[Freesurfer] Pass code

External Email - Use Caution Hello, I have downloaded the FreeSurfer Vitrual VM images for my research project and a pass code is required to open the image. As mentioned in the guidelines https://secure-web.cisco.com/1oZit62PBJoLikTlTdvtgmPiBPc4ThiBZJNpYfu6IvCxQzVN4benp3jbBBux

Re: [Freesurfer] Samseg lesion mask holes

Hi Evie, --save-probabilities and --save-posteriors will save two different things for lesions. The former is an initialization of lesions based on intensity and location constraints, and the latter is a probability map of seg.mgz after we also introduce lesion shape constraints (Cf Fig.4 of h

Re: [Freesurfer] How to extract hippocampus from nu.mgz using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

Hi Minh, I think you can first use mri_binarize to obtain the mask, then apply the mask to nu.mgz using mri_mask. https://surfer.nmr.mgh.harvard.edu/fswiki/mri_binarize https://surfer.nmr.mgh.harvard.edu/fswiki/mri_mask Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of

Re: [Freesurfer] White matter exclusions occurring in v7.3.2 but not v5.3

Frm an automated standpoint, there is not much more to do. That area may be part of the medial wall anyway. If you want to fix it manually, you will have to cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz Then edit the manedit in freeview to fill in those regions with 255 Then rerun recon-a

Re: [Freesurfer] Manual of Freesurfer to Learn the Software from Zero to advanced Level

Hi Ahsan, You can find information on the Freesurfer wiki. https://surfer.nmr.mgh.harvard.edu/fswiki/ There are tutorial videos here: https://surfer.nmr.mgh.harvard.edu/fswiki/TeachYourselfFreeSurfer Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Ahsan Ali Sent: Tues

Re: [Freesurfer] Which motion correction parameters are used in FSFAST?

These are not the basic translations and rotations, rather: mcprextreg - text file of the motion correction parameters assembled into an orthogonalized matrix that can be used as nuisance regressors I don't know what your design is, please send your mkanalysis command lie On 3/29/2023 12:45 AM

[Freesurfer] FLAIRpial bug

External Email - Use Caution Dear developers, We encountered the bug related to the analysis with FLAIR in recon-all (recon-all -s ${subj} -i T1.nii.gz -FLAIR FLAIR.nii.gz -FLAIRpial -all). We obtain a worse segmentation with FLAIR than only with T1. We use FreeSurfer v. 7.3.2

[Freesurfer] Longitudinal processing of single time point data

External Email - Use Caution Dear Freesurfer experts, I am processing longitudinal data from subjects participating in a pre-post analysis; a few subjects do not have follow-up data. I'd like to still include these subjects and plan on using mixed effects analysis methods given

Re: [Freesurfer] How to extract hippocampus from nu.mgz using lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz

Dear Minh, Maybe user mri_binarize on lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz to create a mask, and then use mri_mask to extract the hippocampus? Cheers, /E -- Juan Eugenio Iglesias http://www.jeiglesias.com From: on behalf of Hoang Gia Minh Reply-To: Freesurfer support list Date: Tuesday,

Re: [Freesurfer] Longitudinal processing of single time point data

Hi Chris, Since there is only one timepoint, the base recon-all command will look like this: recon-all -base -tp -all is the subjectID for the one timepoint you have. Not sure how you named . It should be an unique name in your SUBJECTS_DIR. Hope this helps. Best, Yujing From: freesurfer

[Freesurfer] error with synthsr in Mac M1

External Email - Use Caution Hi developers, I'm Using freesurfer-darwin-macOS-dev.pkg (the ) which is developed in march 2023. Also my system is Apple M1 max (MacOS Ventura 13.2.1). When I run synthsr, I receive an error: mri_synthsr --i /Users/Hyperfine/028 --o /Users/Hyperf

[Freesurfer] Autrecon-pial command

External Email - Use Caution Hello all, Does -autorecon-pial flag also recreate the statistics tables with the new surfaces? or do you have to run autorecon3 after to recalculate stats files? Tks, Carlos ___ Freesurfer mailing list Fre

Re: [Freesurfer] Autrecon-pial command

Hi Carlos, It looks like -autorecon-pial has all -autorecon3 steps. I believe it will recreate the statistics tables. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Carlos Alcocer Sent: Wednesday, March 29, 2023 7:10 PM To: Freesurfer support list Subject: [Freesurfe

[Freesurfer] Tracula, trac-all, bug in interreg

External Email - Use Caution Hi, I've been trying to configure Tracula to use different inter-subject registration methods. It fails for type #3 (robust cost) and #4 (nonlinear CVS). From the trac-all script (line #1634), it looks like Tracula points to different trctrain template