Re: [Freesurfer] Hypothalamus segmentation using hypothalamic subunits vs ScLimbic

Dear Asmin, The discrepancies arise from differences in anatomical protocols. You can look at the definitions in the corresponding papers and keep the one that adapts better to your needs. The results should be fairly highly correlated. Kind regards, Eugenio -- Juan Eugenio Iglesias http://www.j

[Freesurfer] Password for Zip file

External Email - Use Caution Hello, I am trying to set up the software using Virtual Box but require the password for the zip file? Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman

[Freesurfer] Hypothalamus segmentation using hypothalamic subunits vs ScLimbic

External Email - Use Caution Dear FreeSurfer Experts, I have a question regarding how the hypothalamus volumes are calculated using the hypothalamic subunits function, as opposed to the ScLimbic deep learning tool which is only currently available in the dev version of Freesurfer.

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

External Email - Use Caution Hello, Please, can someone answer my 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 negative association between FA and clinical score (see attached

Re: [Freesurfer] how the variance calculated for t-value in the first level GLM in fsfast

This is just straight-forward GLM, ie, beta = inv(X'*X)*X'*y (y is the input time series after preproc) yhat = X*beta residual = y - yhat residualstd = sum(residual.^2)/DOF  (DOF = rows of X - cols of X) t = C*beta/sqrt(C'*inv(X'*X)*C*residualstd) where C is the contrast matrix On 3/10/2023 4:50

Re: [Freesurfer] mri_glmfit with age-squared

It is probably a scaling problem with using age^2. Try normalizing the age^2 column (ie, remove the mean and divide by the sum of the squares) On 3/9/2023 3:30 PM, Triebswetter, Curtis wrote: External Email - Use Caution Hello Freesurfer experts, I am attempting to run the command m

Re: [Freesurfer] How to find topological defects

not really. I usually add them to benefit my own work (I'm a user in addition to a developer). I'll try to write them down as I go alonjg On 3/7/2023 5:14 PM, KennethSPrice wrote: External Email - Use Caution Amazing, thanks. Any place to see a list of more shortcuts like this? -Ken -

Re: [Freesurfer] mri_segstats

You can pass it a --mul SCALE option to multiply the output by any scaling factor On 3/7/2023 1:16 PM, John Anderson wrote: External Email - Use Caution Dear Freesurfer community, Please forgive me for the basic nature of my question. I was wondering whether there is an argument that

Re: [Freesurfer] Apply a nonlinear transform to a surface.

or use mris_apply_reg with the --m3z option On 3/4/2023 10:56 AM, Fischl, Bruce R.,PHD wrote: You can try mris_transform, although you might need to convert the nonlinear warp to our format. I’m pretty sure others have done this, so maybe someone else can comment? Cheers Bruce *From:* free

Re: [Freesurfer] Freeview error

Hi, This error suggests that your cluster instance is not able to find the swrast drivers: libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast swrast is a software renderer. It is provided by libgl1-mesa-dri library. If the library is not installed, you c

Re: [Freesurfer] Error using chol

probably something wrong with your stimulus schedule (paradigm). Can you send the X.mat (or Xtmp.mat)? On 2/28/2023 12:12 PM, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi! I am running into an issue with fast_selxavg3b. I am attempting a first level PPI analysis. The

Re: [Freesurfer] white and pial surfaces of the hippocampus

We do not have a way to generate surfaces for hippocampus. You could play with the subfields, eg, like mri_binarize --i subfields.mgz --match M1 M2 ... --surf lh.hippo --surf-smooth 2 This will build a surface around segments M1, M2, ... you can then view with freeview On 2/28/2023 8:42 AM, Kh

Re: [Freesurfer] Freesurfer v. 7.3.2 careg error

Hi Simon, In 7.3.2, as you mentioned if you split recon-all into multi stages, '-careg' needs to be specified on the command line for autorecon2. This has been fixed in dev version. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Simon Jones Sent: Monday, March 13, 2023 6

[Freesurfer] Freesurfer v. 7.3.2 careg error

External Email - Use Caution Dear Freesurfer Support, Under older versions of Freesurfer such as 7.2.0 I can split recon-all into two stages: recon-all -autorecon1 -noskullstrip -s sub -i sub.nii.gz Manually create brainmask.mgz recon-all -autorecon2 -autorecon3 -s sub Using free