Error in Ica
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Asa Borzabadi
May 25, 2022, 3:15:22 PM5/25/22
to hcp-...@humanconnectome.org
Hi,
I am trying to run IcaFixProcessingBatch.sh and I face some problems, I am sorry if it is too basic but could you please let me know of your ideas?
In the error file:
Wed May 25 13:50:15 EDT 2022:hcp_fix_multi_run: While running '/home/asa/projects/HCPpipelines-4.3.0/ICAFIX/hcp_fix_multi_run /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP@/home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA 0 /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP_PA/tfMRI_VISION3_AP_PA FALSE HCP_Style_Single_Multirun_Dedrift.RData 10 FALSE':
Wed May 25 13:50:15 EDT 2022:hcp_fix_multi_run: ERROR: '/usr/local/fsl/bin/immv' command failed with return code: 1
Wed May 25 13:50:15 EDT 2022:hcp_fix_multi_run: ERROR: '/usr/local/fsl/bin/immv' command failed with return code: 1
In the log file get:
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: HCPPIPEDIR: /home/asa/projects/HCPpipelines-4.3.0
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: CARET7DIR: /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSLDIR: /usr/local/fsl
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSL_FIXDIR: /home/asa/Downloads/fix
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: HCPCIFTIRWDIR: :/home/asa/Desktop/CIFTI_MATLAB
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Showing HCP Pipelines version
========================================
DIRECTORY: /home/asa/projects/HCPpipelines-4.3.0
PRODUCT: HCP Pipeline Scripts
VERSION: v4.3.0
========================================
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Showing Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.5.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 76441605d20536d81034a64c9d34ec393aa528b9
Commit Date: 2021-02-16 13:46:47 -0600
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Showing FSL version
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: INFO: Determined that the FSL version in use is 6.0.5.1:57b01774
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSL version: 6.0.5.1:57b01774
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FIX version: 1.06.15
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSL_FIX_MATLAB_MODE: 0
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: fMRI Names: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: highpass: 0
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: hp=0 corresponds to a linear detrend
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: ConcatName: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP_PA/tfMRI_VISION3_AP_PA
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: doMotionRegression: FALSE
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: TrainingData: HCP_Style_Single_Multirun_Dedrift.RData
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FixThresh: 10
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: DeleteIntermediates: FALSE
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: PWD: /home/asa/projects/HCPpipelines-4.3.0/Examples/Scripts
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Looping over files and doing highpass to each of them
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Top of loop through fmris: fmri: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP
parsed 'TCS - MEAN' as 'TCS - MEAN'
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: tr: 0.800000
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: processing FMRI file tfMRI_VISION3_AP with highpass 0
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: MATLAB_COMPILER_RUNTIME: /usr/local/MATLAB/MATLAB_Runtime/v93
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: Run compiled MATLAB with command...
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: /home/asa/Downloads/fix/call_matlab.sh -c /usr/local/MATLAB/MATLAB_Runtime/v93 -b /home/asa/projects/HCPpipelines-4.3.0/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 tfMRI_VISION3_AP /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64/wb_command
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64
Warning: functionhighpassandvariancenormalize: hp=0 will be interpreted as polynomial detrending of order 1
> In functionhighpassandvariancenormalize (line 76)
Elapsed time is 1.362764 seconds.
Non-empty voxels: 231833 (= 25.68% of 902629)
Elapsed time is 0.481835 seconds.
