how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
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Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
External Email - Use Caution
Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Yes, it is MRS.
Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, February 21, 2022 5:25 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
External Email - Use Caution
Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/134Bh1tScyraNIgzY1NDozcY2vE2zhe57dq8hPloJo_3VTI...https://secure-web.cisco.com/1SZ_ZwxUHUoHqP332XFGWKlV1rBGVZpWfjoGbMwovH8RMj2XdDYrM9GgfKAiqt0TrmkE3Gwe0p6N2B-5ZMPuLVZPJXyW0NKljySOhcBqh9dOUag4g2j3zWx5OSaGYVqNRqpWcQ42YvXBRMppsZDyLzqBQ81UYPC_sooTdOYpHFKKb0XXVAHa7OFCexOXG_2VMsjR-B_RlbEy-a8Eog3lcJSSB-mGFDIN8GzE92BZShp4UQHnygF8s7SK9jO7EgXqWIQbb1H5LGnm-TO4arAF8nUF_stbNshv42dAMfwZziQIKRoi36_H65-ZZVLJe5Z-mQrn57AEHzksDP0bz7gLlhA/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257Cb780495e7cc04454891108d9f591850c%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637810827623402419%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DS6AoUqej6ir9sOSfR7h%252Bx0phctkv0%252BTzwCB7XwS2Tww%253D%26reserved%3D0
If you already have the VOI that is aligned to the mprage via the geometry in the volume header, then you can use mri_compute_volume_fractions to compute the composition; specify --regheader subject. To be clear, this assumes that the VOI is a single voxel in a "volume" (eg, nii or mgz) and when you run freeview orig.mgz VOI.mgz you see the VOI in the right place on the orig.mgz. When these conditions are met, mri_compute_volume_fractions will give you what you want. One last thing is that volume_fractions will give you another single-voxel "volume" as output. There are several ways to get the value out, the easiest is probably matlab, something like a = MRIread('singlevoxvol.mgz'); a.vol % will give you the value
On 2/21/2022 6:57 PM, Brown, Alexander wrote:
External Email - Use Caution
Yes, it is MRS.
Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, February 21, 2022 5:25 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
External Email - Use Caution
Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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/1SZ_ZwxUHUoHqP332XFGWKlV1rBGVZpWfjoGbMwovH8RMj2XdDYrM9GgfKAiqt0TrmkE3Gwe0p6N2B-5ZMPuLVZPJXyW0NKljySOhcBqh9dOUag4g2j3zWx5OSaGYVqNRqpWcQ42YvXBRMppsZDyLzqBQ81UYPC_sooTdOYpHFKKb0XXVAHa7OFCexOXG_2VMsjR-B_RlbEy-a8Eog3lcJSSB-mGFDIN8GzE92BZShp4UQHnygF8s7SK9jO7EgXqWIQbb1H5LGnm-TO4arAF8nUF_stbNshv42dAMfwZziQIKRoi36_H65-ZZVLJe5Z-mQrn57AEHzksDP0bz7gLlhA/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257Cb780495e7cc04454891108d9f591850c%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637810827623402419%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DS6AoUqej6ir9sOSfR7h%252Bx0phctkv0%252BTzwCB7XwS2Tww%253D%26reserved%3D0
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Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the terminal output. The output files generated (i.e, cortex.mgz) are the partial volume segmentations for the whole brain. There were no output files that segmented the VOI mask (VOI.mgz). Maybe I didn't specify the input correctly? I inititally recieved errors saying the --regheader flag needs 2 arguments, so I used --regheader <subjid> <path to VOI.mgz>
Now that the tissue maps are generated, Another option I considered is using mri_segstats to extract tissue composition stats from the VOI by using the mri_compute_volume_fractions output volumes (i.e. cortex.mgz) as the segmentation input files and using the VOI.mgz as a mask. However, I am not sure how to address calculating the partial volumes using mri_segstats in coordination with the VOI.mgz mask.
Thanks again for all the help.
