Hi Greg,
I would say there are a variety of possible confounds for cortical thickness
(e.g. changes in cortical myelin content, changes in the closeness of
opposition between grey matter and the dura from brain atrophy), but that
wouldn't be one of the ones I would think of. White matter hyperint
a collaborator just got a grant review that claimed
There's a possibility that changes in cortical thickness in
the insula might be a consequence of lesions (MR-hyperintensities) in the white
matter.
i would think that white matter hyper intensities would tend to enhance
freesur
Hi Doug-
I wanted to follow up on this procedure and ask for a bit of clarification. As
an extension from Ines' efforts, I believe one can produce a ' lobe+aseg.mgz'
lobar volume with both WM and GM for both RH and LH.
1:
mri_annotation2label --s --hemi rh --lobesStrict lobe
mri_annotation2la
We have found Wacom tablets are excellent for editing.
On Apr 4, 2012 4:40 PM, "Jeff Stout" wrote:
> Hi All,
>
> We have a large number of subjects that need minor edits (orbital frontal
> cortex/eye issues subcortical parcellation etc.). To speed up the process
> I was wondering if a stylus inp
Hi All,
We have a large number of subjects that need minor edits (orbital frontal
cortex/eye issues subcortical parcellation etc.). To speed up the process I
was wondering if a stylus input would help with the editing.
Do the graphics tablets (stylus input) work with freesurfer editing? Do they
What version are you using? One of our versions had a problem with
creating bad mgzs. You probably don't need to convert it to mgz. Can you
run mri_label2vol with the original nii and see if it works?
doug
On 04/04/2012 04:50 PM, Anthony Dick wrote:
> No, but the conversion from the original .ni
No, but the conversion from the original .nii works...
[miles:[PATH]] adick% mri_convert chuman_1.mgz junk.mgh
mri_convert chuman_1.mgz junk.mgh
$Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
reading from chuman_1.mgz...
MRIallocIndices: could not allocate 1701979223 elt index arra
so how it is used here?
mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o aseg-in-rawavg.mgz
--regheader aseg.mgz
On 04/04/2012 3:38 PM, Douglas N Greve wrote:
> If you pass it a registration (--reg) then it uses that. It can also
> compute a registration from the information about the geometr
Can you successfully run mri_convert on chuman_1.mgz, eg
mri_convert chuman_1.mgz junk.mgh
doug
On 04/04/2012 12:29 PM, Anthony Dick wrote:
> Hello Bruce,
>
> Sorry--just getting back to this project. The basic problem is that I am
> trying to align a cerebellar parcellation with the underlay i
How are you visualizing the results? Can you send a pic? You should be
using tkmedit.
doug
On 04/04/2012 09:59 AM, René Besseling wrote:
> Dear Freesurfer users,
>
> I've been trying to map a Qdec contrast sig.mgh to the native volume
> of a subject using mri_surf2surf (to get from Qdec fsaverag
If you pass it a registration (--reg) then it uses that. It can also
compute a registration from the information about the geometry in the
header (--regheader) (assuming that the two volumes share a coordinate
system).
doug
On 04/04/2012 01:48 PM, Johnson wrote:
> Hi
> Can anyone tell me please
Hi Tina, sorry for the delay. Most of us are involved in the FS
finishing up today. We don't know anything about a base file created by
recon-all. It looks like your created it with mri_annotation2label? If
so, then it is not a surface, and I'm not sure what mris_convert would
do with it. I'm c
Hi,
I have a few questions about the process flow for the last stable build
(5.0.0). After looking over http://surfer.nmr.mgh.harvard.edu/fswiki/recon-all
, https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable , and
http://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags , it looks l
Hi Rashmi
does it look correct in our visualization tools? If so, you'll need to talk
to the AFNI folks.
cheers
Bruce
On Wed, 4 Apr 2012, Rashmi Singh wrote:
Hello,
I converted the aseg. mgz files to nii format and created a hippcampal mask
with 3dcalc.
