Re: [Freesurfer] Directory

Hi Asa, Give a try of mris_register - https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register Here is the syntax: mris_register [options] All three parameters should take full path to your files. Combining the information I got from surfreg script, is ?h.reg.template.tif from fsaverage_s

Re: [Freesurfer] Directory

External Email - Use Caution Hi Yujing, thanks for your response Yes my subject directory is /tmp/HCP. But I cannot modify it, so I’d like to reference and use the fsaverage_sym template which is located outside of the subjects directory. Is this possible? If not then I’ll have

[Freesurfer] Along- tract multiple comparison result visualisation and summary interpretation

External Email - Use Caution Hello,I have questions regarding the along-tract stats using mri_glmfit and mri_glmfit-sim with permutation for version 7.2.1) I ran it and I found a significant result (see attached summary file) where I expected/found a negative association between

[Freesurfer] MGH35 template

External Email - Use Caution Dear Freesurfer developers, Hi, this message may have slipped through the cracks, hope someone can help us out on this. We're looking for the T1 image that goes along with (i.e. in same space, or at least in same participants) as the MGH35_HCP_F

Re: [Freesurfer] Freeview 'quit unexpectedly' before opening

Would it be possible to send us the full crash report? You can find it in the Console app. Best, Ruopeng On Feb 8, 2023, at 1:48 PM, Rankin McGugin mailto:rankin.mcgu...@gmail.com>> wrote: External Email - Use Caution Here is my error log: Last login: Wed Feb 8 12:03:23 on ttys000

[Freesurfer] Fwd: Freeview 'quit unexpectedly' before opening

External Email - Use Caution Here is my error log: Last login: Wed Feb 8 12:03:23 on ttys000 Rankins-MacBook-Pro:~ rankinmcgugin$ export FREESURFER_HOME=/Applications/freesurfer/7.3.2 Rankins-MacBook-Pro:~ rankinmcgugin$ source $FREESURFER_HOME/SetUpFreeSurfer.sh free

[Freesurfer] Freeview 'quit unexpectedly' before opening

External Email - Use Caution Hello, I am a longtime FS user. I have read threads on this topic but no suggestions work in my case. I have the license file in place. I removed my previous version of FS and have updated to 7.3.2. However, now when I try to start Freeview, I get th

Re: [Freesurfer] Directory

I think you can try to use mris_register directly. https://surfer.nmr.mgh.harvard.edu/fswiki/mris_register From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Huang, Yujing Sent: Wednesday, February 8, 2023 11:05 AM To: Freesurfer support list Subject: Re: [Freesurfer] Directory Hi As

[Freesurfer] password for the developer account of Ubuntu Freesurfer VirtualBox

External Email - Use Caution Could you please send me the password for the developer account of Ubuntu Freesurfer VirtualBox? Thank you, Don ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/m

Re: [Freesurfer] Directory

Hi Asa, I'm wondering if your SUBJECTS_DIR is /tmp/HCP? It looks like surfreg checks if target is 'fsaverage_sym'. Can you try passing just 'fsaverage_sym'? Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Asa Borzabadi Farahani Sent: Wednesday, February 8, 2023 10:38

[Freesurfer] Directory

External Email - Use Caution Hi there experts! I’m hoping to use the surfreg function on some data in which I can’t make any modifications to the subject directory (I’m using a cluster and the data is for public use thus prohibits any changes to it). I want to use the fsaverage