Re: [Freesurfer] Inquiry about creating .label files from .nii file

External Email - Use Caution Hi, The inquiry emerged due to an interest in using prebuilt R and/or Python visualization packages that only accept .annot as input. Is there some method of conversion to .annot given the aforementioned files I have? Thanks again. On Sat, Jun 12, 20

Re: [Freesurfer] Inquiry about creating .label files from .nii file

If you already have it on the surface you don’t need it, do you? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 1:12 PM To: Freesurfer support list Subject: Re: [Freesurfer] Inquiry about creating .label files from .nii file Extern

Re: [Freesurfer] Inquiry about creating .label files from .nii file

External Email - Use Caution Thanks for the info. I have the atlas surface (with vertex data) saved as a .vtk. Would the mris_sample_parc work with this input file type? On Sat, Jun 12, 2021 at 1:01 PM Fischl, Bruce wrote: > I see. And what do you want to do with the annot and l

Re: [Freesurfer] Inquiry about creating .label files from .nii file

I see. And what do you want to do with the annot and label files? Annots are surface parcellations only, so you would need to sample to a surface to get them. If you have a surface you can use mris_sample_parc to sample it onto the surface and create an annotation (I think Doug has something new

Re: [Freesurfer] Inquiry about creating .label files from .nii file

External Email - Use Caution Hi Bruce, It is volumetric. Thanks! On Sat, Jun 12, 2021 at 11:47 AM Fischl, Bruce wrote: > Hi Evan > > > > Is it a volumetric atlas or a surface one? > > > > Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-bo

Re: [Freesurfer] Inquiry about creating .label files from .nii file

Hi Evan Is it a volumetric atlas or a surface one? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Evan Collins Sent: Saturday, June 12, 2021 11:33 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Inquiry about creating .label files from .nii file Ex

[Freesurfer] Inquiry about creating .label files from .nii file

External Email - Use Caution FreeSurfer, I currently have a .nii atlas file and a corresponding LUT (look-up table). The atlas is appropriately segmented and colored as seen in Freeview. How do I create/export the corresponding .label and .annot files? Thank you.

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

External Email - Use Caution Hi Eugenio, Yes, Matlab runtime had already been installed. Copying initial description of checks/troubleshooting already done so far, "... > Things that have been checked/tried or troubleshooting attempted: > - SIP protection is disabled (csrutil st