mri_compute_volume_fractions for a while and thought something would have been
changed meanwhile.
Thanks Joerg
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Bruce Fischl
Sent: Monday, June 10, 2019 12:42 PM
To: Freesurfer support list
Subject: Re: [Freesurfer
Hello,
I always used mri_compute_volume_fractions to compute the volume fractions in
my GE-EPI images (percentage of gm,wm, and csf in each voxel). That does not
seem to be possible anymore. I can still define a registration matrix and an
outstem but no input execpt of the standard FreeSurfer a
Hi Joerg
can you give us more information than that? Why do you say it is not
possible? It should be
cheers
Bruce
On Mon, 10 Jun 2019, Pfannmoeller, Joerg Peter wrote:
> Hello,
>
> I always used mri_compute_volume_fractions to compute the volume fractions
> in my GE-EPI images (percentage of g
gh.harvard.edu] on behalf of Antonin Skoch
> [a...@ikem.cz]
> Sent: Thursday, April 26, 2018 1:09 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_compute_volume_fractions
>
>
> External Email - Use Caution
>
> Dhivya,
>
>
>
> t
, April 26, 2018 1:09 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_compute_volume_fractions
External Email - Use Caution
Dhivya,
this syntax works for me with version 6. With version 5.3.0 I am getting the
same error mesage. I do not know how the correct syntax is
.04 and my freesurfer
version is ,
freesurfer/5.3.0/bin/freesurfer
mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz
still I am getting , unknown option --o
Trying to give as per documentation, which is
--o outstem --regheader subject
I am really sorry to bother you wi
External Email - Use Caution
Yep , I am using "o" .
I am running it on Ubuntu 16.04 and my freesurfer version is ,
freesurfer/5.3.0/bin/freesurfer
mri_compute_volume_fractions --o test --regheader 002_S 002_S/mri/norm.mgz
still I am getting , unknown option --o
eesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, April 26, 2018 10:52 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_compute_volume_fractions
>
> just run the command as I sent it:
>
> mri_compute
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, April 26, 2018 10:52 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_compute_volume_fractions
just run the command as I sent it:
mri_compute_volume_fractions --o test --regheader
__
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 25, 2018 6:21 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_compute_volume_fra
...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 25, 2018 6:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_compute_volume_fractions
try
mri_compute_volume_fractions --o test --regheader
On Wed, 25 Apr
ent: Wednesday, April 25, 2018 6:01 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_compute_volume_fractions
>
> oh, this must be Doug's code, not mine. Try using --regheader instead
>
> And also please send us the full command and all screen output from it in
&
...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 25, 2018 6:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_compute_volume_fractions
oh, this must be Doug's code, not mine. Try using --regheader instead
And also please send u
harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Wednesday, April 25, 2018 4:22 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] mri_compute_volume_fractions
>
> Hi Dhivya
>
> if you are doing it in the space of the anatomicals, then
Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Wednesday, April 25, 2018 4:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_compute_volume_fractions
Hi Dhivya
if you are doing it in the space of the anatomicals, then use
identity.nofile as the reg file (which is a special file name
, 2018 4:22 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] mri_compute_volume_fractions
Hi Dhivya
if you are doing it in the space of the anatomicals, then use
identity.nofile as the reg file (which is a special file name that will
internally create an identity matrix). The output stem is
Hi Dhivya
if you are doing it in the space of the anatomicals, then use
identity.nofile as the reg file (which is a special file name that will
internally create an identity matrix). The output stem is whatever you
pick - it will be prepended to the files that are written with the volume
frac
External Email - Use Caution
Hi,
I would like to get CSF/GM/WM segmentations from aseg.mgz or in other words
from labeled brain. Can I do that with mri_compute_volume_fractions ? Also, I
am not sure about the parameters to supply,
and ?
Could Someone point me to some documen
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
No, there's not, sorry
On 08/07/2015 03:48 PM, Sebastien Proulx wrote:
>
> Hello Freesurfer,
>
> I am trying to obtain csf, wm and gm tissue volume fraction maps that
> matches my distorted high-resolution EPIs.
>
> Is it possible to input a displacement map to the
> mri_compute_volume_fractions
Hello Freesurfer,
I am trying to obtain csf, wm and gm tissue volume fraction maps that matches
my distorted high-resolution EPIs.
Is it possible to input a displacement map to the mri_compute_volume_fractions
command, such that the surfaces will be deformed before computing the csf, wm
and gm
Hi Adrian
this will create a voxel map with the % of each tissue class in each
voxel. If you want the total %s, just read them out of the stats files and
compute them directly.
cheers
Bruce
On Sat, 14 Apr 2012, Adrian Garcia wrote:
> Dear Bruce,
>
> thank you for the reply. So this function
Just the name you give the output
On Apr 14, 2012, at 4:07 AM, Adrian Garcia wrote:
> I would like to have Freesurfer calculate the percentage of wm/gm/csf from an
> MRI volume (produced with mri_volsynth). I have run recon-all to completion
> and have a registration matrix from the MRI to
I would like to have Freesurfer calculate the percentage of wm/gm/csf from an
MRI volume (produced with mri_volsynth). I have run recon-all to completion
and have a registration matrix from the MRI to the Freesurfer anatomical
(tkregister2). It looks like mri_compute_volume_fractions will do
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