It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote:
I beleive it should have a lower case X, as in:
chmod -R a+x freesurfer/bin
-Zeke
On 10/28/2014 01:19 AM, Ali Radaideh wrote:
Dear Douglas
Thanks for your reply.
Hello Freesurfer Experts,
Thanks so much again for all of your help. I am trying to complete the
Anatomical ROI Analysis Tutorial because I will need to use segmentation
volumes for an experiment we`re running in the lab. In particular, I am
trying to complete the group stats files part of the
Hi Adam
underestimated the insula in the aseg or in the surfaces?
cheers
Bruce
On Wed, 29 Oct
2014, Adam Mezher wrote:
Hi Bruce,
Sorry for not clarifying. A number of subjects in our set have underestimated
insula (usually anatomical right insula but sometimes both). I just uploaded an
Dear Freesurfers,
Not sure if my question is at the right place here but I'll give it a
try.
I have a memory disk with white spaces in the name: Seagate Expansion
Drive. There is no simple way to rename the disk on my Linux machine.
In Unix shell scripting problems with finding the directory
You can also use bbregister to register the CT to the anatomical. I'm
not sure what steps beyond that you'd need to do.
doug
On 10/29/14 10:47 PM, Zachary Greenberg wrote:
Rich,
You need SPM preferably (http://www.fil.ion.ucl.ac.uk/spm/) for
matlab, and freesurfer.
First run recon-all on
can you make a symbolic link (ln -s) to the disk and then reference the
symlink instead of the direct path?
On 10/30/14 10:33 AM, Righart, Ruthger wrote:
Dear Freesurfers,
Not sure if my question is at the right place here but I'll give it a
try.
I have a memory disk with white spaces in
Cheap solution, use backticks to evaluate the string, e.g.
--reg /`echo $f1`/fsreg.dat
On 30.10.2014 15:33, Righart, Ruthger wrote:
Dear Freesurfers,
Not sure if my question is at the right place here but I'll give it a
try.
I have a memory disk with white spaces in the name:
Yes, works!!!
Thank you
Ruthger Righart
Le 2014-10-30 15:36, Douglas Greve a écrit :
can you make a symbolic link (ln -s) to the disk and then reference the
symlink instead of the direct path?
On 10/30/14 10:33 AM, Righart, Ruthger wrote:
Dear Freesurfers,
Not sure if my question is at
Ali,
First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are
working properly? I am under the impression that versions of freesurfer
pre-version 5.3 will not work on newer linux distributions?
In regards to your current permision denied issue... What happens if you
try and run
The problem is that the class name exceeds the maximum number of
characters. For some strange reason I set that to be 50 and the class
name is 55. I've changed it in our code tree, but you'll just have to
shorten the name and it should work.
doug
On 10/29/2014 07:15 PM, Bronwyn Overs wrote:
Try this
chmod -R a+x freesurfer/bin/*
On 10/30/2014 06:27 AM, Ali Radaideh wrote:
It does not work. This is really strange
On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu
mailto:zkauf...@nmr.mgh.harvard.edu wrote:
I beleive it should have a lower case X, as in:
You are in a folder that you do not have write permission to. Try cding
to a different folder, or spec a path to a folder where you have write
permissions, eg,
asegstats2table --subjects 004 008 --meas volume --tablefile
/tmp/aseg_stats.txt
doug
On 10/30/2014 08:28 AM, Claire Morley
Notification of the “Isaac Peral” Program to contract one senior
researcher associated with BBVA Foundation-UPM Industry-Academia chairs for
scientific-technological research in Medical Imaging, within Marie Curie
Action COFUND.
This notice provides for a maximum of one position in the
Notification of the “Isaac Peral” Program to contract one senior
researcher associated
with BBVA Foundation-UPM Industry-Academia chairs for
scientific-technological research in Medical Imaging, within Marie Curie
Action COFUND.
This notice provides for a maximum of one position in the area of
Hi Martin,
could you please confirm whether the glm analysis was correctly performed ?
the command line is:mri_glmfit --glmdir DIR --y
lh.thickness-pc1.stack.fwhm15.mgh --label lh.fsaverage.cortex.label --fsgd
FSGD_FILE --C Contrast-010..0.mtx --surf fsaverage lh
I get results, but I when I do
Hi Alex,
the QDEC output (text in the terminal) should have the command line that
was used to call the mri_glmfit command.
Best, Martin
On 10/30/2014 03:08 PM, Alex Hanganu wrote:
Hi Martin,
could you please confirm whether the glm analysis was correctly
performed ?
the command line
Hello,
Previously we have used a lesion of 128 microliters and have filtered out
anything smaller in volume than that for analyses (single subject pothole
analysis). Now we want to do something similar on the surface. So we need
to approximate the surface area of that 128 microliters when
right ! I totally forgot about this !
Thank you Martin !
Sincerely,Alex
On Thursday, October 30, 2014 3:33 PM, Martin Reuter
mreu...@nmr.mgh.harvard.edu wrote:
Hi Alex,
the QDEC output (text in the terminal) should have the command line that was
used to call the mri_glmfit
I believe it's in the surfaces. It is apparent when I load the lh.pial and
lh.white over the brainmask.
thanks,
Adam
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The
Can you send us an image?
On Oct 30, 2014, at 7:48 PM, Adam Mezher adammez...@gmail.com wrote:
I believe it's in the surfaces. It is apparent when I load the lh.pial and
lh.white over the brainmask.
thanks,
Adam
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I uploaded one when I sent the first email, did you receive it? Uploaded to:
ftp.nmr.mgh.harvard.edu ; cd transfer/incoming
The file was titled ‘mezher_insula_fail.tar.gz’ which contains the entire FS
folder for one subject. Should I go ahead and resend it?
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