Hi!
I tried to convert the fsaverage rh.cortex.patch.flat to gifti with
mris_convert lh.cortex.patch.flat lh.cortex.patch.flat.gii
but gives me the error
MRISalloc(16711682, 392): could not allocate vertices
Cannot allocate memory
Same error, when I want to load it in tksurfer with
tksurfer f
chmod 755 is not the solution since it gives writing permission only
to the owner of the directory.
Use:
chmod 777 $SUBJECTS_DIR
Or
chown YOUR_USERNAME $SUBJECTS_DIR
2009/7/15, Barnali Basu :
> Experts
>
> I am stuck up with a real basic issue, which I have done easily manytimes in
> the older
What areas are these where the pial is not extended enough?
In general, the pial surface might extend further if the white surface is
extended further but you would only want to do that if wm was also being
left out of the white surface.
On Tue, 14 Jul 2009, Devdutta W wrote:
Hi,I have been
Hi Barnali,
sorry, this is an issue for your sysadmins. Looks like you don't have
permissions to create that directory.
cheers,
Bruce
On Tue, 14 Jul 2009, Barnali Basu
wrote:
Experts
I am stuck up with a real basic issue, which I have done easily manytimes in
the older version. I have dow
Hi Stephan,
the patches are in a somewhat different format than the full surfaces.
For mris_convert you need to give it a -p, and for tksurfer you need to
load a full surface (e.g. inflated) then load the patch from the file
menu.
cheers
Bruce
On Wed, 15 Jul 2009, Stephan Gerhard wrote:
Hi
Thanks for the answer, but if I do:
$ mris_convert -p rh.cortex.patch.flat rh.cortex.path.flat.gii
The output is not a valid gifti file, seems to have the same size as the
input file and is binary.
But if I do:
$ mris_convert -p rh.cortex.patch.flat rh.cortex.path.flat.asc
The output looks lik
Hi,
I want to run FreeSurfer on a large number of subjects, so I must reduce
run time as much as possible. I'm only interested in the parcellation of
the cortex and the subcortical segmentation. Are there any
(timeconsuming) processing steps I can skip since I'm not interested in
e.g. surface
Hi Stephan,
sorry, I missed the fact that you were trying to convert to gifti. I don't
think we support patches in gifti format, but Nick (who wrote the gifti
code) is on vacation and will get back to you about it next week.
cheers,
Bruce
On Wed, 15 Jul 2009, Stephan Gerhard wrote:
Thanks
sorry, pretty much everything is required to get those two :<. The cortical
parcellation depends on the subcortical segmentation so there is no time
saving there
Bruce
On Wed, 15
Jul 2009, Renske de Boer wrote:
Hi,
I want to run FreeSurfer on a large number of subjects, so I must reduce r
Hi group,
Is there a paper to cite for the subcortical parcellation done by
FreeSurfer?
Thanks,
Vina
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yes, there are a couple:
Whole Brain Segmentation: Automated Labeling of Neuroanatomical
Structures in the Human Brain, Fischl, B., D.H. Salat, E. Busa, M.
Albert, M. Dieterich, C. Haselgrove, A. van der Kouwe, R. Killiany, D.
Kennedy, S. Klaveness, A. Montillo, N. Makris, B. Rosen, and A.M. D
yes, that is correct. Make sure to handle the mean/offset of C in a
rational way. The simple, though somewhat incorrect, way is to simply
demean C. Better to pick a fixed value of C to test it at. If this is
what you do, let's say you test at C=2, then your contrast would be:
0.5 -0.5 -0.5 0.5
Hi there,
is there any FS command to average two .mgz files from the same subject
withouth going through the recons steps. I just need to obtain a new mgz file
resulting from the average of several mprage of the same patient.
Thanks in advance.
Best,
Jose
---
Jose Luis Cantero, Ph.D.
Laborato
with motion correction use mri_motion_correct2 (or mri_motion_correct.fsl).
Without motion correction you can use mri_average.
cheers
Bruce
On Wed, 15 Jul 2009, Jose Luis Cantero Lorente
wrote:
Hi there,
is there any FS command to average two .mgz files from the same subject
withouth goin
or mri_concat or fscalc.fsl
Bruce Fischl wrote:
with motion correction use mri_motion_correct2 (or
mri_motion_correct.fsl). Without motion correction you can use
mri_average.
cheers
Bruce
On Wed, 15 Jul 2009, Jose Luis Cantero Lorente wrote:
Hi there,
is there any FS command to average tw
Douglas N Greve wrote:
or mri_concat or fscalc.fsl
or 'mris_calc'...
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Whenever i try to open two windows(ie.' tkmedit bert orig.mgz 'and'
tksurfer bert rh pial') the original one will not respond or refresh
unless i close the second one,even i turn on the redraw button in the
tksurfer.
Also,i put the two windows side by side and did not overlay them. i've
tried a few
are you opening them from different shells?
On Wed, 15 Jul 2009
yzha...@artsci.wustl.edu wrote:
Whenever i try to open two windows(ie.' tkmedit bert orig.mgz 'and'
tksurfer bert rh pial') the original one will not respond or refresh
unless i close the second one,even i turn on the redraw butt
Are you opening them from the same terminal window? If so, one is running
in the background and so you will not be able to use it.
Open each from a different terminal window.
--
On Wed, 15 Jul 2009 yzha...@artsci.wustl.edu wrote:
Whenever i try to open two windows(ie.' tkmedit bert orig.mgz
Thank you so much for your answer!
Now I meet another problem.
Just as your see, the C in some classes (e.g., A1B1 and A2B1) is all zeros.
When I run the mri_glm. Some error information was shown. I listed them below.
Matrix condition is 1e+08
ERROR: matrix is ill-conditioned or badly scaled, con
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