Validity check at end of stage 1 detected missing files
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Hwee Ling Lee
Apr 6, 2018, 3:50:10 AM4/6/18
to ashs-users
Dear ASHS users,
I hope this email finds you well.
I have installed the latest version of fast ashs software, and I use the 7T atlas provided by Utrecht.
When I tried to run the segmentation preprocessing using this command,
$ASHS_ROOT/bin/ashs_main.sh -a <directory of the Utrecht atlas> -g <directory of my mprage folder> -f <directory of my TSE image folder> -w <new directory> -P
I get an error message that 'validity check at end of stage 1 detected missing files'.
Attached you will find the files from the dump folder of the subject that I'm trying to preprocess.
Thanks.
Cheers,
Hweeling
Paul Yushkevich
Apr 6, 2018, 11:05:48 AM4/6/18
to Hwee Ling Lee, ashs-users
Hi Hwee Ling
The problem is that the T1-MRI is not registering properly to the template. Does this happen for all the images that you run through ASHS with this atlas, or just this particular image?
There is a way to fix this. First get rid of all the files in the subject’s work folder.
You need to perform the registration manually using ITK-SNAP registration mode. Load the ASHS template T1-MRI as the main image in ITK_SNAP and the subject’s T1-MRI as the additional image. Do the registration (Tools->Registration, Manual, followed by automatic) and save the affine registration matrix as ([…] is the path of the subject’s work directory)
[…]/affine_t1_to_template/t1_to_template_affine.mat
Then you also need to compute the inverse of the matrix using this command:
$ASHS_ROOT/ext/Linux/bin/c3d_affine_tool […]/affine_t1_to_template/t1_to_template_affine.mat -inv -o […]/affine_t1_to_template/t1_to_template_affine_inv.mat
Then run ASHS with the -N flag. This should skip the affine registration step and use your matrix instead.
Let me know if this helps.
Paul
Hwee Ling Lee
Apr 9, 2018, 7:38:48 AM4/9/18
to Paul Yushkevich, ashs-users
Dear Paul,
Thanks for the instructions, however, I'm not sure where I could find the ASHS template T1-MRI. Could you please let me know where I could locate this file?
Also, this does not happen in all subjects. In some subjects, the validity check at end of stage 1 is successful, however, when starting stage 2Ö Initial ROI registration to all T2 atlases, there is another error message:
[..]/ashs-1.0.0/bin/ashs_lib.sh: line 223: parallel: command not found.
Thanks!
Cheers,
Hweeling
Hwee Ling Lee
Apr 12, 2018, 5:55:22 AM4/12/18
to Paul Yushkevich, ashs-users
Dear Paul and all,
Sorry for the multiple postings. I was wondering if someone could help me on this.[..]/ashs-1.0.0/bin/ashs_lib.sh: line 223: parallel: command not found
Could someone please help?
Thanks.Paul Yushkevich
Apr 12, 2018, 10:05:45 AM4/12/18
to Hwee Ling Lee, ashs-users
Hi
The second error is occurring because you are (most likely) running ASHS using the -P flag, which requires GNU Parallel software to be present. You will need to install it on your computer, or not use the -P flag. If you have a multi-core computer, using GNU parallel will result in faster performance.
The template is located in the 7T atlas directory, in the directory called "template", file template.nii.gz
Paul
--
Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania
lo...@hrz.tu-chemnitz.de
Mar 11, 2021, 11:42:03 AM3/11/21
to ashs-users
Hi,
as I had the same error "Validity check at end of stage 1 detected missing files" during segmentation for few subjects out of a large sample (the others worked!),
I followed the instructions given above:
1. I performed registration of the subject's T1 image to the atlas template using ITK-Snap
I followed the instructions given above:
1. I performed registration of the subject's T1 image to the atlas template using ITK-Snap
2. I created the inverse transformation matrix using c3d_affine-tool
3. I copied both matrices, "t1_to_template_affine.mat" and "t1_to_template_affine_inv.mat", into the folder "/work/affine_t1_to_template/".
4. I executed ASHS with the -N option.
I obtained the following error message:
"Validity check at end of stage 1 detected missing files. (ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz and 9 other files).
"Validity check at end of stage 1 detected missing files. (ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz and 9 other files).
Is this indicative of some major registration problems that cannot simply be fixed by supplying a custom transform matrix?
