Re: [Freesurfer] make_average_subject error

External Email - Use Caution Yes! Results attached. On Wed, Mar 17, 2021 at 5:54 PM Douglas N. Greve wrote: > > Can you run > ls -l $FREESURFER_HOME/bin/mri_aparc2aseg > $FREESURFER_HOME/bin/make_average_subject > and send the result? > > Also, the result of > which

Re: [Freesurfer] make_average_subject error

Can you run ls -l $FREESURFER_HOME/bin/mri_aparc2aseg $FREESURFER_HOME/bin/make_average_subject and send the result? Also, the result of which mri_aparc2aseg which make_average_subject On 3/17/2021 8:36 PM, Jordan Mullins wrote: External Email - Use Caution Yes, I had seen that

Re: [Freesurfer] make_average_subject error

External Email - Use Caution Yes, I had seen that report and had downloaded the patch, but still got the same error. Are there any other steps I can take? On Wed, Mar 17, 2021 at 2:59 PM Douglas N. Greve wrote: > This problem is documented (along with a fix) on our release

[Freesurfer] Post-doctoral Position in Human Perceptual Neuroscience at NYU

External Email - Use Caution The Perception and Brain Dynamics Laboratory (PI: Biyu J. He, Ph.D.) at New York University is currently recruiting for a post-doctoral fellow to study neural mechanisms of human perception and the interaction between perceptual and cognitive

Re: [Freesurfer] Longitudinal Registration

Where is the non-linear registration coming from? Our long stream uses affine. On 3/11/2021 2:59 PM, Suzan Maleki wrote: External Email - Use Caution Hi FS experts, I appreciate it if you help me with a question on your longitudinal processing pipeline. If I use FreeSurfer to

Re: [Freesurfer] Troubleshooting: Soft Failures

The contrast is pretty low (probably due to the high resolution). Maybe try version 7 or samseg (in version 7). On 3/17/2021 2:01 AM, 崔鹏程 wrote: External Email - Use Caution Hi Douglas: Thanks for your reply.  Please check the attached file for recon-all.log! Cui

Re: [Freesurfer] make_average_subject error

This problem is documented (along with a fix) on our release notes https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes On 3/16/2021 3:39 PM, Jordan Mullins wrote: External Email - Use Caution Yes, I used the make_average_subject command. I've attached a text file below of the

Re: [Freesurfer] Which pial surface to trust, with or without -FLAIR option

We get a lot of variable results with FLAIR. Sometimes it helps, sometimes it hurts. FLAIR scans themselves can be very variable across sites. If it is looking like it is hurting your results, then just run without it. On 3/12/2021 11:07 AM, Xiaojiang Yang wrote: External Email -

Re: [Freesurfer] Difference between V1_exvivo.label and v1.predict.label?

I don't know that anyone has done the comparison before. V1_exvivo.label is based on histological stains (see Fischl, Cortical Folding Patterns and Predicting Cytoarchitecture, 2008, Cerebral Cortex). v1.predict label is from labeling the stria of genari on high-resolution whole hemisphere ex

Re: [Freesurfer] TRACULA error: missing output volume name

Hi Shanika - Can you please send the full log file from scripts/trac-all.log? It's hard to figure out what causes the error without seeing the full output. Nothing looks unusual in the config file. Thanks, Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] mri_vol2surf; --projfrac-avg and --projfrac-max

Yes, 2x the thickness On 3/10/2021 11:17 PM, Horn, Mitchell Jacob wrote: Dear FS Experts, When using --projfrac-max or --projfrac-avg, how is the “min” component defined? If I specify: --projfrac-max -2 1 0.1 Is the min (-2) simply 2x the thickness at each vertex below/inside the GM/WM

[Freesurfer] TRACULA error: missing output volume name

External Email - Use Caution Dear FreeSurfer team I have been running TRACULA for some time now but recently, I come across a message "missing output volume name" and I cannot do preprocessing in new or old subjects (even subjects who completed preprocessing without error) I

Re: [Freesurfer] Freeview segmentation fault on Mac OS X High Sierra

External Email - Use Caution Hello Mikael. I don’t see a crash report/attachment with your posting. You could just cut and paste the error output from the terminal followed by a cut and paste of the first page of the crash report directly into the actual email - if you like. -

[Freesurfer] Software Engineering job annoucement at LCN in the Martinos Center (MGH)

The Lab for Computational Neuroimaging (LCN) at the Martinos Center at MGH is seeking a highly motivated software engineer to be responsible for maintaining and testing existing software as well as to help implement new algorithms in C++ and Python. Members of LCN develop software for the

[Freesurfer] Freeview segmentation fault on Mac OS X High Sierra

External Email - Use Caution Dear experts, I recently updated to FreeSurfer 7.1.1 but this caused Freeview to stop working. I can neither use the terminal command ”freeview” or open it through the .app in Finder. I get a ”Segmentation fault: 11”. I attach the crash report

Re: [Freesurfer] Meylin overlay

External Email - Use Caution Yes. After I updated the freeview it worked! Thanks a lot Matt. Mudathir > On Mar 17, 2021, at 11:49, Glasser, Matthew wrote: > > External Email - Use Caution > > > There is a bug in Freeview, I believe it has been fixed in