Re: [Freesurfer] Longitudinal pipeline {Disarmed}

External Email - Use Caution Dear FreeSurfer experts This is just a gentle reminder of my previous mail. Diers Kersten has replied to my query. He asked me to send a few details pertaining to my issue. I shared all the necessary details with you people and waiting for your respons

Re: [Freesurfer] mri_watershed error: problem in the COG calcuation

Make sure it looks reasonable (that there is a brain in there, and the intensities look ok). You can send it to us if you want From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Julia Yang Sent: Wednesday, December 2, 2020 10:27 PM To: Freesurfer support list Subject: Re: [Freesurfer] m

Re: [Freesurfer] flipped_hemisphere

Hi, If you are interested in checking information on the volume itself, try mri_info. If you would like specific examples for reference, I would recommend using our wiki pages. Cheers, Jocelyn From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Edoardo P

Re: [Freesurfer] recon-all issues debugging

Hi Courtney Can you send us the recon-all.log file and the full screen output from one job that failed? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Courtney Haswell Sent: Thursday, December 3, 2020 9:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] rec

Re: [Freesurfer] segmentHA_T1.sh

Hej Olof, The CA segmentations (along with all the others) are generated when calling segmentHA_T1.sh the standard way: segmentHA_T1.sh [SUBJECT_NAME][SUBJECTS_DIR] Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

[Freesurfer] flipped_hemisphere

External Email - Use Caution Hi, after performing a segmentation with Freesurfer and making a Bem model it looks that some results are flipped between right and left hemispheres. Is there a way to check that Freesurfer is interpreting correctly the mri ? Thanks __

[Freesurfer] segmentHA_T1.sh

External Email - Use Caution Hi, I am trying to run the segmentHA_T1.sh with the suffix CA but I seem not be able to write the call correctly How should I call this? best Olof ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu h

[Freesurfer] recon-all issues debugging

External Email - Use Caution I am trying to debug why all of our T1's are failing Freesurfer recon-all. It seems that most of the files are being created but it isn't getting to the stats steps to output those files. In the recon-all log it does say "recon-all -s 13265 exited wi

[Freesurfer] Does segmentation depend on input orientation {Disarmed}

External Email - Use Caution Hi, I ran recon-all twice, once on a T1w image (nifti) with RAS orientation, and once on this image converted to LAS orientation I would expect the output (especially in volume) to be equal, because freesurfer reconverts it to its own orientation if