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Monday, February 21, 2022 9:21 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
If you already have the VOI that is aligned to the mprage via the geometry in the volume header, then you can use mri_compute_volume_fractions to compute the composition; specify --regheader subject. To be clear, this assumes that the VOI is a single voxel in a "volume" (eg, nii or mgz) and when you run freeview orig.mgz VOI.mgz you see the VOI in the right place on the orig.mgz. When these conditions are met, mri_compute_volume_fractions will give you what you want. One last thing is that volume_fractions will give you another single-voxel "volume" as output. There are several ways to get the value out, the easiest is probably matlab, something like a = MRIread('singlevoxvol.mgz'); a.vol % will give you the value
On 2/21/2022 6:57 PM, Brown, Alexander wrote:
External Email - Use Caution
Yes, it is MRS.
Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ 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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, February 21, 2022 5:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
External Email - Use Caution
Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1P9AFovqdC96y48kqgj6pKi8-rEWf3TskpUoH-HM8YeAtCD...https://secure-web.cisco.com/1e96LBxkUv68RHs1pnQwkmKj0-gaAFawVHvt27a_9svFF4RLXdp8KyQwXNUy36ellLTeVEmcDilRCRCMVwdL_zeBpbbDLtDO_sJmqKF5tm4eIeGT-8hC6hGCzHNv45EyZeEZ42mvwrVyzO8P_xLIttODh6NN3h6X027goG67ASOy6Upo-kKCIx2pPYblDw17MPO-YcBkzXNy8iUnU8xX6wIL9ganVrOrNfkvqx8ylF3JsGNWqOTyMxULXHCI_wy8jfj2dPH-GHO9TWzPLoYwz0zPIkopXcwmpPSsPxc5st98k7gt218ep3x_cy3WhhAn6/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1SZ_ZwxUHUoHqP332XFGWKlV1rBGVZpWfjoGbMwovH8RMj2XdDYrM9GgfKAiqt0TrmkE3Gwe0p6N2B-5ZMPuLVZPJXyW0NKljySOhcBqh9dOUag4g2j3zWx5OSaGYVqNRqpWcQ42YvXBRMppsZDyLzqBQ81UYPC_sooTdOYpHFKKb0XXVAHa7OFCexOXG_2VMsjR-B_RlbEy-a8Eog3lcJSSB-mGFDIN8GzE92BZShp4UQHnygF8s7SK9jO7EgXqWIQbb1H5LGnm-TO4arAF8nUF_stbNshv42dAMfwZziQIKRoi36_H65-ZZVLJe5Z-mQrn57AEHzksDP0bz7gLlhA%252Fhttps%25253A%25252F%25252Fnam02.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Caabgk8%25252540mail.missouri.edu%2525257Cb780495e7cc04454891108d9f591850c%2525257Ce3fefdbef7e9401ba51a355e01b05a89%2525257C0%2525257C0%2525257C637810827623402419%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%252526sdata%25253DS6AoUqej6ir9sOSfR7h%2525252Bx0phctkv0%2525252BTzwCB7XwS2Tww%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257Ceea60b65a946427a2cee08d9f5b28a11%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637810969442216145%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DkXe%252Fdig5AyzwBrBgRfl0VGPjd2vReu%252BzUSYuMUnb0N4%253D%26reserved%3D0
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What is the size of your VOI.mgz? Ie, if you run mri_info --dim VOI.mgz It should be 1 1 1, meaning that it is a single voxel
On 2/22/2022 3:27 PM, Brown, Alexander wrote:
External Email - Use Caution
Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the terminal output. The output files generated (i.e, cortex.mgz) are the partial volume segmentations for the whole brain. There were no output files that segmented the VOI mask (VOI.mgz). Maybe I didn't specify the input correctly? I inititally recieved errors saying the --regheader flag needs 2 arguments, so I used --regheader <subjid>
<path to VOI.mgz>
Now that the tissue maps are generated, Another option I considered is using mri_segstats to extract tissue composition stats from the VOI by using the mri_compute_volume_fractions output volumes (i.e. cortex.mgz) as the segmentation input files and using the VOI.mgz as a mask. However, I am not sure how to address calculating the partial volumes using mri_segstats in coordination with the VOI.mgz mask.
Thanks again for all the help.
