yes, it does
On 2/25/2022 5:14 PM, Jennifer Bramen wrote:
External Email - Use Caution
Hi Doug
I want to confirm that the signal any region flagged as cortex is
restricted to gray matter. If that is the case, then I finally have
what I need. Thank you.
Warm regards,
Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865 | *Fax: *310-315-4069
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Douglas
N. Greve" <dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Date: *Friday, February 25, 2022 at 10:25 AM
*To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] PetSurfer: subcortical volume-based analysis
Are you doing an ROI analysis or a voxel-wise analysis? If an ROI
analysis, then use mri_gtmpvc (with or without PVC). This will give
you GM, WM, and CSF ROIs. Or do you mean you want a single average
across all GM?
On 2/24/2022 1:15 PM, Jennifer Bramen wrote:
* External Email - Use Caution *
I would like to measure uptake exclusively in gray matter. What
would you recommend to accomplish this?
In my previous message, I was wondering if adding a gray matter
mask would be a potential way to restrict the analysis to gray
matter. Thanks!
Warm regards,
Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience Institute &
Foundation | Providence Saint John's Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865 | *Fax: *310-315-4069
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
"Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Tuesday, February 22, 2022 at 3:00 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] PetSurfer: subcortical volume-based
analysis
I don't understand. What mask?
On 2/22/2022 8:55 AM, Jennifer Bramen wrote:
* External Email - Use Caution *
If I only want to extract intensity from gray matter, do I
need to add an additional mask?
Thanks!
Jennifer
Get Outlook for iOS
<https://secure-web.cisco.com/1L8X_xbSuY_t_ihVbCVT-VrYnrnVaUkpY43uE0_YCYKJhAviIYu8oxZ5PPt-xMtue1nKBFFsIIdc4KBLgKFCEwa74gpigVENV1GyuIW9GZY7CdyW1O-DI9kzTj0IqZfoGPgj6xImBezDDXVXDYk72vjK3VGgjUz9iLXe0ZpQBziIaJ_lOjni1eZ5hbGxBsHdweSgAAcH3WrreH39jB3E5W_oCbiM_eemv-N1wxKjATTFgYLmBFmxGUK3F_I7myhQ2giptsjKDwBlg67W0Te63GAUl8h6wI9xpMnF5vpkiBB50ky4Fc1twBGrvBs8O3yh8Jw9cAIYSm4G0yFmFVx77AA/https%3A%2F%2Faka.ms%2Fo0ukef>
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Sent:* Monday, February 21, 2022 7:13:39 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] PetSurfer: subcortical
volume-based analysis
The GTM gives you values for each ROI regardless of whether it
is GM, WM, or CSF. They will probably give you similar
answers, but the GTM will be more robust.
On 2/21/2022 8:48 PM, Jennifer Bramen wrote:
* External Email - Use Caution *
Thanks! Yes, I already mapped my PET to anatomical space
using mri_vol2vol and glmdir/aux/bbpet2anat.lta.
RE: selection of mgx instead of gtm: I am analyzing
amyloid PET data and I believe it is recommended to
extract gray matter localized PET data. Is that what I am
doing by using the mgx image?
Warm regards,
Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience
Institute & Foundation | Providence Saint John's Health
Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865 | *Fax: *310-315-4069
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf
of "Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Monday, February 21, 2022 at 2:02 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] PetSurfer: subcortical
volume-based analysis
You need to first map your pet to the anatomical space
using mri_vol2vol and the registration
glmdir/aux/bbpet2anat.lta
BTW, why are you computing the ROI anlaysis from the mgx
data instead of using the output from the gtm? Note that
you cannot use the white matter values that come from mgx.
On 2/21/2022 12:57 PM, Jennifer Bramen wrote:
* External Email - Use Caution *
I am trying to extract mean intensity in my PET data
for every ROI. Doug said to run mri_segstats passing
the PET with --i and using --seg to spec the
segmentation. *I would like to confirm that I am using
this properly.*
mri_segstats --i
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz
--seg $SUBJECTS_DIR/$ID/mri/aparc+aseg.mgz --annot lh
--slabel lh --sum
$PET_DIR/$ID/gtmpvc.output/lh.PET_aparc.aseg
where
$PET_DIR/$ID/gtmpvc.output/mgx.gm_average.T1.nii.gz is
the PET data registered and resampled into the
individual’s T1-weighrd MRI space.
Warm regards,
Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience
Institute & Foundation | Providence Saint John's
Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865 | *Fax: *310-315-4069
*From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on
behalf of "Douglas N. Greve" <dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Date: *Wednesday, February 16, 2022 at 7:30 AM
*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] PetSurfer: subcortical
volume-based analysis
If you want to do an ROI analysis using FS-based ROIs,
you should do that at the individual level. Resample
the PET to the anatoimical space, then run
mri_segstats passing the PET with --i and using --seg
to spec the segmentation. If you really want to do it
in MNI305 space, then it is the same thing just using
the MNI305-based (2mm) segmentation
On 2/14/2022 6:11 PM, Jennifer Bramen wrote:
* External Email - Use Caution *
Dear Freesurfer Developers
I am doing an ROI--based amyloid PET scan
analysis. I have completed all of the steps from
the PetSurfer wiki. I now have the preprocessed,
averaged, resampled, smoothed PET data in MNI305
space which is constrained to the subcortical gray
matter mask.
