External Email - Use Caution Hi Freesurfer team
I was wondering if you’d have some time to take a look at question below. Thanks! ---------- Forwarded message --------- From: Julie Ottoy <julie.jj.ot...@gmail.com> Date: Thu, 30 Jul 2020 at 13:22 Subject: using own skull stripped t1 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Dear freesurfer team I'm trying to use my own skull stripped T1 when running recon-all. For this, I'm doing following steps: 1) run recon-all with -autorecon-1 -noskullstrip 2) mri_convert --in_type nii --out_type mgz -rl ./FreeSurfer/ID/mri/orig.mgz -rt nearest ./own_skull_strip.nii.gz ./FreeSurfer/ID/mri/brainmask.mgz 3) run recon-all with -autorecon-2 and autorecon-3 My original own_skull_strip.nii.gz has matrix size 192x240x256. Therefore, when transforming to the size of brainmask.mgz (256x256x256), it deforms. I tried nearest, cubic, and interpolate, but none of them gives actually a good result in terms of retaining the contrast. I was wondering if it is important to keep a good contrast for brainmask.mgz , or whether this brainmask.mgz is just used to determine the brain borders for segmentation. (ie.: in which steps of recon-all is the brainmask.mgz actually used?) Any recommendations? Thank you! Julie
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