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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> on behalf of Douglas N. Greve <dgr...@mgh.harvard.edu> Sent: Monday, February 21, 2022 7:13:39 PM To: freesurfer@nmr.mgh.harvard.edu <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! 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