This is a slightly longer part of the log:
====================================
PROGRESS: 0
====================================
+ [[ -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat ]]
+ [[ -n 1 ]]
+ echo 'Skipping Affine Registration'
Skipping Affine Registration
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ job_progress 0.5
+ local PROGRESS=0.5
+ local CHUNK_PSTART CHUNK_PEND
+ read CHUNK_PSTART CHUNK_PEND
++ echo 1
++ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
+ echo 'CHUNK 0.0 0.2'
CHUNK 0.0 0.2
+ echo 1
+ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
0 0.2
+ echo 'CHUNK 0 0.2 0.5'
CHUNK 0 0.2 0.5
+ bash /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_default_hook.sh progress 0 0.2 0.5
====================================
PROGRESS: 0
====================================
+ [[ -n 1 ]]
+ [[ -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz ]]
+ greedy -d 3 -m NCC 2x2x2 -e 0.5 -n 60x20x0 -i /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.nii.gz -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz -oinv /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz -gm /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template_bet_mask.nii.gz
ABORTING PROGRAM DUE TO RUNTIME EXCEPTION -- File '/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.nii.gz' does not exist
[0;31m
**************** !! ERROR !! *******************
Validity check at end of stage 1 detected
missing files.
(ants_t1_to_temp/greedy_t1_to_template_invwarp.n
ii.gz and 9 other files).
************************************************
[0m
PROGRESS: 0
====================================
+ [[ -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat ]]
+ [[ -n 1 ]]
+ echo 'Skipping Affine Registration'
Skipping Affine Registration
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ job_progress 0.5
+ local PROGRESS=0.5
+ local CHUNK_PSTART CHUNK_PEND
+ read CHUNK_PSTART CHUNK_PEND
++ echo 1
++ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
+ echo 'CHUNK 0.0 0.2'
CHUNK 0.0 0.2
+ echo 1
+ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
0 0.2
+ echo 'CHUNK 0 0.2 0.5'
CHUNK 0 0.2 0.5
+ bash /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_default_hook.sh progress 0 0.2 0.5
====================================
PROGRESS: 0
====================================
+ [[ -n 1 ]]
+ [[ -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz ]]
+ greedy -d 3 -m NCC 2x2x2 -e 0.5 -n 60x20x0 -i /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.nii.gz -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz -oinv /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz -gm /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template_bet_mask.nii.gz
ABORTING PROGRAM DUE TO RUNTIME EXCEPTION -- File '/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.nii.gz' does not exist
[0;31m
**************** !! ERROR !! *******************
Validity check at end of stage 1 detected
missing files.
(ants_t1_to_temp/greedy_t1_to_template_invwarp.n
ii.gz and 9 other files).
************************************************
[0m
Best,
Lorenz
Lorenz
Paul Yushkevich
Mar 11, 2021, 4:08:51 PM3/11/21
to lo...@hrz.tu-chemnitz.de, ashs-users
Hi Lorenz
Would you mind sharing the log file in the dump directory corresponding to this stage?
Thank you
paul
paul
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Paul A. Yushkevich, Ph.D.
Professor of Radiology
Professor of Radiology
Penn Image Computing and Science Laboratory
University of Pennsylvania Perelman School of Medicine
lo...@hrz.tu-chemnitz.de
Mar 12, 2021, 3:36:50 AM3/12/21
to ashs-users
Hi Paul,
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ local CHUNK_PSTART CHUNK_PEND
+ read CHUNK_PSTART CHUNK_PEND
++ echo 1
++ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
+ echo 'CHUNK 0.0 0.2'
CHUNK 0.0 0.2
+ echo 1
+ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
0 0.2
I'm pasting the content of the log file for stage 1 in /dump below.