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, February 21, 2022 9:21 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics If you already have the VOI that is aligned to the mprage via the geometry in the volume header, then you can use mri_compute_volume_fractions to compute the composition; specify --regheader subject. To be clear, this assumes that the VOI is a single voxel in a "volume" (eg, nii or mgz) and when you run freeview orig.mgz VOI.mgz you see the VOI in the right place on the orig.mgz. When these conditions are met, mri_compute_volume_fractions will give you what you want. One last thing is that volume_fractions will give you another single-voxel "volume" as output. There are several ways to get the value out, the easiest is probably matlab, something like a = MRIread('singlevoxvol.mgz'); a.vol % will give you the value
On 2/21/2022 6:57 PM, Brown, Alexander wrote:
External Email - Use Caution
Yes, it is MRS.
Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Monday, February 21, 2022 5:25 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
External Email - Use Caution
Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
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Hello,
The output of mri_info --dim VOI.mgz is 344 344 344 1.
VOI.mgz is a mask of the MRS "voxel". "Voxel" is a slightly misleading term in this context, as the MRS "voxel" is the small rectangular volume from which the MRS data is acquired. I basically have a rectangular ROI mask (VOI.mgz) that has been registered to orig.mgz, and would like to extract the tissue composition of the mask (VOI.mgz). Sorry for the poor prior descriptions.
Thanks, Alex
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Tuesday, February 22, 2022 5:20:45 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
What is the size of your VOI.mgz? Ie, if you run mri_info --dim VOI.mgz It should be 1 1 1, meaning that it is a single voxel
On 2/22/2022 3:27 PM, Brown, Alexander wrote:
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Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the terminal output. The output files generated (i.e, cortex.mgz) are the partial volume segmentations for the whole brain. There were no output files that segmented the VOI mask (VOI.mgz). Maybe I didn't specify the input correctly? I inititally recieved errors saying the --regheader flag needs 2 arguments, so I used --regheader <subjid> <path to VOI.mgz>
Now that the tissue maps are generated, Another option I considered is using mri_segstats to extract tissue composition stats from the VOI by using the mri_compute_volume_fractions output volumes (i.e. cortex.mgz) as the segmentation input files and using the VOI.mgz as a mask. However, I am not sure how to address calculating the partial volumes using mri_segstats in coordination with the VOI.mgz mask.
Thanks again for all the help.
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ 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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, February 21, 2022 9:21 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
If you already have the VOI that is aligned to the mprage via the geometry in the volume header, then you can use mri_compute_volume_fractions to compute the composition; specify --regheader subject. To be clear, this assumes that the VOI is a single voxel in a "volume" (eg, nii or mgz) and when you run freeview orig.mgz VOI.mgz you see the VOI in the right place on the orig.mgz. When these conditions are met, mri_compute_volume_fractions will give you what you want. One last thing is that volume_fractions will give you another single-voxel "volume" as output. There are several ways to get the value out, the easiest is probably matlab, something like a = MRIread('singlevoxvol.mgz'); a.vol % will give you the value
On 2/21/2022 6:57 PM, Brown, Alexander wrote:
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Yes, it is MRS.
Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ 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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, February 21, 2022 5:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
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Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
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To use the commands I mentioned. You must have a single voxel volume (dim = 1 1 1). You might be able to make something from you map with something like mri_mask -bb 0 VOI.mgz VOI.mgz VOI.masked.mgz # Get the dimension of this volume with mri_info --dim VOI.masked.mgz # Now create a single voxel with mri_convert -ds DSX DSY DSZ VOI.masked.mgz singlevoxel.mgz Where DSX DXY DSZ are the dimenions from mri_info above Check the dimension of the singlevoxel.mgz to make sure it is 1 1 1 Then load it in freeview over the anatomical to make sure it is in the right place
On 2/22/2022 10:49 PM, Brown, Alexander wrote:
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Hello,
The output of mri_info --dim VOI.mgz is 344 344 344 1.
VOI.mgz is a mask of the MRS "voxel". "Voxel" is a slightly misleading term in this context, as the MRS "voxel" is the small rectangular volume from which the MRS data is acquired. I basically have a rectangular ROI mask (VOI.mgz) that has been registered to orig.mgz, and would like to extract the tissue composition of the mask (VOI.mgz). Sorry for the poor prior descriptions.