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 231833
golden search result: 77134.7593
golden search initial range: 269 to 77134.7593
golden search result: 341.7968
golden search initial range: 448 to 77134.7593
golden search result: 54962.9313
Out =
VNDIM: [1 53]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 54962.9312687276
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 53
c =
2
golden search initial range: 448 to 231833
golden search result: 78993.5445
golden search initial range: 273 to 78993.5445
golden search result: 313.4033
golden search initial range: 448 to 78993.5445
golden search result: 40500.617
Out =
VNDIM: [1 53 69]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
c =
3
golden search initial range: 448 to 231833
golden search result: 78929.0746
golden search initial range: 278 to 78929.0746
golden search result: 290.3848
golden search initial range: 448 to 78929.0746
golden search result: 37501.2693
Out =
VNDIM: [1 53 69 69]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924 37501.269268007]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
dimavg: 69
c =
4
golden search initial range: 448 to 231833
golden search result: 78929.0746
golden search initial range: 273 to 78929.0746
golden search result: 306.6533
golden search initial range: 448 to 78929.0746
golden search result: 38680.5865
Out =
VNDIM: [1 53 69 69 69]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924 37501.269268007 38680.5864693282]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
dimavg: 69
Out =
VNDIM: [1 53 69 69 69]
Out.DOF: 448
DOF: 177
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924 37501.269268007 38680.5864693282]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 176
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 91282
golden search result: 18308.0256
golden search initial range: 278 to 18308.0256
golden search result: 317.6555
golden search initial range: 141 to 317.6555
golden search result: 167.8709
golden search initial range: 448 to 18308.0256
golden search result: 9403.8356
Out =
VNDIM: [1 39]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 9403.83564374992
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 39
c =
2
golden search initial range: 448 to 91282
golden search result: 19789.3514
golden search initial range: 255 to 19789.3514
golden search result: 307.12
golden search initial range: 141 to 307.12
golden search result: 154.6284
golden search initial range: 448 to 19789.3514
golden search result: 7422.7557
Out =
VNDIM: [1 39 41]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 41
c =
3
golden search initial range: 448 to 91282
golden search result: 19822.3381
golden search initial range: 256 to 19822.3381
golden search result: 325.4425
golden search initial range: 147 to 325.4425
golden search result: 162.536
golden search initial range: 448 to 19822.3381
golden search result: 7389.1751
Out =
VNDIM: [1 39 41 42]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644 7389.17505959121]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 42
dimavg: 42
c =
4
golden search initial range: 448 to 91282
golden search result: 19808.5764
golden search initial range: 256 to 19808.5764
golden search result: 334.9353
golden search initial range: 151 to 334.9353
golden search result: 159.1836
golden search initial range: 448 to 19808.5764
golden search result: 7271.9729
Out =
VNDIM: [1 39 41 42 42]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644 7389.17505959121 7271.9728719709]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 42
dimavg: 42
Out =
VNDIM: [1 39 41 42 42]
Out.DOF: 448
DOF: 91
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644 7389.17505959121 7271.9728719709]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 42
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 92
saving tfMRI_VISION3_AP_Atlas_hp0_vn.dscalar.nii
Elapsed time is 0.093841 seconds.
Elapsed time is 0.383644 seconds.
Wed May 25 12:46:42 EDT 2022:hcp_fix_multi_run: Dims: 69 42
Wed May 25 12:46:42 EDT 2022:hcp_fix_multi_run: Bottom of loop through fmris: fmri: tfMRI_VISION3_AP
Wed May 25 12:46:42 EDT 2022:hcp_fix_multi_run: Top of loop through fmris: fmri: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
parsed 'TCS - MEAN' as 'TCS - MEAN'
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: tr: 0.800000
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: processing FMRI file tfMRI_VISION3_PA with highpass 0
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: MATLAB_COMPILER_RUNTIME: /usr/local/MATLAB/MATLAB_Runtime/v93
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: Run compiled MATLAB with command...
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: /home/asa/Downloads/fix/call_matlab.sh -c /usr/local/MATLAB/MATLAB_Runtime/v93 -b /home/asa/projects/HCPpipelines-4.3.0/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 tfMRI_VISION3_PA /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64/wb_command
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64
Warning: functionhighpassandvariancenormalize: hp=0 will be interpreted as polynomial detrending of order 1
> In functionhighpassandvariancenormalize (line 76)
Elapsed time is 1.357488 seconds.
Non-empty voxels: 231831 (= 25.68% of 902629)
Elapsed time is 0.471356 seconds.