Best, Lorenz
Best, Lorenz
+ source /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_lib.sh
++ source /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_version.sh
+++ ASHS_VERSION_MAJOR=1
+++ ASHS_VERSION_MINOR=0
+++ ASHS_VERSION_PATCH=0
+++ ASHS_VERSION_NOTE=
+++ ASHS_VERSION_FULL=1.0.0
+++ ASHS_VERSION_DATE=20170915
+++ ASHS_OLDEST_COMPAT_DATE=20170810
++ source /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_common_master.sh
+++ [[ ! -n /home/h7/goenner/ashs/ashs-fastashs_beta ]]
++++ uname
+++ ARCH=Linux
+++ ASHS_BIN=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin
+++ ASHS_ANTS=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042
+++ ASHS_FSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl
++++ /home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/c3d -version
++++ grep Version
+++ [[ ! -n Version 1.1.0 ]]
+++ PATH=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/sw/installed/MATLAB/2019b:/sw/installed/MATLAB/2019b/bin:/sw/installed/Java/1.8.0_161-OpenJDK:/sw/installed/Java/1.8.0_161-OpenJDK/bin:/usr/lib64/qt-3.3/bin:/sw/taurus/tools/slurmtools/default/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
++ [[ ! /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/ashs_user_config.sh == /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_config.sh ]]
++ source /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_config.sh
+++ ASHS_SIDES='left right'
+++ ASHS_MPRAGE_DENOISE=0
+++ ASHS_MPRAGE_SRUPSAMPLE=0
+++ ASHS_MPRAGE_SRUPSAMPLE_FACTOR='1 1 1'
+++ ASHS_TSE_DENOISE=0
+++ ASHS_TSE_SRUPSAMPLE=0
+++ ASHS_TSE_SRUPSAMPLE_FACTOR='1 1 1'
+++ ASHS_TSE_ISO_FACTOR=100x100x500%
+++ ASHS_TSE_ISO_REGION_CROP='20x20x0% 60x60x100%'
+++ ASHS_FLIRT_MULTIMODAL_OPTS='-searchrx -5 5 -searchry -5 5 -searchrz -5 5 -coarsesearch 3 -finesearch 1 -searchcost normmi'
+++ ASHS_TEMPLATE_ANTS_ITER=60x20x0
+++ ASHS_TEMPLATE_STAGES_TOTAL=4
+++ ASHS_TEMPLATE_STAGES_RIGID=1
+++ ASHS_TEMPLATE_ROI_DILATION=10x10x10vox
+++ ASHS_TEMPLATE_ROI_MARGIN=4x4x4vox
+++ ASHS_TEMPLATE_TARGET_RESOLUTION=0.4688x0.4688x0.4688mm
+++ ASHS_TEMPLATE_MASK_THRESHOLD=0.5
+++ ASHS_TARGET_ATLAS_FOR_HISTMATCH=0
+++ ASHS_HISTMATCH_CONTROLS=5
+++ ASHS_PAIRWISE_AFFINE_ITER=60x60x0
+++ ASHS_PAIRWISE_DEFORM_ITER=60x60x20
+++ ASHS_PAIRWISE_CROSSCORR_RADIUS=2x2x2
+++ ASHS_PAIRWISE_ANTS_STEPSIZE=0.25
+++ ASHS_PAIRWISE_ANTS_T1_WEIGHT=0
+++ ASHS_LABEL_SMOOTHING=0.24mm
+++ ASHS_MALF_STRATEGY='Joint[0.1,2]'
+++ ASHS_MALF_PATCHRAD=3x3x1
+++ ASHS_MALF_SEARCHRAD=3x3x1
+++ ASHS_MALF_PADDING=0x0x2
+++ ASHS_EC_DILATION=1
+++ ASHS_EC_TARGET_SAMPLES=100000
+++ ASHS_EC_DRYRUN_SAMPLE_RATE=0.01
+++ ASHS_EC_ITERATIONS=500
+++ ASHS_EC_PATCH_RADIUS=6x6x0
+++ ASHS_EC_MINIMUM_SAMPLES=100
+++ ASHS_EC_QSUB_EXTRA_OPTIONS=
++ source /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/ashs_user_config.sh
++ [[ -n '' ]]
+ cat
Script: ashs_template_qsub.sh
Root: /home/h7/goenner/ashs/ashs-fastashs_beta
Working directory: /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
PATH: /home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/sw/installed/MATLAB/2019b:/sw/installed/MATLAB/2019b/bin:/sw/installed/Java/1.8.0_161-OpenJDK:/sw/installed/Java/1.8.0_161-OpenJDK/bin:/usr/lib64/qt-3.3/bin:/sw/taurus/tools/slurmtools/default/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
Skip Rigid: 1
Skip Ants: 1
+ WFSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1
+ WANT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp
+ WAFF=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ mkdir -p /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1 /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ TEMP_T1_FULL=/home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template.nii.gz
+ TEMP_T1_MASK=/home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template_bet_mask.nii.gz
+ ashs_subj_vars /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WORK=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WANT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp
+ local WAFF=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ local WFSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1
+ SUBJ_RAWMPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz
+ SUBJ_RAWTSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz
+ SUBJ_MPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz
+ SUBJ_TSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz
+ SUBJ_AFF_T2T1_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat
+ SUBJ_AFF_T2T1_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
+ SUBJ_AFF_T1TEMP_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat
+ SUBJ_AFF_T1TEMP_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat
+ SUBJ_T1TEMP_WARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz
+ SUBJ_T1TEMP_INVWARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz
+ SUBJ_T1TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat'
+ SUBJ_T1TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_T2TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat'
+ SUBJ_T2TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_AFF_T1TEMP_RESLICE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.nii.gz
+ [[ /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -nt /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz ]]