Thanks, Alex
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Tuesday, February 22, 2022 5:20:45 PM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics What is the size of your VOI.mgz? Ie, if you run mri_info --dim VOI.mgz It should be 1 1 1, meaning that it is a single voxel
On 2/22/2022 3:27 PM, Brown, Alexander wrote:
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Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the terminal output. The output files generated (i.e, cortex.mgz) are the partial volume segmentations for the whole brain. There were no output files that segmented the VOI mask (VOI.mgz). Maybe I didn't specify the input correctly? I inititally recieved errors saying the --regheader flag needs 2 arguments, so I used --regheader <subjid>
<path to VOI.mgz>
Now that the tissue maps are generated, Another option I considered is using mri_segstats to extract tissue composition stats from the VOI by using the mri_compute_volume_fractions output volumes (i.e. cortex.mgz) as the segmentation input files and using the VOI.mgz as a mask. However, I am not sure how to address calculating the partial volumes using mri_segstats in coordination with the VOI.mgz mask.
Thanks again for all the help.
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Monday, February 21, 2022 9:21 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics If you already have the VOI that is aligned to the mprage via the geometry in the volume header, then you can use mri_compute_volume_fractions to compute the composition; specify --regheader subject. To be clear, this assumes that the VOI is a single voxel in a "volume" (eg, nii or mgz) and when you run freeview orig.mgz VOI.mgz you see the VOI in the right place on the orig.mgz. When these conditions are met, mri_compute_volume_fractions will give you what you want. One last thing is that volume_fractions will give you another single-voxel "volume" as output. There are several ways to get the value out, the easiest is probably matlab, something like a = MRIread('singlevoxvol.mgz'); a.vol % will give you the value
On 2/21/2022 6:57 PM, Brown, Alexander wrote:
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Yes, it is MRS.
Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu *Sent:* Monday, February 21, 2022 5:25 PM *To:* freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
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Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
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Thanks!!
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu Sent: Thursday, February 24, 2022 11:41 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
To use the commands I mentioned. You must have a single voxel volume (dim = 1 1 1). You might be able to make something from you map with something like mri_mask -bb 0 VOI.mgz VOI.mgz VOI.masked.mgz # Get the dimension of this volume with mri_info --dim VOI.masked.mgz # Now create a single voxel with mri_convert -ds DSX DSY DSZ VOI.masked.mgz singlevoxel.mgz Where DSX DXY DSZ are the dimenions from mri_info above Check the dimension of the singlevoxel.mgz to make sure it is 1 1 1 Then load it in freeview over the anatomical to make sure it is in the right place
On 2/22/2022 10:49 PM, Brown, Alexander wrote:
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Hello,
The output of mri_info --dim VOI.mgz is 344 344 344 1.
VOI.mgz is a mask of the MRS "voxel". "Voxel" is a slightly misleading term in this context, as the MRS "voxel" is the small rectangular volume from which the MRS data is acquired. I basically have a rectangular ROI mask (VOI.mgz) that has been registered to orig.mgz, and would like to extract the tissue composition of the mask (VOI.mgz). Sorry for the poor prior descriptions.
Thanks, Alex
________________________________ 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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Tuesday, February 22, 2022 5:20:45 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
What is the size of your VOI.mgz? Ie, if you run mri_info --dim VOI.mgz It should be 1 1 1, meaning that it is a single voxel
On 2/22/2022 3:27 PM, Brown, Alexander wrote:
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Hi Dr. Greve,
I ran the mri_compute_volume_fractions command and have attached the terminal output. The output files generated (i.e, cortex.mgz) are the partial volume segmentations for the whole brain. There were no output files that segmented the VOI mask (VOI.mgz). Maybe I didn't specify the input correctly? I inititally recieved errors saying the --regheader flag needs 2 arguments, so I used --regheader <subjid> <path to VOI.mgz>
Now that the tissue maps are generated, Another option I considered is using mri_segstats to extract tissue composition stats from the VOI by using the mri_compute_volume_fractions output volumes (i.e. cortex.mgz) as the segmentation input files and using the VOI.mgz as a mask. However, I am not sure how to address calculating the partial volumes using mri_segstats in coordination with the VOI.mgz mask.
