rd.edu
Subject: RE: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
Hi Sebastien
that isn't how the algorithm works. If I had to guess, I would guess that what
you are seeing is locations with high through-plane curvature so even though a
voxel looks like it is
mgh.harvard.edu
Subject: RE: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
there aren't really any workarounds other than using a machine with more ram.
Otherwise you can reduce the resolution. Maybe try -r 0.
Bruce
On Thu, 10
Sep 2015, Sebastien Proulx wrot
To: Sebastien Proulx
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
there aren't really any workarounds other than using a machine with more ram.
Otherwise you can reduce the resolution. Maybe try -r 0.
Bruce
O
AM
To: Sebastien Proulx
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
presumably you mean GB, not MB? That's not enough - a single distance transform
of a 256^3 volumes at 0.25 mm is 1GB of 4-8 byte voxels and we have
-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 10, 2015 10:15 AM
To: Sebastien Proulx
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
presumably you mean GB, not MB? That's not enoug
ginal Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, September 10, 2015 10:06 AM
To: Sebastien Proulx
Subject: Re: [Freesurfer] mri_compute_volume_fractions not filling some sulci
properly
how much ram do you have in the machine? You probably need more. Also, ca
p.s. you can try increasing the resolution of the intermediate volumes
using the -r switch. The default is 0.5. Try 0.25 (although this will
take 8 times the memory and time I think). Make sure to put the -r 0.25
before before the mandatory options. If this does make things look
significantly b
Hi Sebastien
it's pretty hard to tell what's going on from a couple of slices. What was
the command line you used? If you upload the subject I'll take a look (I'll
need the exact command lines you ran as well).
cheers
Bruce
On Tue, 8
Sep 2015, Sebastien Proulx wrote:
My images don’t se
Hello Freesurfers,
I have been using mri_compute_volume_fractions for a while and I just noticed
something weird. Some clearly csf pixels (sometime very large groups) are not
filled in the *.csf.mgz image mri_compute_volume_fractions produces The first
following figure shows a posterior coronal
