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

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!