Thanks again for all the help.
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ 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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, February 21, 2022 9:21 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
If you already have the VOI that is aligned to the mprage via the geometry in the volume header, then you can use mri_compute_volume_fractions to compute the composition; specify --regheader subject. To be clear, this assumes that the VOI is a single voxel in a "volume" (eg, nii or mgz) and when you run freeview orig.mgz VOI.mgz you see the VOI in the right place on the orig.mgz. When these conditions are met, mri_compute_volume_fractions will give you what you want. One last thing is that volume_fractions will give you another single-voxel "volume" as output. There are several ways to get the value out, the easiest is probably matlab, something like a = MRIread('singlevoxvol.mgz'); a.vol % will give you the value
On 2/21/2022 6:57 PM, Brown, Alexander wrote:
External Email - Use Caution
Yes, it is MRS.
Attached is a screenshot showing a mask of the svs VOI overlaid on the structural. This is from Gannet MRS software that uses SPM12 to register and segment the VOI. I have the generated VOI.nii mask from the Gannet output - maybe I could use the mask as the registration input for Freesurfer?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779 ________________________________ 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 Douglas N. Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Sent: Monday, February 21, 2022 5:25 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] how to register single-voxel spectroscopy VOI to Freesufer-processed brain and extract tissue composition statistics
WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. I don't know what an svs is. Is it like MRS?
On 2/21/2022 5:51 PM, Brown, Alexander wrote:
External Email - Use Caution
Hello,
I have been asked to provide tissue composition stats (%GM,%WM,%CSF) for an SVS VOI. How can I register the svs file to the Freesurfer-processed brain and extract these values?
Thanks, Alex
Alex Brown CNS Core Facility Department of Psychological Sciences 115 Melvin H. Marx Building 1416 Carrie Francke Drive Columbia, MO 65211 Contact: 573-884-8779
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gNcJ7xTok8kTnlZTDJRbwa4yv38HGV_scJkgKhlHVH911q...https://secure-web.cisco.com/1rEeaWfRIBGjHB6w-YqYwF2N3a1h3oEQ9DHuCqkw53E_AbllDsEHXON2fo_HQrAJpouLv3k3A6I5PMGj3YRB-VwzsfURalaSN4AExB1wyEikOf1fYKdAM6ClCbrCYDbspqjO1GOeD7A0NQIBaGwY8NZtYV85NI37m8aJR0WOByHcENGJTTbOr7WqJexuBvn3KTh-EtQUBFRc5gEp56YInp2x7Wa7aLcsBYUu7K-O_Yy9-Nd90QaSuAvg74O5O7MqegOkxpE62h3-zui7xihD0-w/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1ANa1tOpaTvVWnyZttnPeA-xK1QGLU_oX9pjDNONK_EqAnpiTmDTPV8KzaXuA6nonsJI91Ec87Y2YKSnm9mkSksBO9M3GhYprRrOUrNRrxrvBNdlCsakEtGFxeFyoNJrUcg14IadaCgAnsENOdq6rma8I3_RXugN4-nXjc24caMcShJeqJL27VCcj4ZCNIGaBLyKM_6riOxF2DIR8tdcs44de9zY151Id2HNTbNxQw-f-YdeCnlWefR-JcfO6AXrKa5x6Q7eBM5GTu1CQZnzFeg%252Fhttps%25253A%25252F%25252Fnam02.