*How do I extract mean intensity within all of the
subcortical ROI?*
Thank you!
Warm regards,
Jennifer Bramen, PhD
(she/her/hers)
Senior Research Scientist, Neuroimaging
Assistant Professor
Pacific Brain Health Center | Pacific Neuroscience
Institute & Foundation | Providence Saint John's
Health Center
1301 20th St. #150 Santa Monica, CA 90404
*Phone:* 310-525-0865 | *Fax: *310-315-4069
_______________________________________________
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/1pHRKHdySejszKCsrs9a5H_HhNUL-CC5YeU4Cl_81vNtgCRYphxx1lXfNUS28oh3w1R-TndgZ47wOf2XFHWg3dBsYow738wDFOOYfSwGLuBCjeJ-FaIOQPsyai7IAeZ1dOxsmP6GuyW5j2bVWEFjAU09qZ4M9zHUa2XyfmlPf4piiqQbo3Ayz3gL78M-vcSa8d1BpjLa9zF3PA4aHAuzSSyumGTLdIAY-5_L_6XgNw7iEG5NYmI7TPk5Phat5eGYdipePAy6m0hB1ibRYO0p1h0wvZVeul211fN1oB8Pwq1PTrPMjeCu2cTqbID6R2Q-DwaPaMHuhE_4IcMArFhh63A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
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/183gHoF2QNWF0XhiYjGNXYG6PPLdbxs7KNgXhQsXHho8xZeK39atN7Jo6IrguyAfg0UBKyIPPcrj8etGhWOIJSNajPkkOaei1R60Wd4bPE580iHNNu_GQG7BBenVzhSh8t2VkqrI4Q6QSCRZqq2EjampfrVY983C-QNTmp78vE1y84HS6yv0YGhl-4D3SbUFqsLCBh2IkABxx72wmJE7GCNlYMkb8ZLiJ_ycvg1ZLF_XkTN4RELwpHwjAuhJ0UJqGWFCl4wzrgr5imnM5q5gpOYtuSlA1riTYcmWbehUIE8csYd3C-9XHdR01xyYX-Prz/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
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/1HhoR3iG7YXh8B4Ixg7EzpDAUjTpD3UqKliUOGNCDvrQn7AfA5AGqz7xcGiGNl6t7jTDPAns3V_l0864tx_-m4WMYrITAqZbDtpUdvbGKxtRT-oG0KVcX8kiw4SXv1HYz9eKSHqzFcgND2HyCO8VUkrVjlVBcNllbFDr2lYs3tE0JC4KNwBKJMRL8XvYD_d3wDjyuyODOa11GzxUbU_T6e0VisXHH35HKqVzbc6Qm4i1HvcPFdoj1uwKGFya_DDP8ZhJMtfxD6uGmGmGxEdt8sYhjnmTtx3BTLi2FtPiRADaXAcFlOBW6mjerbQ5py1WdpOeKwsbXanFjPSpB-_qUdA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
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/1imT65cf6WgjTiJ7F417-ebDtKpGky25DINjoNqTb-LnN05tZMD1P7WJt6ENHSoMsQZWHNRw9QOu5N_QzNNuGGEGbatv8XrVsp1BvbBdyH2Xs3DIaLHPw2U5KzaFAR_nobdg7V84cV48rIcGO8bwdw5vb6ms3eHIURrp1mxMAIqytpzvbauoldGNqBneX_OeR-nKDxz_MujzMm43S-V1g1HY7FWEsYBE5YdgfevSnBuxAI5phFX1OaoSVo0TE5sSqhTLZ-3z-SH7YIizD3L_oI_8F6NA_vD8pJ1GcmIcDri3kxUHPS3KlEOuGqfAPNRxP/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
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/1zKKNT1xqhdSNv8f-sWLmf3R6SOumOtUHpR8NkJyuKe22i17oH02hP53jLrmpizE58St9dRy6ONP74HYKVg__VI2ekAviBmUuzN9L9c7CDlHg3AqOj-QSMihlsiQ3wRobjuMWe-eyb9H-4bJBrkrVpB3rhPfjL7CMX_ziu8-Tk99PcSOmA5KnZ1YgdOCZZgB1ErjYgDCz2_R78LYNCRw9iLVCaiqf27PScrcDOvQxb8-kUxJtItzby4SbgtVfc_T4TylXZzETtbkNWzr2bEpjsiRnEE6n_xe3eN1sTMn0S4a7ZbCKIdHgupKF-HU5qkj7UqcB_PDxul0E9g1Y4kcn9g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
