c3d_affine_tool error
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Catherine Tallman
Jul 29, 2021, 4:02:45 PM7/29/21
to ashs-users
Hello,
Best,
I am running ASHS locally and am receiving the following error:
+ c3d_affine_tool /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat -inv -o /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
terminate called after throwing an instance of 'char const*'
/ashs/ashs-fastashs/bin/ashs_lib.sh: line 401: 24942 Aborted (core dumped) c3d_affine_tool $SUBJ_AFF_T2T1_MAT -inv -o $SUBJ_AFF_T2T1_INVMAT
When I check the /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/ folder, I do not see the flirt_t2_to_t1.mat file. I am also curious about what this warning means and if it would prevent the matrix was being made? IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESvnl_lbfgs: Error. Netlib routine lbfgs failed.
Below is the full log file.
Best,
Catherine
tee: /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/dump/ashs_main.o20210729_190620: Permission denied
ashs_main execution log
timestamp: Thu Jul 29 19:06:20 UTC 2021
invocation: /usr/local/ashs-fastashs/bin/ashs_main.sh -I sub-002 -a /usr/local/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/PMC_atlas/ashs_atlas_upennpmc_20170810 -g /usr/local/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_rec-PURE_T1w.nii.gz -f /usr/local/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_acq-highres_rec-PURE_T2w.nii.gz -w /usr/local/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
directory: /usr/local/mridata/Smith_Merit/Processed_Data/derivatives/ASHS
environment:
ASHS_MPRAGE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_rec-PURE_T1w.nii.gz
ASHS_ROOT=/ashs/ashs-fastashs
ASHS_SUBJID=sub-002
ASHS_TSE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_acq-highres_rec-PURE_T2w.nii.gz
ASHS_WORK=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
Atlas : /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/PMC_atlas/ashs_atlas_upennpmc_20170810
T1 Image : /mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_rec-PURE_T1w.nii.gz
T2 Image : /mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_acq-highres_rec-PURE_T2w.nii.gz
WorkDir : /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
Not using SGE or GNU parallel
****************************************
Starting stage 1: Normalization to T1 population template
****************************************
[0;36m
------------------- INFO ---------------------
Started stage 1: Normalization to T1 population
template
------------------------------------------------
[0m
tee: /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/dump/ashs_stg1.o20210729_190621: Permission denied
+ source /ashs/ashs-fastashs/bin/ashs_lib.sh
++ source /ashs/ashs-fastashs/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 /ashs/ashs-fastashs/bin/ashs_common_master.sh
+++ [[ ! -n /ashs/ashs-fastashs ]]
++++ uname
+++ ARCH=Linux
+++ ASHS_BIN=/ashs/ashs-fastashs/ext/Linux/bin
+++ ASHS_ANTS=/ashs/ashs-fastashs/ext/Linux/bin/ants_1042
+++ ASHS_FSL=/ashs/ashs-fastashs/ext/Linux/bin/fsl
++++ /ashs/ashs-fastashs/ext/Linux/bin/c3d -version
++++ grep Version
+++ [[ ! -n Version 1.1.0 ]]
+++ PATH=/ashs/ashs-fastashs/ext/Linux/bin:/ashs/ashs-fastashs/ext/Linux/bin/ants_1042:/ashs/ashs-fastashs/ext/Linux/bin/fsl:/ashs/ashs-fastashs/ext/Linux/bin:/ashs/ashs-fastashs/ext/Linux/bin/ants_1042:/ashs/ashs-fastashs/ext/Linux/bin/fsl:/home/ctallman/anaconda3/bin:/home/ctallman/anaconda3/condabin:/usr/local/cuda-7.5/bin:/home/ctallman/.local/bin:/usr/local/fsl6/bin:/usr/local/antsbin/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/opt/TurboVNC/bin:/usr/local/cuda-7.5/bin:/home/ctallman/.local/bin:/usr/local/fsl6/bin:/usr/local/antsbin/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/opt/TurboVNC/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/var/cfengine/bin:/home/ctallman/bin:.:/usr/local/mridata:/usr/local/afni/bin:/usr/local/ITKv4/bin:/usr/local/bin:/usr/local/mricrogl:/home/ctallman/bin:.:/usr/local/mridata:/usr/local/afni/bin:/usr/local/ITKv4/bin:/usr/local/bin:/usr/local/mricrogl
++ [[ ! /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/PMC_atlas/ashs_atlas_upennpmc_20170810/ashs_user_config.sh == /ashs/ashs-fastashs/bin/ashs_config.sh ]]
++ source /ashs/ashs-fastashs/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 /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/PMC_atlas/ashs_atlas_upennpmc_20170810/ashs_user_config.sh
+++ ASHS_TEMPLATE_TARGET_RESOLUTION=0.4x0.4x0.4mm
+++ ASHS_EC_TARGET_SAMPLES=40000
++ [[ -n '' ]]
+ cat
Script: ashs_template_qsub.sh
Root: /ashs/ashs-fastashs
Working directory: /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
