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There is a single number for all the gray matter over the entire brain.
They are not broken down into structures or parcel unless it is only in the
aseg (subcortical parcellation).
I have found a way to calculate it. Now, I wanna write this lh.w-g.pct
How about this command:
mri_segstats --seg $FREESURFER_HOME/subjects/bert/mri/aparc+aseg.mgz --i
$FREESURFER_HOME/subjects/bert/mri/orig.mgz --sum bert-orig.aparc+aseg.sum
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 12:52 PM
To:
I guess I still don’t understand what you want. Is it a single number for all
gray matter over the entire brain? Or broken down by structure/parcel?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Wednesday, February 21, 2024 12:52 PM
To: Freesurfer support list
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There is no such flag in mri_segstats to calculate gray matter cortical
parcels. There is a flag for total gray matter rather. Nevertheless, I
think there is a file in recon-all output that has white matter to gray
matter ratio : lh.w-g.pct and
I think that is exactly one of the outputs of mri_segstats. Check the help on
it and see if it does what you want. I believe it is also run by default during
recon-all and the values placed into one of the stats output files
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf
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Yes, please
That's exactly what I mean.
On Wed, Feb 21, 2024, 6:44 PM Fischl, Bruce R.,PHD
wrote:
> Can you clarify what you mean by “measure the intensities for the grey
> matter regions”? You could for example compute the mean gray matter
>
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From: "Perumalla, Sucika"
To: "freesurfer"
Sent: Wednesday, February 21, 2024 4:30:39 PM
Subject: [Freesurfer] Help with Recon-all Errors
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Can you clarify what you mean by “measure the intensities for the grey matter
regions”? You could for example compute the mean gray matter intensity within
each cortical parcel and each subcortical structure. Is that what you want?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of
Hello FreeSurfer Support,
My name is Sucika Perumalla and I hope you can please help me with
troubleshooting recon-all. I’m getting multiple frames errors when trying to
run recon-all with my dicoms even after extracting the multiple frames. I was
wondering if you can please help resolve this
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I think these are not grey matter but cortical parcellation.
FSL can output grey matter segmentation but I do not think freesurfer has
such an output.
In aparc.stats (rh.aparc or lh.aparc), there is only GrayVol and no
intensity measure. I want to know
Recon-all outputs these 3 aparc aseg volumes:
aparc.DKTatlas+aseg.mgz
aparc.a2009s+aseg.mgz
aparc+aseg.mgz
Are these what you are looking for? They should work the same way as aseg
volume.
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of ERNEST KISSI
Sent: Tuesday,
There is an error before the 'multiple frames error':
"
Found 384 DICOM file(s)
load Image
/Applications/freesurfer/7.4.1/subjects/JacquelineOneill/E36409769/Ax_T1_3D_MPRAGE/765855821.dcm,
size 114688
Warning: Unable to determine slice direction: please check whether slices are
flipped
Warning:
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Hello freesurfer Team,
I have the grey matter segmentation from FSL and I have freesurfer
recon-all output but the recon-all outputs do not have regional grey matter
intensities. Can I use MRI_segstats to calculate the regional grey matter
output
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