Applications are invited for two doctoral research positions in a multimodality
neuroimaging project funded by the Zürich Institute of Human Physiology (ZIHP),
to start on the 1st of January 2011. The project will investigate the major
physiological and metabolic markers of typical and atypical
Hello,
Changing the spm path to spm5 did not fix the problem.
Command line: bbregister --s RMCON051 --mov ../bold/009/f.nii --reg
../bold/register.dat
--init-spm --bold
Scripts directory: /space/ventzl/36/users/RespMon12C/scripts
SUBJECTS_DIR: /space/ventzl/36/users/RespMon12C/subjects
termina
Did you happen to notice this error printed by matlab?
Warning: Executing startup failed in matlabrc.
This indicates a potentially serious problem in your MATLAB setup, which
should be resolved as soon as possible. Error detected was:
MATLAB:UndefinedFunction
Undefined function or variable 'mne_
Dear all,
Can tksurfer load both hemispheres at once from command line input?
Hiroyuki
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The information in this e-mail is intended
no, sorry
Oya, Hiroyuki wrote:
> Dear all,
>
> Can tksurfer load both hemispheres at once from command line input?
>
> Hiroyuki
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@
no, sorryOn Thu, 7 Oct 2010, Oya, Hiroyuki wrote:
> Dear all,
>
> Can tksurfer load both hemispheres at once from command line input?
>
> Hiroyuki
>
>
>
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Hi all,
I was curious as to approximately how much memory is required to run a
surface through autorecon 1 and 2, and autorecon 2 and 3. I'm running them
on a new server where I have to request resources, so a ballpark figure is
really all I need. Thanks!
Nathan
Hi all,
I'm having an issue with selxavg3-sess in Stable 4. I've run all commands
up to this point without error. Here was the command I used
selxavg3-sess -s FB0011099AA -analysis fmcsm5_functionals
and the error:
ERROR: cannot find volume matching
/autofs/cluster/roffman/users/folate_subjects
Yes, for TBSS you probably want to use permutation simulation. BTW, why
are you doing the group analysis in FreeSurfer? I think FSL offers TBSS
group analysis. I'm not trying to steer you away from FreeSurfer, but it
might make sense to stick with one software package.
doug
Jacobs H (NP) wrote
Hello, Dr. Fischl,
I asked this quesion about zero thickness in the sulcus next to the lateral
vertricle before, and corrected the wrong label of lateral vertricle in the
aseg.mgz file and added white matter between lateral vertricle and this sulcus
in the wm.mgz. But the problem is still ex
Nathan,
You can find that info here:
https://surfer.nmr.mgh.harvard.edu/fswiki/SystemRequirements
--
On Thu, 7 Oct 2010, Nathan Dankner wrote:
> Hi all,
>
> I was curious as to approximately how much memory is required to run a
> surface through autorecon 1 and 2, and autorecon 2 and 3. I'm ru
3GB (actually, 2GB is sufficient most of the time, but some people have
needed 2.7GB).
n.
On Thu, 2010-10-07 at 10:48 -0500, Nathan Dankner wrote:
> Hi all,
>
> I was curious as to approximately how much memory is required to run a
> surface through autorecon 1 and 2, and autorecon 2 and 3. I'
Nathan,
For recon-all you should have at least 1GB per Core.
If you use a 6-core processor you should have at least 6GB to run 6
recon-all simultaneously
Given the current memory price circumstances, I would ask for at least 1.5GB
per Core
-- PPJ
one more question: I replace the mislabeled lateral ventricle with CSF because
I can not find the "none" in the FreesurfercolorLUT.txt. How to change the
mislabeled lateral ventricle to none?
Thank you,
Xin
From: Wang, Xin
Sent: Thu 10/7/2010 12:04 PM
To:
None should be the first label in the FreeSurferColorLUT.txt (it's labeled
as "Unknown" with an ID# of 0). But really you should be labeling it what
it truly is. Is this the gray matter you are labeling as CSF?
