Hi FS experts,
I just downloaded the latest version again today:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0.tar.gz(
4.2 GB 1/28/13 9:47:00 PM, fsaverage has been copied to /subjects/myproject
location)
When running this
Post-doc position within the Collaborative Research Centre 940 Volition and
Cognitive Control: Mechanisms, Modulators, and Dysfunctions at the Department
of Child and Adolescent Psychiatry, University Hospital C. G. Carus, Dresden
University of Technology, Germany
Job Description: The
Hi list,
I'm trying to run trac-all on one subject and have a problem with the
bvecs file at the -prep stage.
After dtifit is started an error massage occurs: Error: bvecs and bvals don't
have the same number of entries:
[iMac-di-Stefano:/Applications/freesurfer/subjects] Stefano% trac-all -prep
no, the longer time is probably because the mac version you are using is 32
bit.
cheers
Bruce
On Tue, 29 Jan 2013, Varghese Chikku wrote:
Dear All,I ran a test subject on VM and the process took 20 hrs to
complete.But the same images on Mc pro took 58 hours.VM is 8GB and Mpro
is 16
Hi Stefano - Are the files that you're attaching the ones from the dmri
directory or are they the original files that you specified in your
configuration file? I'm guessing they're not the dmri/bv??s files because
then they'd be formatted in rows and not columns.
Without seeing the bvecs
Hi Chikku
note that because you have a 64 bit mac doesn't mean you are running 64
bit software. Until pretty recently we didn't have a 64 bit mac version,
so unless you downloaded a beta in the last month or so, you are likely
running a 32 bit version
cheers
Bruce
On Tue, 29 Jan 2013,
Dear FreeSurfer experts,
I did a group analysis in qdec, found several significant clusters and would
now like to extract the mean cortical thickness of each significant cluster. I
know that I have to run mri_glmfit-sim to do this, but I do not understand
which commands I need to get the
Dear all,
I'm attaching a job offer for a fully-funded neuroimaging position at Frankfurt
University, available immediately. The position is based at the Brain Imaging
Center of Goethe University, a facility that hosts two dedicated research MR
scanners and an MEG facility. A full clinical
Hi Julia, it should just be created when mri_glmfit-sim runs. Is it not?
doug
On 01/29/2013 11:03 AM, Richter, Julia wrote:
Dear FreeSurfer experts,
I did a group analysis in qdec, found several significant clusters and
would now like to extract the mean cortical thickness of each
You have either too many effects that you are trying to fit or you don't
have enough subjects. Decrease one or increase the other!
doug
On 01/28/2013 01:00 PM, Pablo Emanuel wrote:
Hi,
My name is Pablo. I am using the freesurfer in my analyses, but when I
try use the QDEC to statistical
When I run recon-all using freesurfer 5.2 latest beta it will segment
crash.
Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23 16:44:29 UTC 2013
x86_64 x86_64 x86_64 GNU/Linux
/home/knutjbj/freesurfer/ernie
mri_convert /usr/local/freesurfer/subjects/sample-001.mgz
Chikku,
Can you send us your recon-all.log and recon-all.cmd files? I'd like to
investigate why it ran so slowly.
Nick
On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku wrote:
Dear All,
I ran a test subject on VM and the process took 20 hrs to
complete.But the same images on Mc pro
Hi Knut
does it segfault on other systems? Can you email me the 001.mgz and I'll
see if it works here?
thanks
Bruce
On Tue, 29 Jan 2013, Knut J Bjuland wrote:
When I run recon-all using freesurfer 5.2 latest beta it will segment crash.
Linux mypc 3.7.4-204.fc18.x86_64 #1 SMP Wed Jan 23
Knut,
I noticed in the log that there was only 284KB of free memory available,
which is not enough to run freesurfer, although it would seem like it
should be enough to run the mri_convert command. Can you free-up more
memory and re-run? Also, I noticed that you're running the Centos6
build,
it's probably not enough to run gunzip, which for some reason takes
*lots* of ram
On Tue, 29 Jan 2013, Nick Schmansky wrote:
Knut,
I noticed in the log that there was only 284KB of free memory available,
which is not enough to run freesurfer, although it would seem like it
should be enough
Hi Nick
I reran dicom import from /usr/local/freesurfer/subject/sample*. I had
24254940 kB free memory but I still got a segmentation error.I used
sample data from /usr/local/freesurfer/subject. Do you think it is a
glibc bug in Fedora 18. It contain glibc-2.16-28.fc18.x86_64.