+ c3d /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -type short -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz
+ SUBJ_MPRAGE_DENOISE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz
+ echo 'ASHS_MPRAGE_DENOISE = 0'
ASHS_MPRAGE_DENOISE = 0
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz
+ rm -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz
+ [[ /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -nt /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz ]]
+ c3d /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -type short -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz
+ SUBJ_TSE_DENOISE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz
+ rm -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz
+ ashs_align_t1t2 /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local ASHS_WORK=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local OVERRIDE_MAT=
+ local OVERRIDE_MODE=
+ ashs_subj_vars /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WORK=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WANT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp
+ local WAFF=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ local WFSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1
+ SUBJ_RAWMPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz
+ SUBJ_RAWTSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz
+ SUBJ_MPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz
+ SUBJ_TSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz
+ SUBJ_AFF_T2T1_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat
+ SUBJ_AFF_T2T1_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
+ SUBJ_AFF_T1TEMP_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat
+ SUBJ_AFF_T1TEMP_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat
+ SUBJ_T1TEMP_WARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz
+ SUBJ_T1TEMP_INVWARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz
+ SUBJ_T1TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat'
+ SUBJ_T1TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_T2TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat'
+ SUBJ_T2TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ [[ -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat ]]
+ export FSLOUTPUTTYPE=NIFTI_GZ
+ FSLOUTPUTTYPE=NIFTI_GZ
+ c3d /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz -resample 100x100x500% -region 20x20x0% 60x60x100% -type short -o /tmp/ashs.zH6rRpXF/tse_iso.nii.gz
+ [[ -n '' ]]
+ local INIT_RIGID
+ [[ -n '' ]]
+ INIT_RIGID=-ia-identity
+ greedy -d 3 -a -dof 6 -m MI -n 100x100x10 -i /tmp/ashs.zH6rRpXF/tse_iso.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz -ia-identity -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat
Executing with the default number of threads: 24
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -13718.3 GNORM= 22.9664
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -13718.994 7.287 0.002
2 4 -13719.055 1.509 1.000
3 5 -13719.059 1.132 1.000
4 6 -13719.068 0.673 1.000
5 7 -13719.069 0.406 1.000
6 8 -13719.069 0.101 1.000
7 9 -13719.069 0.054 1.000
8 11 -13719.069 0.034 0.405
9 13 -13719.069 0.030 0.401
10 14 -13719.069 0.023 1.000
11 16 -13719.069 0.024 0.321
12 19 -13719.069 0.030 0.019
13 20 -13719.069 0.026 1.000
14 22 -13719.069 0.018 0.235
15 23 -13719.069 0.017 1.000
16 25 -13719.069 0.014 0.235
17 26 -13719.069 0.013 1.000
18 28 -13719.069 0.017 0.172
19 30 -13719.069 0.012 5.000
20 31 -13719.069 0.010 1.000
21 34 -13719.069 0.016 0.063
22 36 -13719.069 0.016 0.251
23 37 -13719.069 0.009 1.000
24 38 -13719.069 0.017 1.000
25 39 -13719.069 0.018 1.000
26 40 -13719.069 0.017 1.000
27 42 -13719.069 0.011 0.062
28 43 -13719.069 0.011 1.000
29 44 -13719.069 0.014 1.000
30 46 -13719.069 0.014 0.306
31 47 -13719.069 0.013 1.000
32 48 -13719.069 0.013 1.000
33 49 -13719.069 0.011 1.000
34 50 -13719.069 0.012 1.000
35 51 -13719.069 0.014 1.000
36 52 -13719.069 0.012 1.000
37 54 -13719.069 0.007 0.371
38 56 -13719.069 0.011 0.442
39 59 -13719.069 0.007 0.085
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESvnl_lbfgs: Error. Netlib routine lbfgs failed.
Final RAS Transform:
1 0.000101283 -4.45839e-05 -0.0308046
-0.000101284 1 -3.68812e-05 0.014514
4.45802e-05 3.68857e-05 1 -0.0573888
0 0 0 1
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -15959.8 GNORM= 85.3138
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -15961.966 19.610 0.001
2 4 -15962.091 1.996 1.000
3 5 -15962.093 1.269 1.000
4 6 -15962.095 1.498 1.000
5 7 -15962.100 2.175 1.000
6 8 -15962.104 1.250 1.000
7 9 -15962.104 0.563 1.000
8 10 -15962.104 0.237 1.000
9 11 -15962.104 0.079 1.000
10 12 -15962.104 0.072 1.000
11 13 -15962.104 0.104 1.000
12 14 -15962.104 0.078 1.000
13 15 -15962.104 0.060 1.000
14 17 -15962.104 0.035 0.464
15 18 -15962.104 0.079 1.000
16 19 -15962.104 0.042 1.000
17 20 -15962.104 0.013 1.000
18 21 -15962.104 0.010 1.000
19 23 -15962.104 0.007 0.335
20 25 -15962.104 0.008 0.276
21 26 -15962.104 0.006 1.000
22 28 -15962.104 0.006 0.510
23 32 -15962.104 0.005 0.004
24 35 -15962.104 0.007 0.039
25 36 -15962.104 0.005 1.000
26 40 -15962.104 0.005 3.348
27 44 -15962.104 0.005 0.073
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESvnl_lbfgs: Error. Netlib routine lbfgs failed.