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 231831
golden search result: 77461.6824
golden search initial range: 264 to 77461.6824
golden search result: 330.343
golden search initial range: 448 to 77461.6824
golden search result: 55999.1251
Out =
VNDIM: [1 51]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 55999.1250862219
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 51
c =
2
golden search initial range: 448 to 231831
golden search result: 80852.4872
golden search initial range: 265 to 80852.4872
golden search result: 313.7238
golden search initial range: 448 to 80852.4872
golden search result: 42239.8884
Out =
VNDIM: [1 51 66]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 66
c =
3
golden search initial range: 448 to 231831
golden search result: 80604.6666
golden search initial range: 270 to 80604.6666
golden search result: 312.7814
golden search initial range: 448 to 80604.6666
golden search result: 41287.4011
Out =
VNDIM: [1 51 66 67]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533 41287.4010529891]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 67
dimavg: 67
c =
4
golden search initial range: 448 to 231831
golden search result: 81213.9505
golden search initial range: 270 to 81213.9505
golden search result: 301.3251
golden search initial range: 448 to 81213.9505
golden search result: 38781.0615
Out =
VNDIM: [1 51 66 67 67]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533 41287.4010529891 38781.0615032408]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 67
dimavg: 67
Out =
VNDIM: [1 51 66 67 67]
Out.DOF: 448
DOF: 160
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533 41287.4010529891 38781.0615032408]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 67
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 159
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 91282
golden search result: 18370.0321
golden search initial range: 268 to 18370.0321
golden search result: 350.3035
golden search initial range: 141 to 350.3035
golden search result: 161.1729
golden search initial range: 448 to 18370.0321
golden search result: 9245.9594
Out =
VNDIM: [1 35]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 9245.95943598597
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 35
c =
2
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 261 to 19892.3084
golden search result: 330.6731
golden search initial range: 154 to 330.6731
golden search result: 167.9455
golden search initial range: 448 to 19892.3084
golden search result: 8171.8565
Out =
VNDIM: [1 35 44]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 44
c =
3
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 262 to 19892.3084
golden search result: 323.7663
golden search initial range: 164 to 323.7663
golden search result: 183.6021
golden search initial range: 448 to 19892.3084
golden search result: 8780.8644
Out =
VNDIM: [1 35 44 46]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 46
dimavg: 46
c =
4
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 262 to 19892.3084
golden search result: 358.8489
golden search initial range: 159 to 358.8489
golden search result: 179.8866
golden search initial range: 448 to 19892.3084
golden search result: 8194.6187
Out =
VNDIM: [1 35 44 46 44]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561 8194.61867397467]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 44
dimavg: 45
c =
5
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 260 to 19892.3084
golden search result: 339.5635
golden search initial range: 158 to 339.5635
golden search result: 173.2438
golden search initial range: 448 to 19892.3084
golden search result: 8171.8565
Out =
VNDIM: [1 35 44 46 44 45]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561 8194.61867397467 8171.85647524673]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 45
dimavg: 45
Out =
VNDIM: [1 35 44 46 44 45]
Out.DOF: 448
DOF: 107
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561 8194.61867397467 8171.85647524673]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 45
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 107
saving tfMRI_VISION3_PA_Atlas_hp0_vn.dscalar.nii
Elapsed time is 0.092566 seconds.
Elapsed time is 0.363751 seconds.
Wed May 25 12:51:07 EDT 2022:hcp_fix_multi_run: Dims: 67 45
Wed May 25 12:51:07 EDT 2022:hcp_fix_multi_run: Bottom of loop through fmris: fmri: tfMRI_VISION3_PA
Wed May 25 12:51:08 EDT 2022:hcp_fix_multi_run: Making concatenated folder: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP_PA
Wed May 25 12:51:08 EDT 2022:hcp_fix_multi_run: WARNING: Previous /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP_PA directory removed
parsed 'TCS + MEAN' as 'TCS + MEAN'
parsed 'TCS * VN' as 'TCS * VN'
Wed May 25 12:53:28 EDT 2022:hcp_fix_multi_run: Removing the concatenated VN'ed time series
Wed May 25 12:53:28 EDT 2022:hcp_fix_multi_run: Removing the concatenated demeaned time series
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run VN'ed and demeaned time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run HP'ed time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run VN'ed and demeaned time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run HP'ed time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Run compiled MATLAB with command...
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: /home/asa/Downloads/fix/call_matlab.sh -c /usr/local/MATLAB/MATLAB_Runtime/v93 -b /home/asa/projects/HCPpipelines-4.3.0/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 -1 tfMRI_VISION3_AP_PA_hp0 /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64/wb_command
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64
Non-empty voxels: 231833 (= 25.68% of 902629)
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 896 to 231833
golden search result: 85882.0142
golden search initial range: 553 to 85882.0142
golden search result: 715.1327
golden search initial range: 896 to 85882.0142
golden search result: 71668.891
Out =
VNDIM: [1 92]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: 71668.8909809099
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 92
c =
2
golden search initial range: 896 to 231833
golden search result: 93316.5252
golden search initial range: 558 to 93316.5252
golden search result: 681.4038
golden search initial range: 896 to 93316.5252
golden search result: 65013.7625
Out =
VNDIM: [1 92 124]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 124
c =
3
golden search initial range: 896 to 231833
golden search result: 92129.262
golden search initial range: 551 to 92129.262
golden search result: 614.0605
golden search initial range: 896 to 92129.262