This error
does v5.1 work on this system?
does the centos4_x86_64 v5.2 build work?
n.
On Tue, 2013-01-29 at 20:33 +0100, Knut J Bjuland wrote:
Hi Nick
I reran dicom import from /usr/local/freesurfer/subject/sample*. I had
24254940 kB free memory but I still got a segmentation error.I used
sample
Dear Freesurfer users and experts,
We are attempting to grow a mask that we have created in FSL, to expand it into
white matter.
At first, we tried this in FSL using the dilM command which dilated the size of
the mask by n voxels. We then multiplied this by a segmented white matter mask
Hello again!
Thank you for all your help so far. Just one more question now... is
there a way to specify these values to be pulled using a script:
GausCurv FoldInd CurvInd
...??
Thanks,
Catherine
On 1/23/13, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote:
They must be in a single folder
yes, use the -m or --meas flags. If you run it with -h, you will get
help and examples
doug
On 01/29/2013 04:12 PM, Nucleos P wrote:
Hello again!
Thank you for all your help so far. Just one more question now... is
there a way to specify these values to be pulled using a script:
GausCurv
Post-doc position available immediately within the Centre for Research on
Ageing, Health and Wellbeing, College of Medicine, Biology and the Environment,
Australian National University, Canberra, Australia.
We are seeking a junior Postdoctoral Fellow to join a small collaborative team
working
Hi Jodie
you can do this on the surface, then project the resulting label 1mm into
the white matter if I understand what you want correctly. You might also
check out the wmparc.mgz and see if it already does what you want.
cheers
Bruce
On Tue,
29 Jan 2013, Jodie Davies-Thompson wrote:
Dear all,
I am trying to calculate the distance from a reference vertex to all other
vertices in a surface mesh (or ideally to a subset of vertices), moving
along the actual surface (e.g. smoothwm).
I am able to loop through the pairs of vertices in which I'm interested,
using mris_pmake in each
Jodie, you might also look into using the white matter parcellation.
That would allow you to select the WM from a particular gyrus.
doug
On 01/29/2013 03:31 PM, Jodie Davies-Thompson wrote:
Dear Freesurfer users and experts,
We are attempting to grow a mask that we have created in FSL, to
Are there commas in the dmri/bvecs file? If so, do setenv LANG
en_US.UTF-8 as described in the archive post that I sent you. Does this
solve the error about bvecs and bvals not having the same size?
On Tue, 29 Jan 2013, std...@virgilio.it wrote:
Hi Anastasia,
I put my files in a folder
Hi Folks,
I have a question about entorhinal cortex volume. The entorhinal cortex is
listed in ?h.aparc.stats and ?h.entorhinal_exvivo.stats. In a previous
post on the mailing list, it was mentioned that we should use the volume
measurement from ?h.entorhinal_exvivo.stats.
We would like to make
Hi Mehul
the entorhinal label in the aparc was drawn by Rahul based on gyral
landmarks. The one in the _exvivo.stats is based on being able to see the
layer II islands in ex vivo MRI and hence we believe it is more accurate.
Not sure why you need to integrate the ex vivo one back into the
Thanks for quick response Bruce. We will use the volume from ex-vivo
stats..
Regarding the need to integrate the ex vivo one back into aparc+aseg.
We noticed the entorhinal volume in aparc is larger than that in
exvivo.stats.
So do the extra entorhinal voxels in aparc need to be re-labelled as
Hello Anastasia and Stefano,
Maybe is of little help but I wanted to let you know that I've
experienced the same problem.
Using exactly the same data, and using 5.1 in both cases, and having
the locale set up as specified according to a solution in the mailing
list:
- in cent os 4 it is working
-
Thanks Nick,
Please find the attached.
On 29 January 2013 19:33, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote:
Chikku,
Can you send us your recon-all.log and recon-all.cmd files? I'd like to
investigate why it ran so slowly.
Nick
On Tue, 2013-01-29 at 06:53 +0100, Varghese Chikku
On 29. jan. 2013 21:16, Nick Schmansky wrote:
does v5.1 work on this system?
no
does the centos4_x86_64 v5.2 build work?
no.
I have filed a bug report on
https://bugzilla.redhat.com/show_bug.cgi?id=905638 . It might be problem
with mri_convert and glibc interaction.
Knut J
n.
On Tue,
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