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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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1bL2PbUa0oBf3uE-dqjk6ArIqlk3Mu1XRZ0Gqm2BSbnknDX... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS... < https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS... .
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It certainly could be, although I defer to Ruopeng. Do you get any errors when you start freeview?
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Haley O Higginbotham Sent: Friday, June 23, 2023 1:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 232, Issue 12 - data not displayed
External Email - Use Caution 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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu> Sent: Monday, June 19, 2023 3:51 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 232, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
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When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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.commailto:jb19790001@gmail.com> Subject: Re: [Freesurfer] Size of overlap between a label and a volume To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <CABPMGjnBVnozT=1BcLNrXPe5fmciy4=7iisRTJ3xbXyVXY4Ctg@mail.gmail.commailto:CABPMGjnBVnozT=1BcLNrXPe5fmciy4=7iisRTJ3xbXyVXY4Ctg@mail.gmail.com> Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
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.camailto:parsatad@student.ubc.ca < parsatad@student.ubc.camailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1bL2PbUa0oBf3uE-dqjk6ArIqlk3Mu1XRZ0Gqm2BSbnknDX... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS... < https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS...https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDSnWFtnDs4dDxmZ0KAaurt7X2ksh15CPKyMoFG1e_bLBE1T_ymhu-QUAx4_yJt_1k-rAAQN4ZiVDIg4Y_tN7C1oy_6FBjRoalfTUF3bw8gpxFTQgq2CkCi1aG7mPoXG2pttMvKyTe22pGcV-hg-84orMuAyku6C8FYMYvBx2wvn9egPVJBsDqGreYKUcqBi-_1Uwrahua-8-GNZRSxA7lkKttOaKGrG44K8d-XZbWzrEmOKseNEhdxJYbTkJ1qa6s-uE-1odtnhsORP79OWVcMhivoexZwjx_N4wT3CvjA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%3e .
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Freeview requires OpenGL engine for fast editing (hardware accelerated hit test). So if you disable your graphics card, it is like not going to work. Maybe you need to update the graphics card driver to the latest?
Ruopeng
On Jun 23, 2023, at 1:27 PM, Haley O Higginbotham <hhigginb@mit.edumailto:hhigginb@mit.edu> wrote:
External Email - Use Caution
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: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be 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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu> Sent: Monday, June 19, 2023 3:51 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Freesurfer Digest, Vol 232, Issue 12
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://secure-web.cisco.com/1NFAytgj_o7SeKzQukc41bipAEO_iD8efSPiiL9lGpNDyHnU24aG7hBviwVPliMdp6rvx3ifddV7rAz92G0sPt_9_9oSbEBKAm0_nHTmebYKIFTbDEaggo7NjKq3Jtj_lWuh_YpQhi-JJ_qhZ3QCWEY4TPFdd7YpfwkyiegWS-rlm5VWWCufAdumAPQlaKd1bVYWMz4f-31g2LFqk0WXKX2fY8jSMbB5w7vmb2Av9s_d9xDstMisi16Y8_y4LKvPquP97g19q-F3_A0ajnF1z8W3WbRCvgoWsIxJ_D-gVfns0iKKOfm4zo9xTJizVzKr2/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu
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When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
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)
----------------------------------------------------------------------
Message: 1 Date: Sat, 17 Jun 2023 07:45:35 -0400 From: John Anderson <jb19790001@gmail.commailto:jb19790001@gmail.com> Subject: Re: [Freesurfer] Size of overlap between a label and a volume To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <CABPMGjnBVnozT=1BcLNrXPe5fmciy4=7iisRTJ3xbXyVXY4Ctg@mail.gmail.commailto: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.camailto:parsatad@student.ubc.ca < parsatad@student.ubc.camailto: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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1bL2PbUa0oBf3uE-dqjk6ArIqlk3Mu1XRZ0Gqm2BSbnknDX... The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS... < https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDS...https://secure-web.cisco.com/1QOro1Z2r3HL9t5oIefcbPfQTo4oxpIuIeCBs3Tp0a1yEDSnWFtnDs4dDxmZ0KAaurt7X2ksh15CPKyMoFG1e_bLBE1T_ymhu-QUAx4_yJt_1k-rAAQN4ZiVDIg4Y_tN7C1oy_6FBjRoalfTUF3bw8gpxFTQgq2CkCi1aG7mPoXG2pttMvKyTe22pGcV-hg-84orMuAyku6C8FYMYvBx2wvn9egPVJBsDqGreYKUcqBi-_1Uwrahua-8-GNZRSxA7lkKttOaKGrG44K8d-XZbWzrEmOKseNEhdxJYbTkJ1qa6s-uE-1odtnhsORP79OWVcMhivoexZwjx_N4wT3CvjA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%3E .
freesurfer@nmr.mgh.harvard.edu
-
Fischl, Bruce R.,PHD -
Haley O Higginbotham -
Wang, Ruopeng