Final RAS Transform:
1 5.36579e-05 -5.33024e-06 -0.00495109
-5.36579e-05 1 -3.30601e-05 0.00503629
5.33024e-06 3.30601e-05 1 -0.00860201
0 0 0 1
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -13882.6 GNORM= 77.4666
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -13883.010 6.942 0.000
2 4 -13883.014 3.763 1.000
3 5 -13883.017 4.290 1.000
4 6 -13883.035 9.789 1.000
5 7 -13883.057 12.484 1.000
6 8 -13883.071 11.596 1.000
7 9 -13883.076 6.203 1.000
8 10 -13883.080 0.973 1.000
9 11 -13883.080 0.207 1.000
Final RAS Transform:
1 -3.49285e-06 8.25228e-06 0.000490804
3.49285e-06 1 2.88827e-06 0.000365437
-8.25228e-06 -2.88827e-06 1 0.000927375
0 0 0 1
+ c3d_affine_tool /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat -inv -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
++ source /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_version.sh
+++ ASHS_VERSION_MAJOR=1
+++ ASHS_VERSION_MINOR=0
+++ ASHS_VERSION_PATCH=0
+++ ASHS_VERSION_NOTE=
+++ ASHS_VERSION_FULL=1.0.0
+++ ASHS_VERSION_DATE=20170915
+++ ASHS_OLDEST_COMPAT_DATE=20170810
++ source /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_common_master.sh
+++ [[ ! -n /home/h7/goenner/ashs/ashs-fastashs_beta ]]
++++ uname
+++ ARCH=Linux
+++ ASHS_BIN=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin
+++ ASHS_ANTS=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042
+++ ASHS_FSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl
++++ /home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/c3d -version
++++ grep Version
+++ [[ ! -n Version 1.1.0 ]]
+++ PATH=/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/sw/installed/MATLAB/2019b:/sw/installed/MATLAB/2019b/bin:/sw/installed/Java/1.8.0_161-OpenJDK:/sw/installed/Java/1.8.0_161-OpenJDK/bin:/usr/lib64/qt-3.3/bin:/sw/taurus/tools/slurmtools/default/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
++ [[ ! /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/ashs_user_config.sh == /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_config.sh ]]
++ source /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_config.sh
+++ ASHS_SIDES='left right'
+++ ASHS_MPRAGE_DENOISE=0
+++ ASHS_MPRAGE_SRUPSAMPLE=0
+++ ASHS_MPRAGE_SRUPSAMPLE_FACTOR='1 1 1'
+++ ASHS_TSE_DENOISE=0
+++ ASHS_TSE_SRUPSAMPLE=0
+++ ASHS_TSE_SRUPSAMPLE_FACTOR='1 1 1'
+++ ASHS_TSE_ISO_FACTOR=100x100x500%
+++ ASHS_TSE_ISO_REGION_CROP='20x20x0% 60x60x100%'
+++ ASHS_FLIRT_MULTIMODAL_OPTS='-searchrx -5 5 -searchry -5 5 -searchrz -5 5 -coarsesearch 3 -finesearch 1 -searchcost normmi'
+++ ASHS_TEMPLATE_ANTS_ITER=60x20x0
+++ ASHS_TEMPLATE_STAGES_TOTAL=4
+++ ASHS_TEMPLATE_STAGES_RIGID=1
+++ ASHS_TEMPLATE_ROI_DILATION=10x10x10vox
+++ ASHS_TEMPLATE_ROI_MARGIN=4x4x4vox
+++ ASHS_TEMPLATE_TARGET_RESOLUTION=0.4688x0.4688x0.4688mm
+++ ASHS_TEMPLATE_MASK_THRESHOLD=0.5
+++ ASHS_TARGET_ATLAS_FOR_HISTMATCH=0
+++ ASHS_HISTMATCH_CONTROLS=5
+++ ASHS_PAIRWISE_AFFINE_ITER=60x60x0
+++ ASHS_PAIRWISE_DEFORM_ITER=60x60x20
+++ ASHS_PAIRWISE_CROSSCORR_RADIUS=2x2x2
+++ ASHS_PAIRWISE_ANTS_STEPSIZE=0.25
+++ ASHS_PAIRWISE_ANTS_T1_WEIGHT=0
+++ ASHS_LABEL_SMOOTHING=0.24mm
+++ ASHS_MALF_STRATEGY='Joint[0.1,2]'
+++ ASHS_MALF_PATCHRAD=3x3x1
+++ ASHS_MALF_SEARCHRAD=3x3x1
+++ ASHS_MALF_PADDING=0x0x2
+++ ASHS_EC_DILATION=1
+++ ASHS_EC_TARGET_SAMPLES=100000
+++ ASHS_EC_DRYRUN_SAMPLE_RATE=0.01
+++ ASHS_EC_ITERATIONS=500
+++ ASHS_EC_PATCH_RADIUS=6x6x0
+++ ASHS_EC_MINIMUM_SAMPLES=100
+++ ASHS_EC_QSUB_EXTRA_OPTIONS=
++ source /home/h7/goenner/ashs/atlases/ashs_atlas_princeton/ashs_user_config.sh
++ [[ -n '' ]]
+ cat
Script: ashs_template_qsub.sh
Root: /home/h7/goenner/ashs/ashs-fastashs_beta
Working directory: /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
PATH: /home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/ants_1042:/home/h7/goenner/ashs/ashs-fastashs_beta/ext/Linux/bin/fsl:/sw/installed/MATLAB/2019b:/sw/installed/MATLAB/2019b/bin:/sw/installed/Java/1.8.0_161-OpenJDK:/sw/installed/Java/1.8.0_161-OpenJDK/bin:/usr/lib64/qt-3.3/bin:/sw/taurus/tools/slurmtools/default/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
