[Freesurfer] Export surface files to 3D Model including the annotation

External Email - Use Caution Dear freesurfer experts, I want to create 3D models (fbx or ply file) of the pial files including the annotation/coloring that is loaded. I tried to use mris_convert to make the pial file that was saved with the annotation to convert the surface into

[Freesurfer] Error: MRInormFindControlPoints: could not find enough control points

External Email - Use CautionDear Freesurfer experts,I was trying this command: $ recon-all -s Desikan -i /path/to/nii -all, to generate the anno files.But it ends up with the errors of MRInormFindControlPoints: could not find enough control points The .nii file I am using is the vol

Re: [Freesurfer] Error: MRInormFindControlPoints: could not find enough control points

External Email - Use Caution Hi Yang The input to recon-all should be a T1-weighted MRI volume. I think what you are giving it instead is a label volume Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Man YANG Sent: Wednesday, June 14, 2023 6:52 AM To:

Re: [Freesurfer] place pial matter on top of the cortex using segmentation volume

External Email - Use Caution I’m not sure if I understood what you are trying to show. If you want to show the cortical thickness on top of the pial surface, you can load it as an overlay. Ruopeng On Jun 14, 2023, at 7:30 AM, Malav Shah mailto:malav.s...@bccn-berlin.de>> wrote

Re: [Freesurfer] place pial matter on top of the cortex using segmentation volume

External Email - Use Caution Thanks for your reply, Wang. Sorry if the question was not clear. I will try to elaborate better. Here is a cropped image from the previous screenshot. This is a T2 sequence, and with a manipulated contrast, so the overall brightness is very high.

Re: [Freesurfer] Error with running retinotopy glm

External Email - Use Caution Hi Loïc, Uncertain if this will address the error you are receiving, but after looking over your analysis.info files and the analysis script, it looks like you are trying to analyze each individual retinotopy run (polar or eccen) separately? If that

[Freesurfer] Question about mri_nu_correct.mni

External Email - Use Caution Hi all, I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with 176*256*256 FOV, 1mm isotropic resolution. I saw that the Ants N4 bias correction is done after the FOV is expanded to 256*256*256, not on the original image. Shouldn't t

Re: [Freesurfer] Question about mri_convert --conform

External Email - Use Caution Hi Yujing, Thanks. I am wondering about the reason why Freesurfer converts data types to uchar. Doesn't this affect the non-uniformity bias correction that follows? Best, Ruifeng On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing wrote: > Extern

Re: [Freesurfer] MANCOVA + Posthoc Testing Design Matrix Setup

External Email - Use Caution Hello, I am looking to run a MANCOVA to examine cortical gray matter differences across three groups (accounting for several covariates), and I was hoping to get input on whether I am setting up my design matrix correctly. Groups: 3 Covariates: Age (d

[Freesurfer] how to manipulate values in m3z file

External Email - Use Caution Hello, I produced an m3z warp file with mri_gradunwarp. Now I need to 0 out all displacement in the z direction, while keeping everything else the same since I need to combine multiple warps from images with different geometries. I see two strateg

Re: [Freesurfer] place pial matter on top of the cortex using segmentation volume

External Email - Use Caution Why can’t you visualize it on the pial surface? Any error message when you attempt to do that? Can you elaborate? On Jun 14, 2023, at 12:12 PM, Malav Shah mailto:malav.s...@bccn-berlin.de>> wrote: External Email - Use Caution Thanks for yo

[Freesurfer] Freesurfer Development Version Apple M1/2 Chip Compatability

External Email - Use Caution Dear Freesurfers, A workaround was previously posted for Apple M1/2 processors to download and run the 7.3.2 release of Freesurfer (here https://secure-web.cisco.com/1rgq3XWhrkT5IzQbYknPjjI7Mi7jKtIiJWP1SE_KD5koSQ-3iSHZ30Nk2GI7phyDpowICRBD3HLzAMmu61OF

Re: [Freesurfer] Error running hippocampus subfields and amygdala nuclei segmentation pipeline

External Email - Use Caution Thank you for the prompt response and looking into the issue. I just checked with the University IT, unfortunately FreeSurfer v7.4 and v7.3 requires Centos7.X + above, whereas the Artemis HPC operating system at my university is based on Centos 6.9,

Re: [Freesurfer] Freesurfer Development Version Apple M1/2 Chip Compatability

External Email - Use Caution The link to msg 74015 did not work for me in the freesurfer mail list archive, so I don’t know how that relates to what you are inquiring about.   But the freesurfer Intel Mac binaries generally run (automatically) using the built-in Rosetta emulatio

Re: [Freesurfer] SynthSR Freesurfer Development Version Apple M1/2 Chip Compatability

External Email - Use Caution Thank you so much, I previously used the workaround to uninstall and reinstall tensorflow that was posted on the forum on 12th December 2022 for 7.3.2. This workaround worked for the development version also this evening, but several tools are failin