Thank you Dr Bruce,
I want to calculate PET signal in each Brodman map! I will give an example:
If I want to caclulate PET singal for every parcellate and segment in the atlas "wmparc.mgz". I do the following:
bbregister --t1 --mov T1.nii.gz --init-fsl --reg t1.reg.dat --s SUBJID
mri_vol2vol --mov PET_MAP.nii --reg t1.reg.dat --fstarg --interp nearest --o PET_MAP.anat.nii
mri_segstats --seg $SUBJECTS_DIR/SUBJID/mri/wmparc.mgz --ctab-default --i PET_MAP.anat.nii --mask PET_MAP.anat.nii --sum PET_MAP.summary.dat
mri_segstats --seg $SUBJECTS_DIR/SUBJID/mri/wmparc.mgz --ctab-default --i PET_MAP.anat.nii --mask PET_MAP.anat.nii --sum PET_MAP.summary.dat
How can I do the same previous steps ( if correct) on the atlas V1. I.e how can I replace the atalas "wmparc" in the command "mri_segstat" with the atals V1 to get PET signal for every brodman?
Bests,
John
John
Sent: Wednesday, May 11, 2016 at 8:10 PM
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] V1 Atlas ( brodman maps)
From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu>
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] V1 Atlas ( brodman maps)
Hi John
recon-all should create lh.BA.annot and rh.BA.annot parcellations that
contain all the Brodmann areas we know how to label
cheers
Bruce
On Thu, 12 May 2016, John Anderson wrote:
> Dear experts,
> I want to use the atlas V1 to calculate PET signal for Brodman areas. How
> can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all
> the BAs in one file) to feed it in the command “mri-segstat”?
> Bests,
> John
>
>_______________________________________________
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recon-all should create lh.BA.annot and rh.BA.annot parcellations that
contain all the Brodmann areas we know how to label
cheers
Bruce
On Thu, 12 May 2016, John Anderson wrote:
> Dear experts,
> I want to use the atlas V1 to calculate PET signal for Brodman areas. How
> can I create this atlas in the form of “aseg.mgz” or ”wmparc.mgz” ( i.e all
> the BAs in one file) to feed it in the command “mri-segstat”?
> Bests,
> John
>
>_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