golden search result: 61165.2824
Out =
VNDIM: [1 92 124 125]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 125
dimavg: 125
c =
4
golden search initial range: 896 to 231833
golden search result: 92090.0203
golden search initial range: 569 to 92090.0203
golden search result: 626.6453
golden search initial range: 896 to 92090.0203
golden search result: 63061.9072
Out =
VNDIM: [1 92 124 125 126]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647 63061.907239727]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 126
dimavg: 125.5
c =
5
golden search initial range: 896 to 231833
golden search result: 92090.0203
golden search initial range: 558 to 92090.0203
golden search result: 627.9624
golden search initial range: 896 to 92090.0203
golden search result: 62767.1797
Out =
VNDIM: [1 92 124 125 126 125]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647 63061.907239727 62767.1797406801]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 125
dimavg: 125.333333333333
Out =
VNDIM: [1 92 124 125 126 125]
Out.DOF: 896
DOF: 345
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647 63061.907239727 62767.1797406801]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 125
EigSAdj: array of size [900 1]
grot_one: array of size [896 1]
grot_two: array of size [896 1]
grot_three: array of size [896 1]
grot_four: array of size [896 1]
grot_five: array of size [896 1]
grot_six: array of size [896 1]
NewDOF: 350
Wed May 25 12:57:47 EDT 2022:hcp_fix_multi_run: Dim: 125
Wed May 25 12:57:47 EDT 2022:hcp_fix_multi_run: Running MELODIC located at: /usr/local/fsl/bin/melodic
Wed May 25 12:57:47 EDT 2022:hcp_fix_multi_run: melodic_cmd: /usr/local/fsl/bin/melodic -i tfMRI_VISION3_AP_PA_hp0_vnts -o tfMRI_VISION3_AP_PA_hp0.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.800000 --vn --dim=125 -m tfMRI_VISION3_AP_PA_brain_mask
Wed May 25 13:30:27 EDT 2022:hcp_fix_multi_run: melodic has been run: return_code = 0
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Running FIX
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: using training data file: /home/asa/Downloads/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: fix_cmd: /home/asa/Downloads/fix/fix tfMRI_VISION3_AP_PA_hp0.ica /home/asa/Downloads/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData 10
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Check tfMRI_VISION3_AP_PA_hp0.ica/fix/logMatlab.txt for log output from feature extraction
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Check tfMRI_VISION3_AP_PA_hp0.ica/.fix_2b_predict.log for log output from component classification
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Check tfMRI_VISION3_AP_PA_hp0.ica/.fix.log for log output from cleanup stage
FIX Feature extraction for Melodic output directory: tfMRI_VISION3_AP_PA_hp0.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: tfMRI_VISION3_AP_PA_hp0.ica using training file: /home/asa/Downloads/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData and threshold 10
No valid labelling file specified
Wed May 25 13:50:14 EDT 2022:hcp_fix_multi_run: Done running FIX
Could not find a supported file with prefix "tfMRI_VISION3_AP_PA_hp0.ica/filtered_func_data_clean"
Wed May 25 13:50:15 EDT 2022:hcp_fix_multi_run: ERROR: '/usr/local/fsl/bin/immv' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: hcp_fix_multi_run
stopped at line: 785
call: $FSLDIR/bin/immv ${concatfmrihp}.ica/filtered_func_data_clean ${concatfmrihp}_clean
expanded call: /usr/local/fsl/bin/immv tfMRI_VISION3_AP_PA_hp0.ica/filtered_func_data_clean tfMRI_VISION3_AP_PA_hp0_clean
exit code: 1
---------------------------------------------------
===> Aborting execution!
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: CARET7DIR: /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSLDIR: /usr/local/fsl
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSL_FIXDIR: /home/asa/Downloads/fix
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: HCPCIFTIRWDIR: :/home/asa/Desktop/CIFTI_MATLAB
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Showing HCP Pipelines version
========================================
DIRECTORY: /home/asa/projects/HCPpipelines-4.3.0
PRODUCT: HCP Pipeline Scripts
VERSION: v4.3.0
========================================
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Showing Connectome Workbench (wb_command) version
Connectome Workbench
Type: Command Line Application
Version: 1.5.0
Qt Compiled Version: 5.7.0
Qt Runtime Version: 5.7.0
Commit: 76441605d20536d81034a64c9d34ec393aa528b9
Commit Date: 2021-02-16 13:46:47 -0600
Compiled with OpenMP: YES
Compiler: g++ (/home/caret/gcc/install/gcc-4.8.5/bin)
Compiler Version: 4.8.5
Compiled Debug: NO
Operating System: Linux
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Showing FSL version
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: INFO: Determined that the FSL version in use is 6.0.5.1:57b01774
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSL version: 6.0.5.1:57b01774
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FIX version: 1.06.15
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FSL_FIX_MATLAB_MODE: 0
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: fMRI Names: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: highpass: 0
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: hp=0 corresponds to a linear detrend
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: ConcatName: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP_PA/tfMRI_VISION3_AP_PA
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: doMotionRegression: FALSE
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: TrainingData: HCP_Style_Single_Multirun_Dedrift.RData
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: FixThresh: 10
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: DeleteIntermediates: FALSE
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: PWD: /home/asa/projects/HCPpipelines-4.3.0/Examples/Scripts
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Looping over files and doing highpass to each of them
Wed May 25 12:42:26 EDT 2022:hcp_fix_multi_run: Top of loop through fmris: fmri: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP
parsed 'TCS - MEAN' as 'TCS - MEAN'
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: tr: 0.800000
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: processing FMRI file tfMRI_VISION3_AP with highpass 0
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: MATLAB_COMPILER_RUNTIME: /usr/local/MATLAB/MATLAB_Runtime/v93
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: Run compiled MATLAB with command...