PATH: /ashs/ashs-fastashs/ext/Linux/bin:/ashs/ashs-fastashs/ext/Linux/bin/ants_1042:/ashs/ashs-fastashs/ext/Linux/bin/fsl:/ashs/ashs-fastashs/ext/Linux/bin:/ashs/ashs-fastashs/ext/Linux/bin/ants_1042:/ashs/ashs-fastashs/ext/Linux/bin/fsl:/home/ctallman/anaconda3/bin:/home/ctallman/anaconda3/condabin:/usr/local/cuda-7.5/bin:/home/ctallman/.local/bin:/usr/local/fsl6/bin:/usr/local/antsbin/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/opt/TurboVNC/bin:/usr/local/cuda-7.5/bin:/home/ctallman/.local/bin:/usr/local/fsl6/bin:/usr/local/antsbin/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/usr/local/fsl/bin:/usr/local/freesurfer/mni/bin:/opt/TurboVNC/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/var/cfengine/bin:/home/ctallman/bin:.:/usr/local/mridata:/usr/local/afni/bin:/usr/local/ITKv4/bin:/usr/local/bin:/usr/local/mricrogl:/home/ctallman/bin:.:/usr/local/mridata:/usr/local/afni/bin:/usr/local/ITKv4/bin:/usr/local/bin:/usr/local/mricrogl
Skip Rigid:
Skip Ants:
+ WFSL=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1
+ WANT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp
+ WAFF=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template
+ mkdir -p /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1 /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template
+ TEMP_T1_FULL=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/PMC_atlas/ashs_atlas_upennpmc_20170810/template/template.nii.gz
+ TEMP_T1_MASK=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/PMC_atlas/ashs_atlas_upennpmc_20170810/template/template_bet_mask.nii.gz
+ ashs_subj_vars /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
+ local WORK=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
+ local WANT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp
+ local WAFF=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template
+ local WFSL=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1
+ SUBJ_RAWMPRAGE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_raw.nii.gz
+ SUBJ_RAWTSE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_raw.nii.gz
+ SUBJ_MPRAGE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage.nii.gz
+ SUBJ_TSE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse.nii.gz
+ SUBJ_AFF_T2T1_MAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat
+ SUBJ_AFF_T2T1_INVMAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
+ SUBJ_AFF_T1TEMP_MAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine.mat
+ SUBJ_AFF_T1TEMP_INVMAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine_inv.mat
+ SUBJ_T1TEMP_WARP=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz
+ SUBJ_T1TEMP_INVWARP=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz
+ SUBJ_T1TEMP_TRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine.mat'
+ SUBJ_T1TEMP_INVTRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine_inv.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_T2TEMP_TRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat'
+ SUBJ_T2TEMP_INVTRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine_inv.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_AFF_T1TEMP_RESLICE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine.nii.gz
+ [[ /mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_rec-PURE_T1w.nii.gz -nt /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_raw.nii.gz ]]
+ c3d /mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_rec-PURE_T1w.nii.gz -type short -o /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_raw.nii.gz
+ SUBJ_MPRAGE_DENOISE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_d.nii.gz
+ echo 'ASHS_MPRAGE_DENOISE = 0'
ASHS_MPRAGE_DENOISE = 0
+ [[ 0 == 1 ]]
+ cp /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_raw.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_d.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage.nii.gz
+ rm -f /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_d.nii.gz
+ [[ /mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_acq-highres_rec-PURE_T2w.nii.gz -nt /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_raw.nii.gz ]]
+ c3d /mnt/pentagon/mridata/Smith_Merit/Processed_Data/nifti/sub-002/ses-str/anat/sub-002_ses-str_acq-highres_rec-PURE_T2w.nii.gz -type short -o /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_raw.nii.gz
+ SUBJ_TSE_DENOISE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_raw.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_d.nii.gz
+ [[ 0 == 1 ]]
+ cp /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_d.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse.nii.gz
+ rm -f /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_d.nii.gz
+ ashs_align_t1t2 /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
+ local ASHS_WORK=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
+ local OVERRIDE_MAT=
+ local OVERRIDE_MODE=
+ ashs_subj_vars /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
+ local WORK=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002
+ local WANT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp
+ local WAFF=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template
+ local WFSL=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1
