[Freesurfer] How to Verify That Cortical Surface Orientation Values are Accurate?

External Email - Use Caution I have created a volume which is supposed to have the cortical surface orientation with respect to b0 at each voxel. To do this I got the 6 frame overlay file from mris_convert. Then I isolated the first 3 values from each row in Matlab to create an

[Freesurfer] B0 distortion correction using 2. FSL epidewarp script

Hi, I am new to fsfast and I trying to create a field map using the AP and PA spin echo maps for B0 distortion correction using the FSL epidewarp script I have two fieldmaps PA_spinecho.nii and AP_spinecho.nii 1. First I want tow know if my code below is about right epidewarp.fsl --mag

[Freesurfer] Tracula statistics outputs for version 7.2

External Email - Use Caution Hi, Upon further examination of pathstats.byvoxel.txt and pathstats.overall.txt, I have 2 more questions. Since my previous 3 questions still have not been answered, I'm including them here so that they are all in one place. The 2 new questions are

[Freesurfer] Quality control of longitudinal recon-all output for >500 participants

External Email - Use Caution Hi all, I am processing a large longitudinal dataset of T1-weighted anatomical images through the recon-all pipeline (N=680). I know that the gold standard for quality control following recon-all is visual inspection of the output surfaces and

[Freesurfer] Getting recon-all stats from SynthSeg 2.0 segmentations

External Email - Use Caution Hello all, I'm trying to perform a comparison of the global and regional phenotype statistics produced by `recon-all` with the outputs of SynthSeg 2.0. Based on the wiki, it looks like I should be able to pass the segmentation from SynthSeg to

Re: [Freesurfer] Freeview does not display image

External Email - Use Caution With regards to WSL, there is probably something preventing the X-server from correctly displaying graphics. Instead of running freeview you could try a simpler command to test X-window graphics. One command is “xeyes” which you can look for and try

Re: [Freesurfer] annex repository missing a lot of files

External Email - Use Caution Hello Ahmed, Maybe you could further explain what you are trying to accomplish, e.g., you don’t need the annex files to compile the freesurfer source. - R. On Oct 4, 2022, at 04:33, Ahmed Abou Aliaa ahmed.s.aboual...@gmail.com wrote:External Email -

Re: [Freesurfer] Freeview does not display image

External Email - Use Caution Hello R, Sorry I wasn’t so clear on my part. I am using ubuntu linux on the windows subsystem linux (WSL). I followed these instructions at