External Email - Use Caution 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 <mich...@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 < > 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/1eutngO8x-cnInx1UiwsTbUiqH_J1FFbPlrpb5nep4tp2FGeHLJWhr62zennTxHmyfhhMHTJzmalKsH0Fdcu6w0oMQfc2GF0N9oMVNXiAEcHqkI4mvXcTc7ePooxDCG5UCgNGiFenjonRI6mPtOMcoDwmSooKSvTh_ksg-rc74kjqKpN6HLspakn60zmk6jXU4w0Bh8htbWlOviPNDEURamRYORlPBiAdDh-wTZe8S_t-ZYsJtMpwRSnt-auni2swkTn_zQMUPp4Ts9hKgR4pQACuUBfP6hDgwqyQ1rfn9Ifboo4di1fuq-Oxq22KB_nq/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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