External Email - Use Caution
Hi all,
I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one (gmwmratio_lh.nii.gz). I've tried doing this as:
fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz
but the result is:
Image Exception: #22 :: Failed to read volume gm_lh.nii.gz Error : Error: Nonsensical ROI for gm_lh.nii.gz
Is there another tool I can use to compute this ratio? Is there a better workflow than making two surfaces and dividing?
Thanks, Dylan
External Email - Use Caution
Hi Dylan,
Give this a try: fscalc gm_lh.nii.gz div wm_lh.nii.gz --o gmwmratio_lh.nii.gz
On Wed, Feb 23, 2022 at 12:24 PM Tisdall, Dylan < mtisdall@pennmedicine.upenn.edu> wrote:
External Email - Use CautionHi all,
I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one (gmwmratio_lh.nii.gz). I've tried doing this as:
fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz
but the result is:
Image Exception: #22 :: Failed to read volume gm_lh.nii.gz Error : Error: Nonsensical ROI for gm_lh.nii.gz
Is there another tool I can use to compute this ratio? Is there a better workflow than making two surfaces and dividing?
Thanks, Dylan
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You can also look in pctsurfcon. This compute the percent gray/white contrast. It does so on the T1w, but you could look inside the script to see how it does it and adapt to your situation.
On 2/23/2022 3:26 PM, Adam Martersteck wrote:
External Email - Use Caution
Hi Dylan,
Give this a try: fscalc gm_lh.nii.gz div wm_lh.nii.gz --o gmwmratio_lh.nii.gz
On Wed, Feb 23, 2022 at 12:24 PM Tisdall, Dylan mtisdall@pennmedicine.upenn.edu wrote:
External Email - Use Caution Hi all, I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one (gmwmratio_lh.nii.gz). I've tried doing this as: fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz but the result is: Image Exception: #22 :: Failed to read volume gm_lh.nii.gz Error : Error: Nonsensical ROI for gm_lh.nii.gz Is there another tool I can use to compute this ratio? Is there a better workflow than making two surfaces and dividing? Thanks, Dylan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://secure-web.cisco.com/1Pyl66I_3XVo-h6e2JTyK2OSc2wi4d_XS3wRzXuOuXVzgG1r0ow6a8GOZwHKNySYyRQ_c4m7Auhad1MuMYtPeZy4jIuGOMRlBrHHYjmt2H4J0lfRLjIeEfLLIJlgBP54gCQzM0s6Qc6gFqXo7KI4HfYajKElx-p3fA-ZM21NQ4ZqSEe_8Q-TsRmhvYaAcg1szVagfGLdsJOOqsvK83x2eI5vAf1xvn9w4dG-veVcpUM9V3LQ0U2a5DoWv7v5RP2jgdPerixssAqhCHKx5cUVDP-bqpqa_mRrYnPzpeZmCema7KFmVBeefC40UqrM01eI8_zEZ7k67i2BDelWGYEu4Rg/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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