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1e96LBxkUv68RHs1pnQwkmKj0-gaAFawVHvt27a_9svFF4RLXdp8KyQwXNUy36ellLTeVEmcDilRCRCMVwdL_zeBpbbDLtDO_sJmqKF5tm4eIeGT-8hC6hGCzHNv45EyZeEZ42mvwrVyzO8P_xLIttODh6NN3h6X027goG67ASOy6Upo-kKCIx2pPYblDw17MPO-YcBkzXNy8iUnU8xX6wIL9ganVrOrNfkvqx8ylF3JsGNWqOTyMxULXHCI_wy8jfj2dPH-GHO9TWzPLoYwz0zPIkopXcwmpPSsPxc5st98k7gt218ep3x_cy3WhhAn6%2525252Fhttps%252525253A%252525252F%252525252Fnam02.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttps%25252525253A%25252525252F%25252525252Fsecure-web.cisco.com%25252525252F1SZ_ZwxUHUoHqP332XFGWKlV1rBGVZpWfjoGbMwovH8RMj2XdDYrM9GgfKAiqt0TrmkE3Gwe0p6N2B-5ZMPuLVZPJXyW0NKljySOhcBqh9dOUag4g2j3zWx5OSaGYVqNRqpWcQ42YvXBRMppsZDyLzqBQ81UYPC_sooTdOYpHFKKb0XXVAHa7OFCexOXG_2VMsjR-B_RlbEy-a8Eog3lcJSSB-mGFDIN8GzE92BZShp4UQHnygF8s7SK9jO7EgXqWIQbb1H5LGnm-TO4arAF8nUF_stbNshv42dAMfwZziQIKRoi36_H65-ZZVLJe5Z-mQrn57AEHzksDP0bz7gLlhA%25252525252Fhttps%2525252525253A%2525252525252F%2525252525252Fnam02.safelinks.protection.outlook.com%2525252525252F%2525252525253Furl%2525252525253Dhttps%252525252525253A%252525252525252F%252525252525252Fmail.nmr.mgh.harvard.edu%252525252525252Fmailman%252525252525252Flistinfo%252525252525252Ffreesurfer%25252525252526data%2525252525253D04%252525252525257C01%252525252525257Caabgk8%2525252525252540mail.missouri.edu%252525252525257Cb780495e7cc04454891108d9f591850c%252525252525257Ce3fefdbef7e9401ba51a355e01b05a89%252525252525257C0%252525252525257C0%252525252525257C637810827623402419%252525252525257CUnknown%252525252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%252525252525253D%252525252525257C3000%25252525252526sdata%2525252525253DS6AoUqej6ir9sOSfR7h%252525252525252Bx0phctkv0%252525252525252BTzwCB7XwS2Tww%252525252525253D%25252525252526reserved%2525252525253D0%2525252526data%252525253D04%25252525257C01%25252525257Caabgk8%252525252540mail.missouri.edu%25252525257Ceea60b65a946427a2cee08d9f5b28a11%25252525257Ce3fefdbef7e9401ba51a355e01b05a89%25252525257C0%25252525257C0%25252525257C637810969442216145%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C3000%2525252526sdata%252525253DkXe%25252525252Fdig5AyzwBrBgRfl0VGPjd2vReu%25252525252BzUSYuMUnb0N4%25252525253D%2525252526reserved%252525253D0%252526data%25253D04%2525257C01%2525257Caabgk8%25252540mail.missouri.edu%2525257Ca2f0131a3a544eecf4c208d9f65a065a%2525257Ce3fefdbef7e9401ba51a355e01b05a89%2525257C0%2525257C0%2525257C637811688788961429%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%252526sdata%25253DwEa1X%2525252FhXvkc%2525252F%2525252BSP%2525252BrYgmrPmc20aFH20KchpA9Jxnbcg%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