[Freesurfer] Question regarding General Linear Model analysis with Freesurfer

External Email - Use Caution Hi! I hope you are doing well! I am working on a paper where we used Freesurfer for whole brain analysis in intergroup comparison (g2v1). The objective of the analysis is to see if there is an association between neuropsychiatric symptoms and brain

[Freesurfer] conversion of .stats to .csv

External Email - Use Caution Dear Team, I would like to convert the .stats files that are being generated in the stats folder as an output from recon-all to csv file or excel file. Is there any way to convert .stats to .csv or .excel format? any help on this would be much apprecia

Re: [Freesurfer] overlay_threshold is ignored when using custom overlay

Hi Maya, Custom color table is always continuous. So it will not automatically mask out a portion in the middle. The overlay_threshold option is not for custom colormap. I think we can add an option to allow specifying colors with 4 components where the last one is for alpha/transparency. Ruop

[Freesurfer] overlay_threshold is ignored when using custom overlay

External Email - Use Caution Hello, I'm trying to use a custom colormap for an overlay in Freeview and I can't get the threshold option to work. Specifically, I want to display positive values with specific colors, and negative values with different colors, similarly to using t

[Freesurfer] acompcor in fsfast

Hi, I am running resting State functional connectivity and I want to run everything in freesurfer and fsfast. I wanted to know is it is possible to run acompcor in fsfast. If so, how do I go about it. Thanks. Get Outlook for iOS __

Re: [Freesurfer] MRI recon-all failed at talairach

External Email - Use Caution It looks like your terminal/character settings are messed up in the current terminal session.  That can happen from trying to look at a raw binary or image file in the terminal window or running something that outputs non-standard characters to the

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

External Email - Use Caution It says "command not found" (when I run 3dvolreg and 3dvolreg.afni)! On Wed, Oct 26, 2022 at 7:24 AM Douglas N. Greve wrote: > What happens when your run 3dvolreg.afni by itself (no options) from the > command line? > > On 10/25/2022 4:41 PM, Gillia

Re: [Freesurfer] Issue with rotation during longitudinal base creation

Hi Nathan, Can you confirm that the error was from mri_robust_template? Not sure what your command line options. I think these options ‘—inittp <>’, ‘--fixtp’, ‘—seed <>’ might help. Best, Yujing Forwarded Message Subject: [Freesurfer] Issue with rotation during longitudina

Re: [Freesurfer] dt_recon eddy correction fail and freeview errors

Do you see a filed called dwi-ec.nii.gz? That should be the output of eddy_correct. The log file says it is running it. Two min does seem a little fast for 60 directions; I have another case that does 340 in about 40min. Try running eddy_correct outside of dt_recon and see what happens., On 1

Re: [Freesurfer] Preproc-sess crashed - 3dvolreg.afni error

What  happens when your run 3dvolreg.afni by itself (no options) from the command line? On 10/25/2022 4:41 PM, Gillian Grennan wrote: External Email - Use Caution Hello FreeSurfer Developers, I downloaded Freesurfer v7.3.2

Re: [Freesurfer] MRI recon-all failed at talairach

What is the error? The funny characters? Can you just send the entire logs (recon-all and avi.log)? On 10/25/2022 11:49 AM, Jonany, Vincent Joe wrote: External Email - Use Caution Dear FreeSurfer Developers, I am encountering a weird error in performing recon-all in my dicom direct

[Freesurfer] PostDoc (or qualified PhD) in Cognitive Computational Modeling (fMRI) in Copenhagen

External Email - Use Caution We are hiring a PostDoc (or qualified PhD student) on cognitive computational neuroimaging. This position is for you if you are interested in how the dopamine system works and like computational modeling. You would be part of a small and dynamic res

[Freesurfer] dt_recon eddy correction fail and freeview errors

External Email - Use Caution Dear Freesurfer Developers, I am trying to perform the dt_recon command for a single participant of my dataset. The original data comes from a philips scanner and was in the PAR/REC format. I converted these files to nifti’s using dcm2niix. This se