So when I fixed those two _thresh errors in

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The script runs all the way through without any errors but there is still one big problem and some smaller niggles:

1) The lateral ventricles are missing e.g. in mri/brain.mgz. I tried two different T1 input images of the same brain.

2) The stats/aseg.stats file is missing

3) (Minor) It doesn't tell me how long it took to run which I found helpful in the recon-all script

On Thu, Jun 22, 2023 at 4:30 PM Michael Mc Laughlin <michael@thecurate.com> wrote:

Actually, that is not the problem at all.

I have found two errors in your script (the one on Github)

There are two lines which refer to colortable_BA_thresh.txt that should say /colortable_BA.txt

The script gets further when I fix those but I still have errors. The first one is:

vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
Writing annot to /home/michael/subjects/jun23mpsynfix/label/rh.BA_exvivo.thresh.annot
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading volume /home/michael/subjects/jun23mpsynfix/mri/wm.mgz...
reading input surface /home/michael/subjects/jun23mpsynfix/surf/rh.white...
Using TH3 vertex volume calc
Total face volume 254138
Total vertex volume 253934 (mask=0)
reading input pial surface /home/michael/subjects/jun23mpsynfix/surf/rh.pial...
reading input white surface /home/michael/subjects/jun23mpsynfix/surf/rh.white...
error: No such file or directory
error: could not read annot file ./rh.BA_exvivo.annot
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
I think the first line here is writing to the wrong filename.

On Thu, Jun 22, 2023 at 1:22 PM Michael Mc Laughlin <michael@thecurate.com> wrote:

I found the problem. Your script has the following lines :

You need to delete the fsaverage from the $SUBJECTS_DIR definition because the lines following it put it in also.

ln -s $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/
cd ../label

# labels
set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject $SNAME --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface"

On Thu, Jun 22, 2023 at 11:23 AM Michael Mc Laughlin <michael@thecurate.com> wrote:
I tried recon-all-clinical and there are two main problems

1) I ran it on a T1-MPRAGE image and it looks fine except that there are no lateral ventricles in the output. See attached.

2) I get lots of errors at the end.

I read the following note in the release notes:

Please replace $FREESURFER_HOME/bin/recon-all-clinical.sh with the latest version HERE. Development versions newer than June 15th 2023 do not have this problem.]

I am not a linux expert, so I don't know how to download that file. If I could download it I am sure I could manage to replace it in the bin directory.

I made an attempt by clicking on the link and copying the text from my browser into a new text file. I used this to replace the supplied file, but I still get errors. Maybe I screwed up.

Michael McLaughlin,
Island View, Beulah Court,
Harbour Road, Dalkey
Co. Dublin
Ph:+353 87 688 2514

ln -s $FREESURFER_HOME/subjects/fsaverage $SUBJECTS_DIR/
	cd ../label

	# labels
	set cmd="mri_label2label --srcsubject fsaverage --srclabel $SUBJECTS_DIR/fsaverage/label/lh.BA1_exvivo.label --trgsubject $SNAME --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface"