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Hi Freesurfer Community and developers! First time poster here!
I am running freesurfer version 7.1: freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
We have 2 sessions of MRI-data from each participant, separated with about 1-2 months. We don't want to compare Freesurfer parcels, but we use Freesurfer to get good parcelations which we later use as masks in the fMRI-analysis. Since we do have two T1w images per subject, I thought to use the longitudinal pipeline to get more stable results as per: https://secure-web.cisco.com/1C82j67WZziPcBPH-8KbA5rOwb-isVXVvr87pgVrBwGd2MV...
"...a longitudinal design can significantly reduce the confounding effect of inter-individual morphological variability by using each subject as his or her own control"
I know this gude is for FS <= 6.0 but I could not find any specfic instructions for FS 7.1, which meant that I used an old script from when I did this sucessfully in the past with FS6.0.
The pipeline is basically: TP1=/path_to_timepoint1/1_sT1W_3D.nii TP2=/path_to_timepoint2/2_sT1W_3D.nii
#Run each TP seperatley #TP1 recon-all -all -s TP1 -i $TP1 -sd $subject_dir -parallel & PIDT1=$! #TP2 recon-all -all -s TP2 -i $TP2 -sd $subject_dir -parallel & PIDT2=$! wait $PIDT1 wait $PIDT2
#Wait until TP 1-2 are done and create template recon-all -base ${subject}_Template -tp TP1 -tp TP2 -all -sd $subject_dir -parallel
These two steps generates, in each subject-dir, the directories TP1, TP2 and subX_Template. The recon-all.log files under scripts say all these processes finished without errors (TP1+TP2+Template), which is really good.
Then comes the final step: #TP1 recon-all -long TP1 ${subject}_Template -all -sd $subject_dir & PIDT1=$! #TP2 recon-all -long TP2 ${subject}_Template -all -sd $subject_dir & PIDT2=$!
wait $PIDT1 wait $PIDT2
Which generates the dirs TP1.long.subX_Template TP2.long.subX_Template
So far so good. But these two finished WITH ERRORS. When searching the recon-all.log files under TP1.long.subX_Template/scripts and TP2.long.subX_Template/scripts it is the same error for both TPs:
Half way through the recon-all.log file:
SUBJECTS_DIR /home/robka/BG_FS_temp/sub102 FREESURFER_HOME /usr/local/freesurfer Loading source label. error: Invalid argument error: mri_label2label: could not open label file /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label\00 ERROR reading /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label Command exited with non-zero status 1 @#@FSTIME 2021:08:20:16:47:37 mri_label2label N 12 e 0.00 S 0.00 U 0.00 P 100% M 5672 F 0 R 202 W 0 c 0 w 1 I 0 O 0 L 12 4 44 @#@FSLOADPOST 2021:08:20:16:47:37 mri_label2label N 12 12 4 44 Linux maul 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:21:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s TP1.long.sub102_Template exited with ERRORS at fre 20 aug 2021 16:47:37 CEST
And at the very bottom:
SUBJECTS_DIR /home/robka/BG_FS_temp/sub102 FREESURFER_HOME /usr/local/freesurfer Loading source label. error: Invalid argument error: mri_label2label: could not open label file /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label\00 ERROR reading /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label Command exited with non-zero status 1 @#@FSTIME 2021:08:20:19:47:29 mri_label2label N 12 e 0.00 S 0.00 U 0.00 P 100% M 5680 F 0 R 203 W 0 c 0 w 1 I 0 O 0 L 93 2 97 @#@FSLOADPOST 2021:08:20:19:47:29 mri_label2label N 12 93 2 97 Linux maul 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:21:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s TP1.long.sub102_Template exited with ERRORS at fre 20 aug 2021 19:47:29 CEST
To report a problem, see http://secure-web.cisco.com/15tLPkzOOjinGp7ztirAETf15D3Q8ETWtMs3R1sqMS9rpNUy...
Output of TP2s recon-all.error log (sampe for TP1): ------------------------------ SUBJECT TP2.long.sub102_Template DATE fre 20 aug 2021 19:47:02 CEST USER robka HOST maul PROCESSOR x86_64 OS Linux Linux maul 4.15.0-147-generic #151-Ubuntu SMP Fri Jun 18 19:21:19 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux 7.1.0 (freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b) /usr/local/freesurfer/bin/recon-all PWD /home/robka/BG_FS_temp/sub102/TP2.long.sub102_Template/label CMD mri_label2label --srcsubject fsaverage --srclabel /home/robka/BG_FS_temp/sub102/fsaverage/label/lh.BA1_exvivo.label --trgsubject TP2.long.sub102_Template --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface
Output of unknown-args.txt (same for both TPs): -long TP1 sub102_Template -all -sd /home/robka/BG_FS_temp/sub102
Only warning I can see is that TP1 and TP2 has different resolutions. Both have exactly the same matrix dims but differ a little in mm resolution: 1x1x1 mm vs 0.9999x0.99999x1 mm. I.e. minor difference.
I also ran the script with the two commands using -parallel: #TP1 recon-all -long TP1 ${subject}_Template -all -sd $subject_dir -parallel & PIDT1=$! #TP2 recon-all -long TP2 ${subject}_Template -all -sd $subject_dir -parallel & PIDT2=$! This also failed but only with one error that I could not figure out.
Any ideas of how to find the problem here? =) The two images don't have apparent issues:
[cid:ceb92c6f-2d9d-484a-8221-71760fdcca23]
Thanks!
Robin Kämpe Research engineer
CSAN, Center for Social and Affective Neuroscience Department of Clinical and Experimental Medicine, IKE Phone: +4673-8005561