Skip Rigid: 1
Skip Ants: 1
+ WFSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1
+ WANT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp
+ WAFF=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ mkdir -p /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1 /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ TEMP_T1_FULL=/home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template.nii.gz
+ TEMP_T1_MASK=/home/h7/goenner/ashs/atlases/ashs_atlas_princeton/template/template_bet_mask.nii.gz
+ ashs_subj_vars /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WORK=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WANT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp
+ local WAFF=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ local WFSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1
+ SUBJ_RAWMPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz
+ SUBJ_RAWTSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz
+ SUBJ_MPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz
+ SUBJ_TSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz
+ SUBJ_AFF_T2T1_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat
+ SUBJ_AFF_T2T1_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
+ SUBJ_AFF_T1TEMP_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat
+ SUBJ_AFF_T1TEMP_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat
+ SUBJ_T1TEMP_WARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz
+ SUBJ_T1TEMP_INVWARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz
+ SUBJ_T1TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat'
+ SUBJ_T1TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_T2TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat'
+ SUBJ_T2TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_AFF_T1TEMP_RESLICE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.nii.gz
+ [[ /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -nt /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz ]]
+ c3d /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -type short -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz
+ SUBJ_MPRAGE_DENOISE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz
+ echo 'ASHS_MPRAGE_DENOISE = 0'
ASHS_MPRAGE_DENOISE = 0
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz
+ rm -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_d.nii.gz
+ [[ /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -nt /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz ]]
+ c3d /home/h7/goenner/ashs/Structural_scans/10100115_1/T1/s1055_006437-0004-00001-000240-01.nii -type short -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz
+ SUBJ_TSE_DENOISE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz
+ rm -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_d.nii.gz
+ ashs_align_t1t2 /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local ASHS_WORK=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local OVERRIDE_MAT=
+ local OVERRIDE_MODE=
+ ashs_subj_vars /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WORK=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115
+ local WANT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp
+ local WAFF=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template
+ local WFSL=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1
+ SUBJ_RAWMPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage_raw.nii.gz
+ SUBJ_RAWTSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse_raw.nii.gz
+ SUBJ_MPRAGE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz
+ SUBJ_TSE=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz
+ SUBJ_AFF_T2T1_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat
