External Email - Use Caution
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/1by8vHZBkgali1lqEExldl9RRMDAvkcckApenn9NS-6rjgSKLo5qIUqnPNUWVuYYrqvir3eOqxfthWszlQKDrjt3tr2uHkrrhgVrTq4elS80ju5M0rcS9ZeaaV2rkeNGFpkdZ38977iDCM0cplU4GLNw7nhbpUvRKmAe0E2iulNqPEbWRFWtyBTTVcfQ-4I4RYaVNO_3uV-m6YlKOpz-c1cN0GmLvdHUiXO9WyKwgZwiLdVNQaZCn4DNQKVNwotbRtsPPxVOxzmb3oiKZpjnyCUNOgf5lHFQf1qh0xdTi0kHPu-2TirBonKyJbwuw3lDw/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
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 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
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 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
- 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/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
External Email - Use Caution
So when I fixed those two _thresh errors in
https://secure-web.cisco.com/1NSg93ccyJ-d1nRYxQp22qqxh0VpV5ftKk_nXjpyVVwbCeR...
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
- 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/1NSg93ccyJ-d1nRYxQp22qqxh0VpV5ftKk_nXjpyVVwbCeR6Hrc55wa7clBot2_7TwVB60Mr2knHiVv8A4Mfl2qmBr5BYBGmlurvKxK7tkVb_5cRm_5FEI_GvOXQuD2koygzRKJ-i9xNxRvWZdKOxuYG-tyuRwO9v-AdgHd7Hh9JHtaZBxs_lSVtIP240zo9HyXSvshgmuVe4pfIrL4_Wvod_9PgcTNm9cAuaW-RaJK_zO9AOe8CixcXkaG_SLZQp9Ou86eoY5TJMOnUVWCBf_opB5Pl4QyOFRI0arqOWt-I6cur7E-SZu4pjFrkCzr3oJjVJhHsxQnclEt4462twOg/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
freesurfer@nmr.mgh.harvard.edu
-
Michael Mc Laughlin