+ SUBJ_RAWMPRAGE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage_raw.nii.gz
+ SUBJ_RAWTSE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse_raw.nii.gz
+ SUBJ_MPRAGE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage.nii.gz
+ SUBJ_TSE=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse.nii.gz
+ SUBJ_AFF_T2T1_MAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat
+ SUBJ_AFF_T2T1_INVMAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
+ SUBJ_AFF_T1TEMP_MAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine.mat
+ SUBJ_AFF_T1TEMP_INVMAT=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine_inv.mat
+ SUBJ_T1TEMP_WARP=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz
+ SUBJ_T1TEMP_INVWARP=/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz
+ SUBJ_T1TEMP_TRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine.mat'
+ SUBJ_T1TEMP_INVTRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine_inv.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ SUBJ_T2TEMP_TRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_warp.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat'
+ SUBJ_T2TEMP_INVTRAN='/mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/affine_t1_to_template/t1_to_template_affine_inv.mat /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/ants_t1_to_temp/greedy_t1_to_template_invwarp.nii.gz'
+ [[ -f /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat ]]
+ export FSLOUTPUTTYPE=NIFTI_GZ
+ FSLOUTPUTTYPE=NIFTI_GZ
+ c3d /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/tse.nii.gz -resample 100x100x500% -region 20x20x0% 60x60x100% -type short -o /tmp/ashs.Cnby5Lqj/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.Cnby5Lqj/tse_iso.nii.gz /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/mprage.nii.gz -ia-identity -o /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat
Executing with the default number of threads: 20
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -2794.25 GNORM= 149.621
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 2 -2924.146 109.067 0.007
2 4 -3034.373 37.773 0.524
3 5 -3044.939 30.753 1.000
4 6 -3049.976 15.754 1.000
5 7 -3052.379 4.685 1.000
6 8 -3052.545 3.139 1.000
7 9 -3052.612 1.684 1.000
8 10 -3052.635 0.824 1.000
9 11 -3052.637 0.255 1.000
10 12 -3052.637 0.315 1.000
11 13 -3052.638 0.220 1.000
12 16 -3052.638 0.294 0.412
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:
0.999306 0.0356028 0.0109462 0.653613
-0.0351229 0.99853 -0.0412838 0.139346
-0.0124 0.0408707 0.999087 -0.121772
0 0 0 1
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -3919.27 GNORM= 44.3568
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -3923.373 15.202 0.004
2 4 -3923.831 10.722 1.000
3 5 -3924.122 9.218 1.000
4 6 -3924.783 14.661 1.000
5 8 -3925.033 1.642 0.473
6 9 -3925.047 0.640 1.000
7 10 -3925.049 0.254 1.000
8 11 -3925.049 0.196 1.000
9 13 -3925.049 0.116 0.405
10 14 -3925.049 0.078 1.000
11 16 -3925.049 0.116 0.472
12 17 -3925.049 0.072 1.000
13 18 -3925.049 0.051 1.000
14 19 -3925.049 0.073 1.000
15 21 -3925.049 0.047 0.458
16 22 -3925.049 0.017 1.000
17 23 -3925.049 0.024 1.000
18 24 -3925.049 0.011 1.000
19 25 -3925.049 0.014 1.000
20 26 -3925.049 0.008 1.000
21 27 -3925.049 0.008 1.000
22 29 -3925.049 0.007 0.489
23 31 -3925.049 0.015 0.281
24 32 -3925.049 0.008 1.000
25 34 -3925.049 0.006 0.288
26 35 -3925.049 0.006 1.000
27 36 -3925.049 0.003 1.000
28 37 -3925.049 0.008 1.000
29 39 -3925.049 0.004 0.400
30 40 -3925.049 0.005 1.000
31 43 -3925.049 0.008 0.340
32 48 -3925.049 0.003 0.414
IFLAG= -1 LINE SEARCH FAILED. SEE DOCUMENTATION OF ROUTINE MCSRCH ERROR RETURN OF LINE SEARCH: INFO= 6 POSSIBLE CAUSES: FUNCTION OR GRADIENT ARE INCORRECT OR INCORRECT TOLERANCESvnl_lbfgs: Error. Netlib routine lbfgs failed.
Final RAS Transform:
0.999296 0.0355927 0.0118783 0.650936
-0.0351086 0.998632 -0.0387397 0.390916
-0.0132409 0.0382954 0.999179 -0.116638
0 0 0 1
*************************************************
N=6 NUMBER OF CORRECTIONS=5 INITIAL VALUES F= -3713.44 GNORM= 31.8025
*************************************************
I NFN FUNC GNORM STEPLENGTH
1 3 -3713.934 10.942 0.001
2 4 -3714.043 9.879 1.000
3 5 -3714.473 13.575 1.000
4 6 -3714.972 19.125 1.000
5 7 -3715.444 23.062 1.000
6 8 -3715.819 8.760 1.000
7 9 -3715.917 6.194 1.000
8 10 -3716.026 6.770 1.000
9 11 -3716.185 8.393 1.000
Final RAS Transform:
0.999293 0.0354505 0.0125347 0.689164
-0.0349685 0.998711 -0.0367817 0.434762
-0.0138225 0.0363174 0.999245 -0.0946095
0 0 0 1
+ c3d_affine_tool /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1.mat -inv -o /mnt/pentagon/mridata/Smith_Merit/Processed_Data/derivatives/ASHS/sub-002/flirt_t2_to_t1/flirt_t2_to_t1_inv.mat
terminate called after throwing an instance of 'char const*'
/ashs/ashs-fastashs/bin/ashs_lib.sh: line 401: 24942 Aborted (core dumped) c3d_affine_tool $SUBJ_AFF_T2T1_MAT -inv -o $SUBJ_AFF_T2T1_INVMAT
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