--
On Thu, 7 Oct 2010, Wang, Xin wrote:
> one more question: I replace the mislabe
Hi Xin,
can you upload this dataset so we can take a look?
Bruce
On Thu, 7 Oct 2010, Wang,
Xin wrote:
>
> Hello, Dr. Fischl,
>
> I asked this quesion about zero thickness in the sulcus next to the
lateral vertricle before, and corrected the wrong label of lateral
vertricle in the aseg.mgz fil
set it to "Unknown" which is 0
On Thu, 7 Oct 2010, Wang, Xin wrote:
> one more question: I replace the mislabeled lateral ventricle with CSF
> because I can not find the "none" in the FreesurfercolorLUT.txt. How to
> change the mislabeled lateral ventricle to none?
>
> Thank you,
>
> Xin
>
> __
Thank you, Allison.
Is Unknown for the empty space between gyri? I did label the gray matter
vertices as cortex.
Xin
From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Thu 10/7/2010 12:16 PM
To: Wang, Xin
Cc: freesurfer@nmr.mgh.harvard.edu
Sub
yes it is
On Thu, 7 Oct 2010, Wang, Xin wrote:
> Thank you, Allison.
> Is Unknown for the empty space between gyri? I did label the gray matter
> vertices as cortex.
>
> Xin
>
>
>
> From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
> Sent: Thu 10/7/2010
Thank you, Dr. Fischl.
I will try another round of correction, and please instruct me how to upload a
subject data to your workstation? so we can look into this problem at same time.
Xin
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thu 10/7/201
you can find it on our wiki
On Thu, 7 Oct 2010, Wang, Xin wrote:
> Thank you, Dr. Fischl.
> I will try another round of correction, and please instruct me how to upload
> a subject data to your workstation? so we can look into this problem at same
> time.
>
> Xin
>
>
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
use the Upload button.
On Thu, 2010-10-07 at 12:25 -0400, Wang, Xin wrote:
> Thank you, Dr. Fischl.
> I will try another round of correction, and please instruct me how to
> upload a subject data to your workstation? so we can look into
you can just re-run motion correction for that one session
doug
Adam Nitenson wrote:
> Hi all,
>
> I'm having an issue with selxavg3-sess in Stable 4. I've run all commands
> up to this point without error. Here was the command I used
>
> selxavg3-sess -s FB0011099AA -analysis fmcsm5_functionals
Hi Adam,
mcextreg files are generated by preproc-sess. If you don't have these
files in your bold/015/ folder than preproc-sess might not have been
completed.
Pratap
> Hi all,
>
> I'm having an issue with selxavg3-sess in Stable 4. I've run all commands
> up to this point without error. Here wa
Hi All:
This is for the FSL VBM experts out there. I have finished all the pre
processing steps for a dataset using FSL VBM and I am trying to design a
matrix for statistical analysis. I am having difficulty with the *design.mat
* file and the* design.con* files. Do any of you know an easy of crea
Hi all,
I am encountering a similar error with spmregister, although it is a bit
different. When my startup.m is configured to add the SPM2 paths,
spmregister works without issue. However, when my startup.m uses either
the SPM5 or 8 paths, it fails with the following error:
Welcome to MATLAB
Hello All:
I read the paper by Kouwe et al. (2008 NeuroImage 40 p.559).
I was wondering if FreeSurfer (v4.5) is able utilize the multi echo
(especially T2-SPACE) sequence in order achieve better segmentation of
GM from dura. The paper mentions the code was altered to do this.
If it is possible,
Hi Deniz,
yes, it should be in the mris_make_surfaces of that version. You need to
run it with -dura memprage_echo%d.mgz 4
where 4 is the # of echoes, and the names would be memprage_echo0.mgz,
memprage_echo1.mgz, memprage_echo2.mgz, and memprage_echo3.mgz. These must
all be "conformed" to be
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