I don't think it will improve it all that much to run the long stream on this. Just pick one of the TPs and use that. If you still want help on the long stream. Start with the first error and send the recon-all.log file.
On 8/23/2021 4:21 AM, Robin Kämpe wrote:
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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://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing
"...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 *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://secure-web.cisco.com/15tLPkzOOjinGp7ztirAETf15D3Q8ETWtMs3R1sqMS9rpNUyXq5QtXPJBc6IUBOsrORBwvjjYZ6yuY4lvRsccwYYtIC31m-x32QocRXvaXWu9ChRX71Pd3kArpUJeanX14T6qiyLlK5__JTetaviKvbUPzKeqoGmBfdTKPb_pWwbBxTRuRlfK3LW_uhU2AV5XZeWmI6q9tGKlpndCxp-O7y9dDa9lIY47FUnVdm0ahrcK6_-6RoVoH6PqTRqLNBN8NriuOdgzbCHUQn3BStmqcg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting
*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:
Thanks!
Robin Kämpe Research engineer
CSAN, Center for Social and Affective Neuroscience
Department of Clinical and Experimental Medicine, IKE Phone: +4673-8005561
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1VwaRz0BJ8E8eH6oUwdVjt5UXwbX5eZbUtGlNA02Q-q5H7W...
