External Email - Use Caution 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 <mich...@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 > <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 > >
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