257C91246e9c45c54412556308d9f7bd59b6%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637813214911551663%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DQ2LTHFbDr4Z%252BUZHV8v1uD8amBecbAJFh%252B%252FH%252Fk7dBkvo%253D%26reserved%3D0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gNcJ7xTok8kTnlZTDJRbwa4yv38HGV_scJkgKhlHVH911q...https://secure-web.cisco.com/1dFVAmj8GJsOim2XXdLCyjxf-gGSWSNA2P8ub4JifUil31jwwN_UTMHaW1hk31QVUUHtcqrqf3bb4kh-0-ATrQ2lycjJoyCEr3V7tS31ajUdmoZm5X2LdQxkc3cb0R9VfjG3e-KARj9Ty7BQfR7OqVUJae6dpJX2bCclU6mKg2_3c6SuOsmwdBRdOQ7zxMh80lq7KhUxz6HeliAxdoEEIs9JLf0KqwhBJrKgg0v3OfH6pJhklEec-Czrc3ib0QnSbRGt0u_S51EMOFXYZegy1ew/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1K_Cr-hgPuql50SxK_-Ls9NtuG8cRwkhVn5GMR0ssvWTzOf9QGoj6p5aaTSUViWExFCdV4gwIkySARfJLzFUSFEoepG97l0OwgrWKbWOyTIEm_1vXPydx9ErJGdfVG1EMbOE4T3R2weLXXiv3TncvZLn1EfkG9d_QWuauzPQV0dL--iXwwTmJAqPoRtTg9yPT-4sA6T4U1AsqATTTcNrv_oUuMr4dB7IScnd06eD2eKzExjg8xc_z6m-qyYI3xZcCDHqFBVweOTvd1zklsOu_UiP0nvHiK6poal7XMLe8ZUIvg2MZhWk73iLwhcDCjeeFcxAMjPdIg0jyxAlBvSZH8A%252Fhttps%25253A%25252F%25252Fnam02.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fsecure-web.cisco.com%2525252F1BiaIw6BEdt5FnYKCXMadJG7BSrx_lL3ILoKARigG3TZ2OM2hf3RY5jyY17VCH6BcCkZ0LS0IMdbtmIfwuosftv2RymwXmNgFTCtPmxBYGu1tu7atS0sGtktVP-bFLeA8yTBIuygeM8rqRSxosJh55BdF0cNLtKFXwerNE3hiGzj_veVEnZVIFRCqQb06XeJQ_LFlk88BkDpYrS6yWQvReXrvgsgxgoefVr16Ub0tN_zASQS3x8JUAInAW9nkzXQYOfm0mXVsP2lJLp_e6FBYYAbgOg6INGusesHSU427Sl8v9LA50tfx3HCbltE48uqV%2525252Fhttps%252525253A%252525252F%252525252Fnam02.safelinks.protection.outlook.com%252525252F%252525253Furl%252525253Dhttps%25252525253A%25252525252F%25252525252Fmail.nmr.mgh.harvard.edu%25252525252Fmailman%25252525252Flistinfo%25252525252Ffreesurfer%2525252526data%252525253D04%25252525257C01%25252525257Caabgk8%252525252540mail.missouri.edu%25252525257Ceea60b65a946427a2cee08d9f5b28a11%25252525257Ce3fefdbef7e9401ba51a355e01b05a89%25252525257C0%25252525257C0%25252525257C637810969442216145%25252525257CUnknown%25252525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%25252525253D%25252525257C3000%2525252526sdata%252525253DMPB4k%25252525252Fmmto5WlFXhajwfONAGqOnVdqW%25252525252FNyIV7j2YH5Y%25252525253D%2525252526reserved%252525253D0%252526data%25253D04%2525257C01%2525257Caabgk8%25252540mail.missouri.edu%2525257Ca2f0131a3a544eecf4c208d9f65a065a%2525257Ce3fefdbef7e9401ba51a355e01b05a89%2525257C0%2525257C0%2525257C637811688788961429%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%252526sdata%25253DCSxOEu7IbcfbAuT2v9DGluPzAy7MwnJqtcOIFjHXh4c%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257C91246e9c45c54412556308d9f7bd59b6%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637813214911551663%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DvKmlifDKOP642%252FC6prHfG6TAUjZiXaeJFXiqcyP1gvw%253D%26reserved%3D0