See this tutorial
https://surfer.nmr.mgh.harvard.edu/fswiki/MultiModalTutorialV6.0 on
multimodal integration. Basically, you will need to run mri_vol2vol to
map your MPF volume to the anatomical/conformed space, then run
mri_segstats passing it the segmentation you want to use and the
converted MPF image.
On 1/24/2024 11:04 AM, ERNEST KISSI wrote:
External Email - Use Caution
When MPF images are registered on T1 images, I think the intensity
represents the MPF values, not the T1 values. This is because the
registration process only transforms the spatial coordinates of the
MPF images to match the T1 images, but does not alter the signal
intensity or contrast of the MPF images. Therefore, the registered MPF
images still reflect the macromolecular proton fraction of the brain
tissue, which is independent of the T1 values.
Just wanna confirm. This is from a colleague.
On Wed, Jan 24, 2024 at 6:50 PM ERNEST KISSI
<ernestkissi...@gmail.com> wrote:
I want to use the intensity of the macromolecular proton fraction
(MPF). I want to compare the intensity of the MPF of the various
brain regions or structures between two groups. I am not using the
volumes. The MPF was registered on the T1 so does it mean that
the intensity is from the MPF.
On Wed, Jan 24, 2024 at 6:44 PM ERNEST KISSI
<ernestkissi...@gmail.com> wrote:
I want to use the intensity of the macromolecular proton
fraction (MPF). I want to compare the intensity of the MPF
between two groups.
On Wed, Jan 24, 2024 at 6:11 PM Fischl, Bruce R.,PHD
<bfis...@mgh.harvard.edu> wrote:
It is whatever volume you gave as input to recon-all. If
you tell us which statistics you want to regenerate for
another volume we can tell you know what commands to run.
cheers
Bruce
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of
*ERNEST KISSI
*Sent:* Wednesday, January 24, 2024 9:05 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [Freesurfer] Freesurfer Intensity representation
* External Email - Use Caution *
Hi,
Please I made an initial enquiry about using freesurfer
for MPF maps. The feedback was that I register the MPF
maps on their corresponding T1 images using multimodal
registration. I used FSL to do the multimodal registration
and then use recon-all in freesurfer.
Now I want to know what the intensity and the volume of
the output in the aseg file represent. Is it the intensity
of the MPF or the TI and MPF?
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