Wed May 25 12:43:15 EDT 2022:hcp_fix_multi_run: /home/asa/Downloads/fix/call_matlab.sh -c /usr/local/MATLAB/MATLAB_Runtime/v93 -b /home/asa/projects/HCPpipelines-4.3.0/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 tfMRI_VISION3_AP /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64/wb_command
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64
Warning: functionhighpassandvariancenormalize: hp=0 will be interpreted as polynomial detrending of order 1
> In functionhighpassandvariancenormalize (line 76)
Elapsed time is 1.362764 seconds.
Non-empty voxels: 231833 (= 25.68% of 902629)
Elapsed time is 0.481835 seconds.
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 231833
golden search result: 77134.7593
golden search initial range: 269 to 77134.7593
golden search result: 341.7968
golden search initial range: 448 to 77134.7593
golden search result: 54962.9313
Out =
VNDIM: [1 53]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 54962.9312687276
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 53
c =
2
golden search initial range: 448 to 231833
golden search result: 78993.5445
golden search initial range: 273 to 78993.5445
golden search result: 313.4033
golden search initial range: 448 to 78993.5445
golden search result: 40500.617
Out =
VNDIM: [1 53 69]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
c =
3
golden search initial range: 448 to 231833
golden search result: 78929.0746
golden search initial range: 278 to 78929.0746
golden search result: 290.3848
golden search initial range: 448 to 78929.0746
golden search result: 37501.2693
Out =
VNDIM: [1 53 69 69]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924 37501.269268007]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
dimavg: 69
c =
4
golden search initial range: 448 to 231833
golden search result: 78929.0746
golden search initial range: 273 to 78929.0746
golden search result: 306.6533
golden search initial range: 448 to 78929.0746
golden search result: 38680.5865
Out =
VNDIM: [1 53 69 69 69]
DOF: 448
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924 37501.269268007 38680.5864693282]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
dimavg: 69
Out =
VNDIM: [1 53 69 69 69]
Out.DOF: 448
DOF: 177
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [54962.9312687276 40500.6169522924 37501.269268007 38680.5864693282]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 69
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 176
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 91282
golden search result: 18308.0256
golden search initial range: 278 to 18308.0256
golden search result: 317.6555
golden search initial range: 141 to 317.6555
golden search result: 167.8709
golden search initial range: 448 to 18308.0256
golden search result: 9403.8356
Out =
VNDIM: [1 39]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 9403.83564374992
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 39
c =
2
golden search initial range: 448 to 91282
golden search result: 19789.3514
golden search initial range: 255 to 19789.3514
golden search result: 307.12
golden search initial range: 141 to 307.12
golden search result: 154.6284
golden search initial range: 448 to 19789.3514
golden search result: 7422.7557
Out =
VNDIM: [1 39 41]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 41
c =
3
golden search initial range: 448 to 91282
golden search result: 19822.3381
golden search initial range: 256 to 19822.3381
golden search result: 325.4425
golden search initial range: 147 to 325.4425
golden search result: 162.536
golden search initial range: 448 to 19822.3381
golden search result: 7389.1751
Out =
VNDIM: [1 39 41 42]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644 7389.17505959121]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 42
dimavg: 42
c =
4
golden search initial range: 448 to 91282
golden search result: 19808.5764
golden search initial range: 256 to 19808.5764
golden search result: 334.9353
golden search initial range: 151 to 334.9353
golden search result: 159.1836
golden search initial range: 448 to 19808.5764
golden search result: 7271.9729
Out =
VNDIM: [1 39 41 42 42]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644 7389.17505959121 7271.9728719709]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 42
dimavg: 42
Out =
VNDIM: [1 39 41 42 42]
Out.DOF: 448
DOF: 91
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9403.83564374992 7422.75567750644 7389.17505959121 7271.9728719709]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 42
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 92
saving tfMRI_VISION3_AP_Atlas_hp0_vn.dscalar.nii
Elapsed time is 0.093841 seconds.
