Hi,
My FreeSurfer installation was working fine several months ago, but
recently when trying to launch tkmedit or tksurfer (from x11), I got:
GLUT: Fatal Error in tksurfer.bin: could not open display: localhost:0.0
GLUT: Fatal Error in tkmedit.bin: could not open display: localhost:0.0
I tri
Tiger).
Nick
On Wed, 2008-12-17 at 00:02 -0500, Catherine Hartley wrote:
Hi,
My FreeSurfer installation was working fine several months ago, but
recently when trying to launch tkmedit or tksurfer (from x11), I got:
GLUT: Fatal Error in tksurfer.bin: could not open display:
localhost:0.0
GLUT
Hi,
If recon-all is interrupted after several hours of processing (someone
shutdown the machine), if I run recon-all again on the same set of data,
will it go through all of the processing steps again, or will it note the
progress made and essentially check through until it reaches the prior point
Hi,
I ran autorecon1 on a group of data consisting of a single set of mprage
DICOMs per subject, acquired on a Siemens Allegra 3T scanner. Several of
the brainmask.mgz images had large portions of the brainstem and cerebellum
removed. A couple had portions of the neck which were not removed. Th
Hi,
I'm hoping to get a hold of the function mris_divide_parcellation
which automatically subdivides the cortical parcellations for a
region into sub-regions. It's not a part of the current Freesurfer
release but would it be possible to get a copy of the development
version?
Thanks,
Ca
Thanks! However when i try to execute the command, i get a message
saying "Permission denied". Any ideas?
Thanks,
Cate
On May 10, 2007, at 5:30 PM, Doug Greve wrote:
here you go ...
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
mris_divide_parcellation
From: Catherine Hartley <[EMAIL PROTECTED]>
Date: May 10, 2007 7:10:19 PM EDT
To: Doug Greve <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] mris_divide_parcellation
then i get: Exec format error. Binary file not executable.
[catemac:/Applications] cate% cd freesurfer/
PowerPC, macintel dir is for the new Intel
Macs.
Nick
On Thu, 2007-05-10 at 19:45 -0400, Catherine Hartley wrote:
From: Catherine Hartley <[EMAIL PROTECTED]>
Date: May 10, 2007 7:10:19 PM EDT
To: Doug Greve <[EMAIL PROTECTED]>
Subject: Re: [Freesurfer] mris_divide_parcellation
then
Hi,
I'm trying to get the anatomical statistics for a new parcellation, ?
h.aparc.splitcingulate.annot, I've created using
mris_divide_parcellation. I've tried using mris_anatomical_stats
with various argument structures (specifying output filenames, not
specifiying output filenames) and
Hi,
When I attempt to load a custom annotation file (that I created using
mris_divide_parcellation) within tksurfer, I get a bus error which
seems to result from a problem with the colortable:
% reading colortable from annotation file...
CTABreadFrom: could not allocate -2 bin table
Cannot
On May 11, 2007, at 1:38 PM, Catherine Hartley wrote:
Hi Jenni,
This doesn't work either:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats
mm103184 lh inflated -f mm103184/stats/
lh.aparc.splitcingulate.stats -a mm103184/label/
lh.aparc.splitcingulate.annot
\
mm103184 lh inflated
Nick
On Fri, 2007-05-11 at 13:39 -0400, Catherine Hartley wrote:
On May 11, 2007, at 1:38 PM, Catherine Hartley wrote:
Hi Jenni,
This doesn't work either:
[catemac:freesurfer/subjects/reruns] cate% mris_anatomical_stats
mm103184 lh inflated -f mm103184/
Hi,
I'm having a problem with the development version of tksurfer. When
I try to load a sig.mgh file as an overlay, I get the following error:
% surfer: couldn't load /Applications/freesurfer/subjects/reruns/
glmleft/ReappCSplusContrast/sig.mgh
sclv_read_from_volume: error in FunD_New
Tha
Hi,
I've used mris_divide_parcellation to generate split the automatic
parcellation into subregions. When I view the resulting annotation
in tksurfer, the label names do not correspond to the subdivision
names, so I am unable to tell which division is which (ie, which is
rostralanteriorc
. Did you regenerate the
surface after generating the .mgh file?
On Sun, 2007-05-13 at 15:29 -0400, Catherine Hartley wrote:
Hi,
I'm having a problem with the development version of tksurfer. When
I try to load a sig.mgh file as an overlay, I get the following
error:
% surfer: cou
Hi,
I'm trying to run mri_motion_correct.fsl to generate the rawavg.mgz file,
and it's failing somewhere before the process completes. I can't seem to
figure out from reading the log file just what is going wrong. Any insight
would be much appreciated!
Thanks
--
mri_motion_correct.fsl log
are the mri/orig/XXX.mgz files ok? What about the mri/rawavg.mgz?
>
> Catherine Hartley wrote:
>>
>> Hi,
>>
>> I just ran autorecon1 on a batch of data and when I view the brainmask in
>> tkmedit, selecting the coronal orientation actually displays th
ok? What about the mri/rawavg.mgz?
>
> Catherine Hartley wrote:
>>
>> Hi,
>>
>> I just ran autorecon1 on a batch of data and when I view the brainmask in
>> tkmedit, selecting the coronal orientation actually displays the sagittal
>> orienation and vice ve
show up fine in tkmedit, but the rawavg.mgz
doesn't? Can you send us the recon-all.log file?
Bruce
On Mon, 18 Jun 2007, Catherine Hartley wrote:
Hi,
Just resending as I sent this at the end of the day Friday. Also,
if this
is difficult to correct, for whatever reason, then could yo
Hi,
I'm still having problems with the rawavg.mgz volume being generated
with incorrect orientations. I gave Jenni two 00?.mgz volumes and
she was able to generate a correctly-oriented rawavg. Our two log
files look very different, but I'm not able to figure out the problem
by looking a
x?
>
> doug
>
>
>
>
>
> Catherine Hartley wrote:
>> Hi,
>>
>> I'm still having problems with the rawavg.mgz volume being generated with
>> incorrect orientations. I gave Jenni two 00?.mgz volumes and she was able
>> to generate a correctly-o
Hi,
I'm getting a bus error when I run mri_glmfit on my Intel Mac. When
I had this problem before, I got a development version of mri_glmfit
which solved the problem. Unfortunately I've reinstalled a newer
version of Freesurfer since then and overwrote that binary file and
it's no longe
Hi,
I'm wondering whether it is possible to create an overlay consisting
of a subset of clusters from a sig.mgh file, filtered according to
custom criteria and preserving the significance value of each vertex
in the remaining clusters so that the overlay can be thresholded as I
choose.
, 11 Feb 2008, Catherine Hartley wrote:
Hi,
I'm wondering whether it is possible to create an overlay
consisting of a subset of clusters from a sig.mgh file, filtered
according to custom criteria and preserving the significance value
of each vertex in the remaining clusters so that th
Hi,
I can't seem to figure out how to save two or more labels as a
conjoined single label.
Thanks in advance,
-Cate
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Hi,
I understand that there are tools under development implementing
Gaussian Random Field correction for multiple comparisons. If there
is a usable version available (and a brief description of how to use
it), I'd like to try it out.
Thanks in advance,
Cate Hartley
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