+ SUBJ_AFF_T2T1_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
+ SUBJ_AFF_T1TEMP_MAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat
+ SUBJ_AFF_T1TEMP_INVMAT=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat
+ SUBJ_T1TEMP_WARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz
+ SUBJ_T1TEMP_INVWARP=/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz
+ SUBJ_T1TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat'
+ SUBJ_T1TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_T2TEMP_TRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat'
+ SUBJ_T2TEMP_INVTRAN='/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine_inv.mat /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ [[ -f /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat ]]
+ export FSLOUTPUTTYPE=NIFTI_GZ
+ FSLOUTPUTTYPE=NIFTI_GZ
+ c3d /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/tse.nii.gz -resample 100x100x500% -region 20x20x0% 60x60x100% -type short -o /tmp/ashs.zH6rRpXF/tse_iso.nii.gz
+ [[ -n '' ]]
+ local INIT_RIGID
+ [[ -n '' ]]
+ INIT_RIGID=-ia-identity
+ greedy -d 3 -a -dof 6 -m MI -n 100x100x10 -i /tmp/ashs.zH6rRpXF/tse_iso.nii.gz /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/mprage.nii.gz -ia-identity -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat
Executing with the default number of threads: 24
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -13718.3 GNORM= 22.9664
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -13718.994 7.287 0.002
2 4 -13719.055 1.509 1.000
3 5 -13719.059 1.132 1.000
4 6 -13719.068 0.673 1.000
5 7 -13719.069 0.406 1.000
6 8 -13719.069 0.101 1.000
7 9 -13719.069 0.054 1.000
8 11 -13719.069 0.034 0.405
9 13 -13719.069 0.030 0.401
10 14 -13719.069 0.023 1.000
11 16 -13719.069 0.024 0.321
12 19 -13719.069 0.030 0.019
13 20 -13719.069 0.026 1.000
14 22 -13719.069 0.018 0.235
15 23 -13719.069 0.017 1.000
16 25 -13719.069 0.014 0.235
17 26 -13719.069 0.013 1.000
18 28 -13719.069 0.017 0.172
19 30 -13719.069 0.012 5.000
20 31 -13719.069 0.010 1.000
21 34 -13719.069 0.016 0.063
22 36 -13719.069 0.016 0.251
23 37 -13719.069 0.009 1.000
24 38 -13719.069 0.017 1.000
25 39 -13719.069 0.018 1.000
26 40 -13719.069 0.017 1.000
27 42 -13719.069 0.011 0.062
28 43 -13719.069 0.011 1.000
29 44 -13719.069 0.014 1.000
30 46 -13719.069 0.014 0.306
31 47 -13719.069 0.013 1.000
32 48 -13719.069 0.013 1.000
33 49 -13719.069 0.011 1.000
34 50 -13719.069 0.012 1.000
35 51 -13719.069 0.014 1.000
36 52 -13719.069 0.012 1.000
37 54 -13719.069 0.007 0.371
38 56 -13719.069 0.011 0.442
39 59 -13719.069 0.007 0.085
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESvnl_lbfgs: Error. Netlib routine lbfgs failed.
Final RAS Transform:
1 0.000101283 -4.45839e-05 -0.0308046
-0.000101284 1 -3.68812e-05 0.014514
4.45802e-05 3.68857e-05 1 -0.0573888
0 0 0 1
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -15959.8 GNORM= 85.3138
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -15961.966 19.610 0.001
2 4 -15962.091 1.996 1.000
3 5 -15962.093 1.269 1.000
4 6 -15962.095 1.498 1.000
5 7 -15962.100 2.175 1.000
6 8 -15962.104 1.250 1.000
7 9 -15962.104 0.563 1.000
8 10 -15962.104 0.237 1.000
9 11 -15962.104 0.079 1.000
10 12 -15962.104 0.072 1.000
11 13 -15962.104 0.104 1.000
12 14 -15962.104 0.078 1.000
13 15 -15962.104 0.060 1.000
14 17 -15962.104 0.035 0.464
15 18 -15962.104 0.079 1.000
16 19 -15962.104 0.042 1.000
17 20 -15962.104 0.013 1.000
18 21 -15962.104 0.010 1.000
19 23 -15962.104 0.007 0.335
20 25 -15962.104 0.008 0.276
21 26 -15962.104 0.006 1.000
22 28 -15962.104 0.006 0.510
23 32 -15962.104 0.005 0.004
24 35 -15962.104 0.007 0.039
25 36 -15962.104 0.005 1.000
26 40 -15962.104 0.005 3.348
27 44 -15962.104 0.005 0.073
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 3 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESvnl_lbfgs: Error. Netlib routine lbfgs failed.
