Hi Bruce,
They have the same geometry, but didn't have the same center (128 128
128 vs 128 118 72). I guess freeview doesn't not show this difference,
or handle it in a different way than mris_calc.
Nevertheless, when both volumes have the same center (mri_convert -oc 0
0 0), the mris_calc -o
Hi, everyone.
The tksurfer can't initial a window in iOS 10.7.5. Has anyone met this
before?
Last login: Mon Oct 15 10:57:04 on ttys001
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME
Hi free surfer users and developers,
for the first time I got this error after running recon-all:
CORRECTING DEFECT 76 (vertices=36299, convex hull=8085)
mris_fix_topology(74305) malloc: *** mmap(size=1148719104) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in
Don't use the -I, just give it an input (the dicoms) and and output
On Oct 15, 2012, at 1:23 AM, Knut J Bjuland knut...@hotmail.com wrote:
Hi Bruce
I converted the dicom into 001.mgz. Then I tried to reslice.
mri_convert -rl -i orig/001.mgz -o orig/001.mgz
mri_convert -rl -i
I am able to convert using mri_convert, but when I try to reslice with
mri_convert -rl input output. I get the error message shown below. I
according to the documentation I could use mri_convert to reslice, but
it does not mention how I should set an vaule for the -rl input. Should
I use
Hi
I think i understood it. Should i use mri_convert -rl template input output
from mri_convert.c
printf(reading template info from volume %s...\n,
reslice_like_name);
template = MRIreadInfo(reslice_like_name);
if(template == NULL)
{
fprintf(stderr,
Hi Pietro
that's a pretty big defect. Have you checked the ?h.orig.nofix to see
why it is so large? The other problem is that the current FS mac release is
32 bit, which is why you are running out of memory. It would work properly
on a Linux box with more ram I suspect. We are hoping to have
yes
On Mon, 15 Oct 2012, Knut J Bjuland wrote:
Hi
I think i understood it. Should i use mri_convert -rl template input output
from mri_convert.c
printf(reading template info from volume %s...\n,
reslice_like_name);
template = MRIreadInfo(reslice_like_name);
Thanks Bruce.
is it possible that this is a problem of the scan I was running? The other
5 scans I was running in parallel went through without errors...
I'm checking control points and wm.mgz anyway...
2012/10/15 Bruce Fischl fis...@nmr.mgh.harvard.edu
Hi Pietro
that's a pretty big defect.
Hi Pietro,
yes, possibly. Subject motion can cause this to happen.
cheers
Bruce
On Mon, 15 Oct 2012,
pietro de rossi wrote:
Thanks Bruce.
is it possible that this is a problem of the scan I was running? The other 5
scans I was running in parallel went through without errors...
I'm checking
Hi Knut,
It should run by default. Did you check the summary log file,
$SUBJECTS_DIR/QA/recon_checker.ALL.summary.log? Otherwise, could you send
the terminal output when you run QAtools on a single subject?
-Louis
On Sun, 14 Oct 2012, Knut J Bjuland wrote:
Hi,
I have downloaded the
Dear all,
I think in the following webpage there is a very small mistake:
http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats
It states that SubCortGray is the sum of the thalamus, caudate, putamen,
pallidum, hippocampus, amygdala, accumbens, and VentralDC from both
hemispheres. But I
Dear Freesurfers,
I computed the functional activation in a sensory task using freesurfer's
fsfast stream. In the cortex surface line like activated regions are present.
Their extension is much larger than the extension of the expected regions.
Therefore, I suppose that those regions are due
you were right Bruce, motion artefacts are VERY bad in that scan. I don't
think I can even edit it properly.
Talking about editing however, I posted something last week but no-one
replied, I'm afraid the email was blocked due to attachment issues.
It was about control points and topological
Hi Pietro,
you will want to fix things if the pial surface doesn't correctly contain
portions of cortical gray matter.
cheers
Bruce
On Thu, 11 Oct 2012, pietro de rossi
wrote:
Dear FreeSurfer users and developers,
I'm getting very frequently some bilateral inferior temporal lobe
Dear Experts,
I apologise for the repost but I was wondering if anyone could guide me with
respect to deriving lobar measures and whether the commands below are correct .
Thanks. M
GM Lobar Values
(1) mri_annotation2label --subject subject1 --hemi ?h --lobesStrict lobesfile
(2)
Hi Mahinda, sorry for the delay, answers below
On 10/15/2012 02:13 PM, Mahinda Yogarajah wrote:
Dear Experts,
I apologise for the repost but I was wondering if anyone could guide
me with respect to deriving lobar measures and whether the commands
below are correct . Thanks. M
_GM Lobar
Hi Louis
I manage to replicate the error by using wm-anat-snr directly on bert
in /usr/local/freesurfer/subjects. I think think the error is in
wm-anat-snr and it interactions with mri_segstats.
mri_segstats -all-info
ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion:
Hi Harry
As Martin said, longitudinal linear
mixed-effects models (lme) are the recommended tool for analyzing
longitudinal data obtained from the Freesurfer longitudinal image
processing pipeline. The increase in power can be dramatic. Coming
up there is a paper about this subject. We are
Hi Fernando, thanks for catching that error. I have corrected it. I'll
also point out now that in version 5.2 brain stem will not be included.
doug
On 10/15/2012 10:52 AM, Fernando Ventrice wrote:
Dear all,
I think in the following webpage there is a very small mistake:
Hi Jorg, can you tell us a little more? A picture would be good. Also,
describe how you have done your analysis (eg, on the surface or in the
volume, how much smoothing).
doug
On 10/15/2012 11:01 AM, Jörg Pfannmöller wrote:
Dear Freesurfers,
I computed the functional activation in a sensory
Hey all,
Can I send through some shell scripts that I wrote to run all the
hemisphere-specific steps so that the lh and rh steps are run together.
If I could send them through to make sure I'm doing autorecon2-wm and
autorecon3-pial correctly?
Thank you.
Chris.
--
Dr Christopher Adamson, PhD
Hi Chris,
I think you can do this with -perhemi, but Nick or Doug can verify.
cheers
Bruce
On Tue,
16 Oct 2012, Chris Adamson wrote:
Hey all,
Can I send through some shell scripts that I wrote to run all the
hemisphere-specific steps so that the lh and rh steps are run together.
If I
Hi Martin,
If you could make available that lme toolbox link, that would be great!
Thanks for the help.
Cheers,
Harry
From: jorge luis [jbernal0...@yahoo.es]
Sent: Tuesday, 16 October 2012 8:16 AM
To: Martin Reuter; Harry Hallock [hhal5...@uni.sydney.edu.au]
Cc:
Dear Bruce/freesurfer community,
Thank-you for offering to take a look at our data.
I have uploaded two files to the ftp. They are called Subject_Before_CP.zip and
Subject_After_Cpedit.zip. Please let me know if you haven't received them. I
uploaded these last Friday but haven't as yet had a
Hi Vanessa
I'm running some tests now
Bruce
On Oct 15, 2012, at 9:10 PM, Vanessa Louise Cropley vcrop...@unimelb.edu.au
wrote:
Dear Bruce/freesurfer community,
Thank-you for offering to take a look at our data.
I have uploaded two files to the ftp. They are called
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