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:

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------------------------------ 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

-long /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: