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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
- I ran it on a T1-MPRAGE image and it looks fine except that there are
no lateral ventricles in the output. See attached.
- 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 https://secure-web.cisco.com/1_vORA_tz_YuBXs18YSfr78M9KFHdcIIdcFRpK9sJiXFWpDjRtIMGcvvfTMZVhsdauKhorZfLyJi2bfjzXqDn9tixg1gQF5EsPxfOBDPN77Kr8gLSFZGynmnEMr9Ldka2Pps0pmxTcjKDlejbd0GssQTFZ1B8yW3vF7Hm_BZhyNalK89E7wlJThaMfKgYFmQeDUYUujBdqoqtIoo_0gX_NdxhbRKvHAPvmKoUEXS_HeCNXLh71cV0OKYsMfGNxcF2EfnBD8loiai1iOOsw-jKhiSBMxzWB8Y1GBW_4OrlWt0xMBJir842mjFGy69XXhEc/https%3A%2F%2Fgithub.com%2Ffreesurfer%2Ffreesurfer%2Fblob%2Fdev%2Frecon_all_clinical%2Frecon-all-clinical.sh. 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