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1gNcJ7xTok8kTnlZTDJRbwa4yv38HGV_scJkgKhlHVH911q...https://secure-web.cisco.com/12V8PIY4eOMAgdXoZgfAe-x417BK16tqitMkpELXg_Z5RL6zhu0pAtxjDhwNxbyLBtC3PwAneDQAQqrFy_5jAb5i458nybHdW_i06nNvtWB52Hzg7H0ZydOen_uG1ztC7nN7vU2JxRcIlPNPtsz256WrxZpl9osFO0gxWeO-b5kNoP0XkBjlvoBSfhlpEUhDozVy6krpy765LnC6vELarJfx5ZWkvCFX8f06w-oFS8wcKa2U2TD5K3s6HdlU2bctCecDudC1XoRcI9lfL9hTWaexpxZvDWIa1yqfz3Y2BVAFANjDHDE4GZAXmt-lK2pXVWYUvh_d6FnjTG2BJlrAl5Q/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fsecure-web.cisco.com%252F1ePEVOwcGIpm1jLE1Ljj2fmtck-1Upsg6x7sOwuJ_nQ5TEaeOu3SHKp2i6gZFdcvStTgyogrp8rhxCO3lP7ZlSWV-U6AAZ79fugSb1GA2QN3vQS3XvLbe0JsTmLNmC3nPrOSDpR3tkDEbQKgK7lwJhJsBsvV_LlPri1LO-13AkGlrVrNXYB5RbErYKkI0cGi0iPb6sbyQuCbvxe27nzJmyj0k3K_bOLz7iZg_Twwirp3ACkz7rol5CjHVcnYbqhACJXoLbe0R5CN_4_RUvTs6gmmKJUvkz8VpTQAtDBmeaiku535ESRrjMt-FlhZ1AzFloH2U0t8WXIdaiKD6TJso7g%252Fhttps%25253A%25252F%25252Fnam02.safelinks.protection.outlook.com%25252F%25253Furl%25253Dhttps%2525253A%2525252F%2525252Fmail.nmr.mgh.harvard.edu%2525252Fmailman%2525252Flistinfo%2525252Ffreesurfer%252526data%25253D04%2525257C01%2525257Caabgk8%25252540mail.missouri.edu%2525257Ca2f0131a3a544eecf4c208d9f65a065a%2525257Ce3fefdbef7e9401ba51a355e01b05a89%2525257C0%2525257C0%2525257C637811688788961429%2525257CUnknown%2525257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%2525253D%2525257C3000%252526sdata%25253DVK6HZU5o%2525252Fw%2525252BRAx%2525252BexcnJ7Rygekp%2525252FgDC6Re8tIWLRubs%2525253D%252526reserved%25253D0%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257C91246e9c45c54412556308d9f7bd59b6%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637813214911551663%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3D3SHC7nIuCdKyx9rqOK3DQjcNlABXOPd0YhkJeShQi5c%253D%26reserved%3D0
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1gNcJ7xTok8kTnlZTDJRbwa4yv38HGV_scJkgKhlHVH911q...https://secure-web.cisco.com/1npMnZtI-hFNcAjdfKgV28U86o7ZrMyzkuhOr_s-h-LtnWJdgtsl5wJTTlPhF-ytuW2i_ha51ocS9J-Kbi4UBnxH_4_0hcsenWXVlB4U9Gp2fOnxNWcJGqCx4EsQ30Cw1uppO_cjqfhcZ3T2j2BrL6SSyRYNNts-YEm_nUBGUji96nbeHv2Y3dKPDA7kKomUOCPXyC8wM5xIvHq9V48fgDfeMzczWGXgfZT3qKTj2CE9bHgFdPM8jMYXkxykd5eIQ9PtS38cK_lbIHBhxFjII633us_RMoVPqCQufhlMZoV0FHxjcphYrSAllpdhPGbRSTrH6lUJG9VekMV_D1Q9Q4Q/https%3A%2F%2Fnam02.safelinks.protection.outlook.com%2F%3Furl%3Dhttps%253A%252F%252Fmail.nmr.mgh.harvard.edu%252Fmailman%252Flistinfo%252Ffreesurfer%26data%3D04%257C01%257Caabgk8%2540mail.missouri.edu%257C91246e9c45c54412556308d9f7bd59b6%257Ce3fefdbef7e9401ba51a355e01b05a89%257C0%257C0%257C637813214911551663%257CUnknown%257CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%253D%257C3000%26sdata%3DqAtFVgYQ0pBCZUyimvjxPaxPY6QJMNovuckEARPBE%252Fk%253D%26reserved%3D0
freesurfer@nmr.mgh.harvard.edu
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Brown, Alexander -
Douglas N. Greve