Elapsed time is 0.383644 seconds.
Wed May 25 12:46:42 EDT 2022:hcp_fix_multi_run: Dims: 69 42
Wed May 25 12:46:42 EDT 2022:hcp_fix_multi_run: Bottom of loop through fmris: fmri: tfMRI_VISION3_AP
Wed May 25 12:46:42 EDT 2022:hcp_fix_multi_run: Top of loop through fmris: fmri: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
parsed 'TCS - MEAN' as 'TCS - MEAN'
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: tr: 0.800000
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: processing FMRI file tfMRI_VISION3_PA with highpass 0
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: MATLAB_COMPILER_RUNTIME: /usr/local/MATLAB/MATLAB_Runtime/v93
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: Run compiled MATLAB with command...
Wed May 25 12:47:34 EDT 2022:hcp_fix_multi_run: /home/asa/Downloads/fix/call_matlab.sh -c /usr/local/MATLAB/MATLAB_Runtime/v93 -b /home/asa/projects/HCPpipelines-4.3.0/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 0 tfMRI_VISION3_PA /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64/wb_command
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64
Warning: functionhighpassandvariancenormalize: hp=0 will be interpreted as polynomial detrending of order 1
> In functionhighpassandvariancenormalize (line 76)
Elapsed time is 1.357488 seconds.
Non-empty voxels: 231831 (= 25.68% of 902629)
Elapsed time is 0.471356 seconds.
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 231831
golden search result: 77461.6824
golden search initial range: 264 to 77461.6824
golden search result: 330.343
golden search initial range: 448 to 77461.6824
golden search result: 55999.1251
Out =
VNDIM: [1 51]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 55999.1250862219
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 51
c =
2
golden search initial range: 448 to 231831
golden search result: 80852.4872
golden search initial range: 265 to 80852.4872
golden search result: 313.7238
golden search initial range: 448 to 80852.4872
golden search result: 42239.8884
Out =
VNDIM: [1 51 66]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 66
c =
3
golden search initial range: 448 to 231831
golden search result: 80604.6666
golden search initial range: 270 to 80604.6666
golden search result: 312.7814
golden search initial range: 448 to 80604.6666
golden search result: 41287.4011
Out =
VNDIM: [1 51 66 67]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533 41287.4010529891]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 67
dimavg: 67
c =
4
golden search initial range: 448 to 231831
golden search result: 81213.9505
golden search initial range: 270 to 81213.9505
golden search result: 301.3251
golden search initial range: 448 to 81213.9505
golden search result: 38781.0615
Out =
VNDIM: [1 51 66 67 67]
DOF: 448
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533 41287.4010529891 38781.0615032408]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 67
dimavg: 67
Out =
VNDIM: [1 51 66 67 67]
Out.DOF: 448
DOF: 160
noise_unst_std: array of size [231831 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [55999.1250862219 42239.8884166533 41287.4010529891 38781.0615032408]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 67
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 159
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 448 to 91282
golden search result: 18370.0321
golden search initial range: 268 to 18370.0321
golden search result: 350.3035
golden search initial range: 141 to 350.3035
golden search result: 161.1729
golden search initial range: 448 to 18370.0321
golden search result: 9245.9594
Out =
VNDIM: [1 35]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: 9245.95943598597
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 35
c =
2
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 261 to 19892.3084
golden search result: 330.6731
golden search initial range: 154 to 330.6731
golden search result: 167.9455
golden search initial range: 448 to 19892.3084
golden search result: 8171.8565
Out =
VNDIM: [1 35 44]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 44
c =
3
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 262 to 19892.3084
golden search result: 323.7663
golden search initial range: 164 to 323.7663
golden search result: 183.6021
golden search initial range: 448 to 19892.3084
golden search result: 8780.8644
Out =
VNDIM: [1 35 44 46]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 46
dimavg: 46
c =
4
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 262 to 19892.3084
golden search result: 358.8489
golden search initial range: 159 to 358.8489
golden search result: 179.8866
golden search initial range: 448 to 19892.3084
golden search result: 8194.6187
Out =
VNDIM: [1 35 44 46 44]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561 8194.61867397467]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 44
dimavg: 45
c =
5
golden search initial range: 448 to 91282
golden search result: 19892.3084
golden search initial range: 260 to 19892.3084
golden search result: 339.5635
golden search initial range: 158 to 339.5635
golden search result: 173.2438
golden search initial range: 448 to 19892.3084
golden search result: 8171.8565
Out =
VNDIM: [1 35 44 46 44 45]
DOF: 448
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561 8194.61867397467 8171.85647524673]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 45
dimavg: 45
Out =
VNDIM: [1 35 44 46 44 45]
Out.DOF: 448
DOF: 107
noise_unst_std: array of size [91282 1]
lambda_pcaNorm: array of size [450 1]
EN: array of size [448 1]
x: [9245.95943598597 8171.85647524673 8780.86442561561 8194.61867397467 8171.85647524673]
lambdaAdj: array of size [448 1]
pcaDim_lambdaAdj: struct
calcDim: 45
EigSAdj: array of size [450 1]
grot_one: array of size [448 1]
grot_two: array of size [448 1]
grot_three: array of size [448 1]
grot_four: array of size [448 1]
grot_five: array of size [448 1]
grot_six: array of size [448 1]
NewDOF: 107
saving tfMRI_VISION3_PA_Atlas_hp0_vn.dscalar.nii
Elapsed time is 0.092566 seconds.
