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Thanks Bruce,
Changing the coordinates still left me with a blank screen, but I tried using glxgears to further troubleshoot and that also resulted in a blank black screen. I was able to fix this by disabling my graphics card (Intel Iris XE). While this enabled freesurfer then to display the mri data, I discovered that I am not able to click on anything within the voxel edit or recon edit pop-up menus (like in this post: Re: [Freesurfer] Freeview Edit options restricted (mail-archive.com)https://secure-web.cisco.com/1mhxyoaRo0TPOzY61gZ72Ihv17F6eoLxQkrIKSVeF9WmwBbwFTfbJouz6qsqQSRdz0Uk2WJfvXwaW6obKEujB6RrViM4R4AtQHcyvw0s5Tv02rV5vVVNxaAQUzePsE4J-taB4ZdiArX0pqI79a-82dF0d5bz5ZH5kTzltCSPWFxMbefYCekHanVzKPReFwgzsuSejjoEGXHy9NKaW7Ghq6no3rgWcW9964k1EwqI7x7HZgkOOK7L8_aSbKL8d2WOL-PuMiYvqw1pdrfBJ94PeBY3FIIp-JGWZrKv4vxId9DB3o7aEtH4fVdjo1B_hZHLypqW0m8SJPadhz4FJEVQ7zw/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg74529.html) and I wonder if this may be related to my graphics card?
Best, Haley ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Monday, June 19, 2023 3:51 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 232, Issue 12
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Today's Topics:
1. Re: Size of overlap between a label and a volume (John Anderson) 2. Freeview: data not displayed (Haley O Higginbotham) 3. Re: Freeview: data not displayed (Fischl, Bruce R.,PHD) 4. [FreeSurfer] Talairach Failure Detection (Krystal Xiwing Yau)
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Message: 1 Date: Sat, 17 Jun 2023 07:45:35 -0400 From: John Anderson jb19790001@gmail.com Subject: Re: [Freesurfer] Size of overlap between a label and a volume To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: CABPMGjnBVnozT=1BcLNrXPe5fmciy4=7iisRTJ3xbXyVXY4Ctg@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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Let's say the red spot is overlay.nii.gz 1) convert aparc+aseg from mgz to nii.gz using: mri_convert aparc+aseg.mgz aparc+aseg.nii.gz 2) create mask between overlay and the atlas using fslmaths: fslmaths aparc+aseg.nii.gz -mas overlay.nii.gz overlay_overlap.nii.gz 3) use fslstats (or mris_cacl) to compute volume: fslstats aparc+aseg.nii.gz -k overlay_overlap.nii.gz -V this output #voxels and volume
Alternatively, you might consider mri_seg_overlap https://secure-web.cisco.com/1yEdORqlIEup_8SwhRxwcP4XoV0QdvHT3rxvRNSBm4KwTJa...
On Fri, Jun 16, 2023 at 10:37?PM parsatad@student.ubc.ca < parsatad@student.ubc.ca> wrote:
External Email - Use CautionHello,
Hope you are doing well. I'm new to freesurfer so I was wondering if you could help me out with something please.
I'm looking for a simple way to find the size (i.e. volume in mm3) of overlap between a particular label (1027 ctx-lh-rostalmiddlefrontal) ) in an aparc+aseg file and a NIfTI volume file that can be overlayed on the aparc+aseg file. Please look at the attached file for a better visualization of what I'm describing.
I'd really appreciate it if you could point me in the right direction.
Thank you,
Parsa
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