Final RAS Transform:
1 5.36579e-05 -5.33024e-06 -0.00495109
-5.36579e-05 1 -3.30601e-05 0.00503629
5.33024e-06 3.30601e-05 1 -0.00860201
0 0 0 1
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -13882.6 GNORM= 77.4666
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -13883.010 6.942 0.000
2 4 -13883.014 3.763 1.000
3 5 -13883.017 4.290 1.000
4 6 -13883.035 9.789 1.000
5 7 -13883.057 12.484 1.000
6 8 -13883.071 11.596 1.000
7 9 -13883.076 6.203 1.000
8 10 -13883.080 0.973 1.000
9 11 -13883.080 0.207 1.000
Final RAS Transform:
1 -3.49285e-06 8.25228e-06 0.000490804
3.49285e-06 1 2.88827e-06 0.000365437
-8.25228e-06 -2.88827e-06 1 0.000927375
0 0 0 1
+ c3d_affine_tool /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1.mat -inv -o /home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ [[ 0 == 1 ]]
+ job_progress 0.25
+ local PROGRESS=0.25
+ local PROGRESS=0.25
+ local CHUNK_PSTART CHUNK_PEND
+ read CHUNK_PSTART CHUNK_PEND
++ echo 1
++ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
+ echo 'CHUNK 0.0 0.2'
CHUNK 0.0 0.2
+ echo 1
+ awk -v bs=0.0 -v be=0.2 -v j=0 -v n=1 '{print bs + ((be - bs) * j) / n, bs + ((be - bs) * (j+1)) / n}'
0 0.2
+ echo 'CHUNK 0 0.2 0.25'
CHUNK 0 0.2 0.25
+ bash /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_default_hook.sh progress 0 0.2 0.25
CHUNK 0 0.2 0.25
+ bash /home/h7/goenner/ashs/ashs-fastashs_beta/bin/ashs_default_hook.sh progress 0 0.2 0.25
Paul Yushkevich
Mar 12, 2021, 9:33:09 AM3/12/21
to lo...@hrz.tu-chemnitz.de, ashs-users
Hi Lorenzo,
I think the problem line is here:
ABORTING PROGRAM DUE TO RUNTIME EXCEPTION -- File '/home/h7/goenner/ashs/ashs-fastashs_beta/ashs_work/10100115/affine_t1_to_template/t1_to_template_affine.nii.gz' does not exist
ASHS is expecting the file t1_to_template_affine.nii.gz, i.e., the T1 resliced into the template after affine registration. But since you are supplying your own .mat file, the code that generates this file is being skipped. I think you need to manually run greedy to generate this file, i.e., using the -rf, -rm, -r options.
This is of course a bug in ASHS.
Thanks!
Paul
Paul
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lo...@hrz.tu-chemnitz.de
Mar 15, 2021, 6:15:33 AM3/15/21
to ashs-users
Hi Paul,
thanks a lot, I will try this and keep you updated.
Lorenz
thanks a lot, I will try this and keep you updated.
Lorenz
Yi-En Quek
Jun 2, 2021, 12:41:02 AM6/2/21
to ashs-users
Hi Paul (and other ASHS developers),
I have also encountered a validity check error at the end of stage 1, but the issue seems to be different from those discussed previously. I think the error is related to:
+ NLMDenoise -i [..]/myworkdir/subj001/tse_raw.nii.gz -o [..]/myworkdir/subj001/tse_d.nii.gz
dyld: Library not loaded: libvtkDomainsChemistryOpenGL2-7.1.1.dylib
Referenced from: [..]/ashs-fastashs_beta/ext/Darwin/bin/NLMDenoise
Reason: image not found
[..]/ashs-fastashs_beta/bin/ashs_template_qsub.sh: line 155: 1513 Abort trap: 6 NLMDenoise -i $SUBJ_RAWTSE -o $SUBJ_TSE_DENOISE
Full output is attached.
Any assistance is greatly appreciated!
Regards,
Yi-En
Paul Yushkevich
Jun 2, 2021, 9:06:59 AM6/2/21
to Yi-En Quek, Xie, Long, ashs-users
Hi Yi-En,
This seems like a bug related to NLMDenoise binary - seems like some dependencies are not being distributed with the main ASHS code. Long, have you seen this error before?
Thanks!
To view this discussion on the web visit https://groups.google.com/d/msgid/ashs-users/ac73fb97-a493-4c47-a2d2-5265c2ab9368n%40googlegroups.com.
Yi-En Quek
Jun 2, 2021, 9:35:16 PM6/2/21
to Xie, Long, Paul Yushkevich, ashs-users
Hi Long and Paul,
I did suspect a compatibility issue. I tried running ASHS-T1 on a Linux machine and it worked great. Thank you for your assistance in this matter!
Regards,
Yi-En
On 3 Jun 2021, at 00:05, Xie, Long <Long...@pennmedicine.upenn.edu> wrote:Hi Yi-En,Thank you for your feedback. Currently, the NLMDenoise binary has not been compiled to work in Mac OS. I will work on incorporating this into the code. For now, please run ASHS-T1 on a Linux machine. Let us know if you come across any issues.Best,LongFrom: Paul Yushkevich <pyush...@gmail.com>
Sent: Wednesday, June 2, 2021 9:06 AM
To: Yi-En Quek <yien...@gmail.com>; Xie, Long <Long...@pennmedicine.upenn.edu>
Cc: ashs-users <ashs-...@googlegroups.com>
Subject: [External] Re: Validity check at end of stage 1 detected missing files
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