Using AFNI I opened the hippocampal
Hello,
I converted the aseg. mgz files to nii format and created a hippcampal mask
with 3dcalc.
Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image
as underlay. For some subjects the hippocampus is not at the correct position.
Please advise.
Thanks,
Rashmi.
__
Hi Nick,
Here's the error that I'm getting:
asegstats2table --meas volume --tablefile
/mnt/haley/Sonya/qdec/stats_tables/aseg.volume.stats.dat --subjects 1001
1002 1003 1004 1005 1006 1009 1010 1012 1013 1014 1015 1016 1017 1018 1020
1022 1023 1024 1025 1028 1029 1030 1031 1033 1034 1036 1037 1038
Hi
Can anyone tell me please how mri_label2vol works, I know what it does,
but I need to know how it works to take the FS space to the original
anatomy space: does it do registration or does it use a transformation
matrix. If the latest which one, where can I find it?
regards
--
Johnson J. Ga
wow, that's pretty dark. Maybe a susceptibility problem? It looks like
the wm further posterior along the strand is already dark even though it
was segmented properly, so you might try putting some control points there
and see if it brings the intensities up enough to recover much of the
stran
Hi Ed,
It seems that the 5.1.0 release for the Mac was composed two days
after the one for Linux, and during exactly those two days one of us
made a change to the file $FREESURFER_HOME/FreeSurferColorLUT.txt.
To correct this issue, please make a back-up copy of your
FreeSurferColorLUT.txt file, a
Hello Bruce,
Sorry--just getting back to this project. The basic problem is that I am
trying to align a cerebellar parcellation with the underlay in tkmedit.
I was working on this with Doug, and his suggestion actually worked, and
now I can't get it to work again (see thread:
http://www.mail-a
Doug or any freesurfer experts can you please answer this question it is quite
urgent:
I have created some manual cortical labels in freesurfer using tksurfer. The
.labels file containing the vertices of the cortical labels does not correspond
to the labels of the pial surface even though they
Dear Freesurfer users,
I've been trying to map a Qdec contrast sig.mgh to the native volume of a
subject using mri_surf2surf (to get from Qdec fsaverage surface to native
surface) and mri_surf2vol (to map from native surface to native volume
cortical ribbon). However, the last step goes wrong: I g
I have downloaded the file
freesurfer-Darwin-leopard-i686-stable-pub-v51.0..dmg,
date 26/05/2011.
Ed
On 4 Apr 2012, at 13:09, Koen Van Leemput wrote:
> OK, I see why this is not working. We've been changing some name
> conventions in our internal FreeSurfer repository after the public
> release
OK, I see why this is not working. We've been changing some name
conventions in our internal FreeSurfer repository after the public
release of version 5.1, and somehow you managed to get an incompletely
updated version.
It appears from
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.1.0 tha
Hi Koen,
No worries.
The result of grep is:
500 right_CA2_3 17 85 136 0
550 left_CA2_3 17 85 137 0
Ed
On 4 Apr 2012, at 12:41, Koen Van Leemput wrote:
> Hi Ed,
>
> Can you please do
>
> "grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt"
>
> and let me know wha
Hi Ed,
Can you please do
"grep _CA2 $FREESURFER_HOME/FreeSurferColorLUT.txt"
and let me know what the result is?
Thanks, and sorry this seems so difficult to sort out.
Koen
On Wed, Apr 4, 2012 at 6:14 AM, Ed Gronenschild
wrote:
> Hi Koen,
>
> As already mentioned, I'm using v5.1.0, Mac Inte
Hi Koen,
As already mentioned, I'm using v5.1.0, Mac Intel
Leopard version.
The voxel values of posterior_left_CA2-3.mgz and
posterior_right_CA2-3.mgz are between 0 and 255,
if that is what you mean by "results".
By the way: I always get the 8 lines with "invalid
drawable" messages from freeview.
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