Re: [Freesurfer] register to mni space

External Email - Use Caution Dear Douglas N. GreveAs you commented, the command, you suggested, transformed well from the aparc+aseg.mgz with native space to MNI 152 space. I also tried the command to transform fiber bundles (the merged_avg33_mni_bbr.mgz), extracted from TRACULA, t

[Freesurfer] Request for password to unzip pre-installed VM freesurfer.

External Email - Use Caution Hi, could anyone inform me what is the the pass code needed to unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z archive? I requested it a few days ago but got no response, so I'm asking once again in case my message got somehow unnoticed. (P.S.: I also check

Re: [Freesurfer] mris_register options

External Email - Use Caution FYI, there is also a make_folding_atlas script, though you won't be able to fine tune the parameters when it runs mris_register On 5/8/2023 10:12 AM, Fischl, Bruce R.,PHD wrote: External Email - Use Caution Hi Jan If you create a family t

Re: [Freesurfer] Hemisphere Volume

External Email - Use Caution No, it is not there explicitly. You can compute it yourself using these measures # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 226058.544078, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter v

Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

External Email - Use Caution what is the justification for using half that? 7.3 is not high in general. what scanner are you using? On 5/8/2023 4:27 AM, Federica Di Antonio wrote: External Email - Use Caution Dear experts, I am here again because I'd like to  ask a spe

Re: [Freesurfer] Question about volumetric atlas ROIs overlap

External Email - Use Caution I don't understand what you are referring to. Can you elaborate? On 5/5/2023 7:53 PM, Nadvar, Negin wrote: External Email - Use Caution Hello, I have a general question about handing atlas ROIs after applying recon-all on a T1W image. Coul

Re: [Freesurfer] mris_register options

External Email - Use Caution Hi Jan If you create a family template you will only be able to compare within family, unless you also align the templates I guess? -nonorm will disable z-normalization of curv and sulc. We typically start with a single subject atlas, do a nonlinear

Re: [Freesurfer] error with mri_convert from nii made from TIFFs

External Email - Use Caution Hi Andrew, Freesurfer currently doesn’t support RGB and RGBA datatypes. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Andrew M Sent: Sunday, May 7, 2023 3:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] erro

[Freesurfer] mris_register options

External Email - Use Caution Dear Doug Dear Bruce Martin Reuter suggested me to write you since you are familiar with true inner workings of free surfer. In my project I try to create a family specific template that is based on three or more family members. We try to avoid the

[Freesurfer] Hemisphere Volume

External Email - Use Caution Dear FreeSurfer administrator *I hope everything is alright. I want to get some help from you.* I'm using FreeSurfer version 7.2.0. I want to obtain the total volumes of the left and right hemispheres separately. However, I could not see this infor

Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

External Email - Use Caution Dear experts, I am here again because I'd like to ask a specification about the fwhm that the alghoritm evaluates: the main value that I obtained was 7.3 mm; It is an high value for a pv correction. May I put in half the value? Because I wonder if the