Hey all,
Is anyone using freesurfers mri_watershed to strip macaque skulls? If so what
options are you using? I am currently trying to use it but am getting really
bad results. I am also open to suggestions of other programs to try.
-Eric
___
Free
Hey all,
I was wondering if anyone knows the format for the Talairach.bnd file?
Specifically what I am looking for is what the matrix at the bottom actually
represents. I am going to use them in a script to actually trim the brain so I
need a way to compute the 6 planes that make up the box a
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and
try to draw control points I can see a little green cross about 1 voxel down
and to the right of the red cross, but as soon as I move the red cross they
vanish and I can no longer see them. FreeSurfer is saving the po
: Faden, Eric (NIH/NIMH) [F]
Sent: Tue 8/1/2006 9:49 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Vanishing Control Points
I am currently running 3.0.3 on RedHat EL v4. Whenever I load up a brain and
try to draw control points I can see a little green cross about 1 voxel down
and to
So my images are 256x256x192 x 1.0mm. One of them works and the other doesn't.
Should I add blank slices to bring it to 256?
-Eric
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 8/1/2006 2:04 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc: frees
mri_convert -c worked.
-Eric
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 8/1/2006 2:39 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Vanishing Control Points
no, you should use mri_convert -c to "co
/NIMH) [F]
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] Vanishing Control Points (Updated: MNC to MGZ
problems)
can you give us details about how you did the conversion?
On Tue, 1 Aug
2006, Faden, Eric (NIH/NIMH) [F] wrote:
> Upon further investigation it seems to be someth
I am working on running some scans through FreeSurfer. I have scans at both
0.5mm and 0.8mm that have all been skull stripped and N3 corrected. The images
have good contrast in general and specifically are fairly good in the
subcortical regions. I am skipping a bunch of the FreeSurfer pipelin
Right, but is there a way I can fix the subcortical structures so that I can
get accurate measures of them?
-Eric
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 8/9/2006 12:29 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc: Freesurfer Mailing List
Subject: Re
I was going to create surfaces and then export them to Caret to use the Atlas
made for Caret.
-Eric
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 8/9/2006 12:35 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc: Freesurfer Mailing List
Subject: RE: [Freesurfer] Non Human
After reading the paper I am still a little confused about how the Subcortical
Parcellation labels the parasingulate gyri when some people have one and others
have two? Can anyone shed a little light on this issue?
-Eric
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Freesurfer mailing list
F
I am trying to run nu_correct inside of a script using perl. It keeps crashing
with a "Termination Status=512".
Processing:.DoneNot
implemented yet in cache_volume_range_has_changed()
Not implemented yet in cache_volume_range_has_c
I have scans that are at .8 and .5 resolution as dicoms. Currently I am using
to3d to rotate the images to the proper orientation. After that I have tried
using 3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 to "resize" the image so that
mri_convert doesn't resample the image, but this is also messing
The monkeys are scanned in different orientation than normal. I also can't use
recon-all because it doesn't work correctly with monkeys.
-Eric
-Original Message-
From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Tue 2/7/2006 12:57 PM
To: Faden, Eric (NIH/NIMH) [F]
Cc:
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