Re: [Freesurfer] Import Matlab SynthSeg labels to FS

External Email - Use Caution Dear Haley, The Matlab version of SynthSeg writes nifty files. You could run the FreeSurfer command to convert to mgz (and rename to aseg, along the way): mri_convert synthseg.nii.gz aseg.mgz Now: I don’t know if it’s possible to simply replace FreeS

Re: [Freesurfer] Questions about the different ways in which metrics such as the cortical surface area can be extracted in Freesurfer

External Email - Use Caution It looks like you are transforming it to fsaverage space before computing the statistics. If this is correct, then that will explain the differences as that transform will involve some interpolation which will change the values. But they should be ver

Re: [Freesurfer] Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged

External Email - Use Caution Sorry, I don't have your previous email so I don't know what the context is. Can you resend this email with the previous exchanges included at the bottom? Also, please remember to send to the FS list instead of us personally. thanks! doug On 8/24/2

Re: [Freesurfer] CSF map

External Email - Use Caution You can try mri_binarize --i aseg.mgz --csf --o csf.mgz to get a binary map Note that the aseg does not have sulcal CSF labeled. But you can get that with something like samseg --i orig.mgz --o samseg Then run mri_binarize on the seg.mgz file On 8/2

Re: [Freesurfer] Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged

External Email - Use Caution Sorry for sending to the wrong place, will do in the future. Here it is. Thanks for the suggestion! The two fov indeed don't align in freeview. I played a little with the --no-resample option but did not acheive what I wanted. Here I simplified the p

Re: [Freesurfer] CSF map

External Email - Use Caution Very interesting. Thanks. On Mon, Aug 28, 2023 at 2:52 PM Douglas N. Greve wrote: > External Email - Use Caution > > You can try > mri_binarize --i aseg.mgz --csf --o csf.mgz > to get a binary map > Note that the aseg does not have sulcal CS

Re: [Freesurfer] Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged

External Email - Use Caution To confirm, the two volumes *without any transformation (ie, "untouched")* do not align in FV but they do align in fslview? In other words, they align in voxel space but not in RAS space? To just copy the geometry, run mri_convert run2.nii.gz --in_lik

[Freesurfer] Cerebellum ROI

External Email - Use Caution Hello Freesurfer developers, I want to create a ROI in fsaverage space including only certain regions of the cerebellum cortex. Is it possible to use/extract the labels from the "# Cerebellar parcellation labels from SUIT" or "# Cerebellar lobule par

Re: [Freesurfer] Copy geometry (fov position) from one header to another while keeping voxel and matrix sizes unchanged

External Email - Use Caution Exactly, the two runs align in voxel space but not in RAS space. mri_convert with the --in_like did the trick, thank you very much. Now I have another scenario where the two runs also don’t align in RAS space but where they would align in voxel space