Elapsed time is 0.363751 seconds.
Wed May 25 12:51:07 EDT 2022:hcp_fix_multi_run: Dims: 67 45
Wed May 25 12:51:07 EDT 2022:hcp_fix_multi_run: Bottom of loop through fmris: fmri: tfMRI_VISION3_PA
Wed May 25 12:51:08 EDT 2022:hcp_fix_multi_run: Making concatenated folder: /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP_PA
Wed May 25 12:51:08 EDT 2022:hcp_fix_multi_run: WARNING: Previous /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP_PA directory removed
parsed 'TCS + MEAN' as 'TCS + MEAN'
parsed 'TCS * VN' as 'TCS * VN'
Wed May 25 12:53:28 EDT 2022:hcp_fix_multi_run: Removing the concatenated VN'ed time series
Wed May 25 12:53:28 EDT 2022:hcp_fix_multi_run: Removing the concatenated demeaned time series
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run VN'ed and demeaned time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run HP'ed time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_AP/tfMRI_VISION3_AP
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run VN'ed and demeaned time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Removing the individual run HP'ed time series for /home/asa/100102/MNINonLinear/Results/tfMRI_VISION3_PA/tfMRI_VISION3_PA
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: Run compiled MATLAB with command...
Wed May 25 12:53:29 EDT 2022:hcp_fix_multi_run: /home/asa/Downloads/fix/call_matlab.sh -c /usr/local/MATLAB/MATLAB_Runtime/v93 -b /home/asa/projects/HCPpipelines-4.3.0/ICAFIX/scripts/Compiled_functionhighpassandvariancenormalize -f functionhighpassandvariancenormalize 0.800000 -1 tfMRI_VISION3_AP_PA_hp0 /home/asa/Downloads/workbench-linux64-v1.5.0/workbench/bin_linux64/wb_command
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64
Non-empty voxels: 231833 (= 25.68% of 902629)
icaDim: No empty voxels -- not masking
c =
1
golden search initial range: 896 to 231833
golden search result: 85882.0142
golden search initial range: 553 to 85882.0142
golden search result: 715.1327
golden search initial range: 896 to 85882.0142
golden search result: 71668.891
Out =
VNDIM: [1 92]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: 71668.8909809099
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 92
c =
2
golden search initial range: 896 to 231833
golden search result: 93316.5252
golden search initial range: 558 to 93316.5252
golden search result: 681.4038
golden search initial range: 896 to 93316.5252
golden search result: 65013.7625
Out =
VNDIM: [1 92 124]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 124
c =
3
golden search initial range: 896 to 231833
golden search result: 92129.262
golden search initial range: 551 to 92129.262
golden search result: 614.0605
golden search initial range: 896 to 92129.262
golden search result: 61165.2824
Out =
VNDIM: [1 92 124 125]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 125
dimavg: 125
c =
4
golden search initial range: 896 to 231833
golden search result: 92090.0203
golden search initial range: 569 to 92090.0203
golden search result: 626.6453
golden search initial range: 896 to 92090.0203
golden search result: 63061.9072
Out =
VNDIM: [1 92 124 125 126]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647 63061.907239727]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 126
dimavg: 125.5
c =
5
golden search initial range: 896 to 231833
golden search result: 92090.0203
golden search initial range: 558 to 92090.0203
golden search result: 627.9624
golden search initial range: 896 to 92090.0203
golden search result: 62767.1797
Out =
VNDIM: [1 92 124 125 126 125]
DOF: 896
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647 63061.907239727 62767.1797406801]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 125
dimavg: 125.333333333333
Out =
VNDIM: [1 92 124 125 126 125]
Out.DOF: 896
DOF: 345
noise_unst_std: array of size [231833 1]
lambda_pcaNorm: array of size [900 1]
EN: array of size [896 1]
