[Freesurfer] Turning Significant Cluster (sig.cluster.summary or sig.mgh) into binary .nii ROI

External Email - Use Caution Hello, I have been struggling to figure out a way to get the significant results of a freesurfer group analysis (just one significant cluster) from either the sig.cluster.summary or sig.mgh file into a binarized ROI in .nii format. I used mri_glmfit

Re: [Freesurfer] MACBOOK PRO M1 Monterey

External Email - Use Caution Hello Zaenab, The package you highlighted, freesurfer-darwin-macOS-dev.pkg, is the one to install on the Mac to use the development build with the latest updates.  If you’ve run other Mac package installers, then the steps should be familiar to you w

[Freesurfer] MACBOOK PRO M1 Monterey

External Email - Use Caution Hello, For downloading the development version of FS which package of the ones available you recommend (attached screen shot), Since the new computer I have is Macbook Pro M1 Monterey ( brand new with no other OS installed other than its built in MacOS

[Freesurfer] FWHM errors for mri_glmfit-sim for lgi?

External Email - Use Caution I receive FWHM values much larger than what average/mult-comp-cor/fsaverage/rh/cortex has (around ~50) w/ LGI, but normal when looking at GM thickness. Is this expected? Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- cd /mnt/V/Data

[Freesurfer] Tkregister2 not opening GUI

External Email - Use Caution Good afternoon, I am trying to verify the registration and for some reason the GUI is not opening. I am using a Macbook Pro running macOS Montery with a 2.4 Gz Quad-Core Intel Core i5 I have Freesurfer version: maOS-7.2.0 I do not get an error whe

Re: [Freesurfer] recon-all outpputs for deep learning

External Email - Use Caution I have a python module that extracts everything I considered useful from a full recon-all output folder for machine learning. I actually used it for predicting ASD. Have a look here: https://secure-web.cisco.com/1y2aCFTmfPbByJKeWu1_Uh_jIlFUNKJ_d_VL4

Re: [Freesurfer] recon-all outpputs for deep learning

External Email - Use Caution great .. I want the sizes of the sub-cortical regions, will I depend here on the output of the mri folder, for example the image wmparc .mgz, or do I need another image or other data? Is there a reference that can help me extract image features for de

Re: [Freesurfer] GLM analysis - volume and surface area

External Email - Use Caution Of course! To do GLM for volume and surface area analysis, is there any change in commands in relation to cortical thickness analysis? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the

[Freesurfer] how to load flat surface in freeview

External Email - Use Caution Dear Freesurfer experts, I'm trying to load the flat surface that I created with this command line: mris_flatten -w 10 lh.full.patch.3d lh.full.flat.patch.3d I tried loading the patch inside freeview but I got this error message: [francesca@GIOVE sur