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Dear Freesurfer experts,
Hello, I am a student currently working in Frank Guenther's lab at Boston University. I am quite new to freesurfer, so forgive me if the following question may be elementary.
I am interested in using freesurfer to compare the level of atrophy (preferably for different brain areas) in an individual subject to several controls. I'm wondering if there is any way to determine the volume of the '?h.pial-outer-smoothed', and corresponding '?h.pial' file generated from running the 'recon-all -s <subj> -localGI' command. The idea is that I could generate a metric representing a general level of atrophy in subjects by comparing these two volumes (or by comparing the '?h.pial-outer-smoothed' to intracranial volume), however, I have been unable to find a way to retrieve these values. Does anyone have any suggestions? I would greatly appreciate any help in this regard.
Thank you for your help!
Best, Riccardo Falsini
Hi Riccardo
when you say "compute the volume", what exactly do you mean? If you want the interior volume of the two surfaces, you can use mris_volume, which uses the divergance formula to do the calculation
cheers Bruce
On Tue, 30 Oct 2018, Riccardo Falsini wrote:
External Email - Use Caution
Dear Freesurfer experts, Hello, I am a student currently working in Frank Guenther's lab at Boston University. I am quite new to freesurfer, so forgive me if the following question may be elementary.
I am interested in using freesurfer to compare the level of atrophy (preferably for different brain areas) in an individual subject to several controls. I'm wondering if there is any way to determine the volume of the '?h.pial-outer-smoothed', and corresponding '?h.pial' file generated from running the 'recon-all -s <subj> -localGI' command. The idea is that I could generate a metric representing a general level of atrophy in subjects by comparing these two volumes (or by comparing the '?h.pial-outer-smoothed' to intracranial volume), however, I have been unable to find a way to retrieve these values. Does anyone have any suggestions? I would greatly appreciate any help in this regard.
Thank you for your help!
Best, Riccardo Falsini
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Hello Bruce,
I believe the mris_volume program / command is exactly what I was looking for.
Thanks a bunch!
Best, Riccardo
On Tue, Oct 30, 2018 at 3:57 PM Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Riccardo
when you say "compute the volume", what exactly do you mean? If you want the interior volume of the two surfaces, you can use mris_volume, which uses the divergance formula to do the calculation
cheers Bruce
On Tue, 30 Oct 2018, Riccardo Falsini wrote:
External Email - Use CautionDear Freesurfer experts, Hello, I am a student currently working in Frank Guenther's lab at
Boston University.
I am quite new to freesurfer, so forgive me if the following question
may be elementary.
I am interested in using freesurfer to compare the level of atrophy
(preferably for different brain
areas) in an individual subject to several controls. I'm wondering if
there is any way to determine
the volume of the '?h.pial-outer-smoothed', and corresponding '?h.pial'
file generated from running
the 'recon-all -s <subj> -localGI' command. The idea is that I could
generate a metric representing
a general level of atrophy in subjects by comparing these two volumes
(or by comparing the
'?h.pial-outer-smoothed' to intracranial volume), however, I have been
unable to find a way to
retrieve these values. Does anyone have any suggestions? I would greatly
appreciate any help in this
regard.
Thank you for your help!
Best, Riccardo Falsini
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freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Riccardo Falsini