x: [71668.8909809099 65013.7625377075 61165.2823596647 63061.907239727 62767.1797406801]
lambdaAdj: array of size [896 1]
pcaDim_lambdaAdj: struct
calcDim: 125
EigSAdj: array of size [900 1]
grot_one: array of size [896 1]
grot_two: array of size [896 1]
grot_three: array of size [896 1]
grot_four: array of size [896 1]
grot_five: array of size [896 1]
grot_six: array of size [896 1]
NewDOF: 350
Wed May 25 12:57:47 EDT 2022:hcp_fix_multi_run: Dim: 125
Wed May 25 12:57:47 EDT 2022:hcp_fix_multi_run: Running MELODIC located at: /usr/local/fsl/bin/melodic
Wed May 25 12:57:47 EDT 2022:hcp_fix_multi_run: melodic_cmd: /usr/local/fsl/bin/melodic -i tfMRI_VISION3_AP_PA_hp0_vnts -o tfMRI_VISION3_AP_PA_hp0.ica/filtered_func_data.ica --nobet --report --Oall --tr=0.800000 --vn --dim=125 -m tfMRI_VISION3_AP_PA_brain_mask
Wed May 25 13:30:27 EDT 2022:hcp_fix_multi_run: melodic has been run: return_code = 0
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Running FIX
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: using training data file: /home/asa/Downloads/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: fix_cmd: /home/asa/Downloads/fix/fix tfMRI_VISION3_AP_PA_hp0.ica /home/asa/Downloads/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData 10
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Check tfMRI_VISION3_AP_PA_hp0.ica/fix/logMatlab.txt for log output from feature extraction
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Check tfMRI_VISION3_AP_PA_hp0.ica/.fix_2b_predict.log for log output from component classification
Wed May 25 13:30:37 EDT 2022:hcp_fix_multi_run: Check tfMRI_VISION3_AP_PA_hp0.ica/.fix.log for log output from cleanup stage
FIX Feature extraction for Melodic output directory: tfMRI_VISION3_AP_PA_hp0.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory: tfMRI_VISION3_AP_PA_hp0.ica using training file: /home/asa/Downloads/fix/training_files/HCP_Style_Single_Multirun_Dedrift.RData and threshold 10
No valid labelling file specified
Wed May 25 13:50:14 EDT 2022:hcp_fix_multi_run: Done running FIX
Could not find a supported file with prefix "tfMRI_VISION3_AP_PA_hp0.ica/filtered_func_data_clean"
Wed May 25 13:50:15 EDT 2022:hcp_fix_multi_run: ERROR: '/usr/local/fsl/bin/immv' command failed with return code: 1
===> ERROR: Command returned with nonzero exit code
---------------------------------------------------
script: hcp_fix_multi_run
stopped at line: 785
call: $FSLDIR/bin/immv ${concatfmrihp}.ica/filtered_func_data_clean ${concatfmrihp}_clean
expanded call: /usr/local/fsl/bin/immv tfMRI_VISION3_AP_PA_hp0.ica/filtered_func_data_clean tfMRI_VISION3_AP_PA_hp0_clean
exit code: 1
---------------------------------------------------
===> Aborting execution!
Glasser, Matt
May 25, 2022, 3:32:49 PM5/25/22
to hcp-...@humanconnectome.org
Please follow the instructions to troubleshoot this error in FIX “No valid labelling file specified”
Matt.
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Asa Borzabadi
May 29, 2022, 5:58:15 PM5/29/22
to hcp-...@humanconnectome.org
Thank you so much,
The problem seems to be solved.
For anyone facing the same problem in the future: "pay attention to the version of R packages you use and also add gifti to your maltab path"
Regards,
Asa Farahni
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Harms, Michael
May 29, 2022, 6:15:13 PM5/29/22
to hcp-...@humanconnectome.org
As an aside, the QuNex container really simplifies the issues around getting an operational version of FIX, since all the dependencies are taken care of inside the container.
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: Asa Borzabadi <asa.bo...@gmail.com>
Reply-To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Date: Sunday, May 29, 2022 at 5:00 PM
To: "hcp-...@humanconnectome.org" <hcp-...@humanconnectome.org>
Subject: [hcp-users] Re: Error in Ica
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