Hi again,
Any suggestion? I haven't any idea about this error. Why does it happen?
Thank you.
alexandra.cristo...@urjc.es escribió:
Hi Bruce,
This is the information about my version:
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
As you can see, it runs in a iMac version 10.6.8
Hi Doug,
Not really clear, I do agree.
1/ I would like to measure the area of the surface called
lesionMask_surf.mgh obtained with mri_vol2surf.
2/ In addition, I have two methods (M1 and M2) to measure a resected
volume. The binary volumes M1_vol and M2_vol are processed with
mri_vol2surf to
On 3/12/13 10:12 AM, Christopher wrote:
Hi Doug,
Not really clear, I do agree.
1/ I would like to measure the area of the surface called
lesionMask_surf.mgh obtained with mri_vol2surf.
You can use mri_segstats, something like
mri_segstats --i $SUBJECTS_DIR/$subject/surf/lh.area --seg
I think the right way to do it is to use the symmetric template
(fsaverage_sym) as the target (instead of fsaverage). You will need to
run the symmetric registration. See
http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi (if you have 5.2, you do
not need to download anything). You can map
Hi FS experts,
I just installed 5.2 for Snow Leopard in a machine who already had 5.1.
When running tkmedit in 5.1 X11 works well, but when running it from 5.2 it
gives the following error:
BRODMANN80:~ glerma$ tkmedit bert T1.mgz
dyld: Library not loaded: /opt/X11/lib/libGLU.1.dylib
it doesn't look like it's exiting, is it? That is, it keeps running after
printing that message?
I would run mri_info on the input volumes (norm.mgz) and check their
parameters
Bruce
On Tue, 12 Mar 2013,
alexandra.cristo...@urjc.es wrote:
Hi again,
Any suggestion? I haven't any idea
Hi again,
The script doesn't keep running after that. I've run mri_info for my
two subject, and there is a little difference between them. In the
dicom header this parameters have, for example, the value for echo
time as 4.568 and 4.56. Could it be the reason?
iAlba-2:mri Alexandra$
yes, that is definitely the reason. Can you remind me what version you
are running? I think the current one doesn't do this check. If it's not
current, can you grab a new mri_ca_train and see if it fixes your problem?
Bruce
On Tue, 12
Mar 2013, alexandra.cristo...@urjc.es wrote:
Hi
The version is 5.1.0. I don't know how to fix it.
I'm running the script with two subjects with the same values (to
check if it is the problem). It's very strange, because we are
acquiring all subjects with the same parameters, and I don't know why
it has a different decimal value.
Thanks!
if you let us know the hardware/software environment you are using we'll
get you a new version of mri_ca_train
On Tue, 12 Mar 2013,
alexandra.cristo...@urjc.es wrote:
The version is 5.1.0. I don't know how to fix it.
I'm running the script with two subjects with the same values (to check if
We have two enviroments:
- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
- freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Thanks!
Bruce Fischl fis...@nmr.mgh.harvard.edu escribió:
if you let us know the hardware/software environment you are using
we'll get you a new version of
Hi Doug,
This is the terminal output. The output volumes don't seem to be smoothed.
preproc-sess -s 8003 -fsd bold -stc up -fwhm 5 -per-run
--
preproc-sess logfile is log/preproc-sess.8003.log
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Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in
the dlabel/diff/ directory has been mapped to the same space as the DWI,
so those are the volumes that can be compared directly to dwi.nii.gz.
a.y
On Tue, 12 Mar 2013, std...@virgilio.it wrote:
Hi list,
I have two
Can you please answer my question? I can't really tell if the issue is due
poor dwi-aseg overlap unless you tell me where you got that aseg volume
from.
On Tue, 12 Mar 2013, std...@virgilio.it wrote:
Thank you Anastasia. What do you think about the issue in the file attacked
(I'm noting
Update: tkmedit 5.1 is working with Xquartz installed in Snow Leopard,
tkmedit 5.2 is not working again.
Any suggestion?
thanks,
Gari
On Tue, Mar 12, 2013 at 1:16 PM, Garikoitz Lerma-Usabiaga
gariko...@gmail.com wrote:
Hi FS experts,
I just installed 5.2 for Snow Leopard in a machine who
Hi freesurfers!
I am curious about corrections for multiple comparisons. I use mkcontrast
to generate my statistical maps and am curious if the function provides any
internal corrections for multiple comparisons
Does mkcontrast-sess correct for multiple comparisons? If so, how?
thank you,
Hi!
how can I translate a coordinate in talairach space of one subject
(Colin27), to every subject in a study? For example, I would like to know
where is the coordinate Y = +30 Talairach of Colin27 in Subject_00,
Subject_01, etc.
Should I use vol2vol to create a volume for every subject? Is there
Hi Rosa, it does not. Usually correction is done at the group level. Do
you need to do it on an individual?
doug
On 3/12/13 6:27 PM, Rosa Lafer-Sousa wrote:
Hi freesurfers!
I am curious about corrections for multiple comparisons. I use
mkcontrast to generate my statistical maps and am
Hi Gary, check out this wiki page and let me know if you still have
questions
http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
doug
On 3/12/13 8:04 PM, Garikoitz Lerma-Usabiaga wrote:
Hi!
how can I translate a coordinate in talairach space of one subject
(Colin27), to every subject
Hi Rosa, the sig maps are uncorrected at the individual level. To
correct them, run selxavg3-sess with the -fwhm option. This will compute
the FWHM of the residuals. When that is done, look for the fwhm.dat file
and get its contents.
Did you run this in the subject's native space? If so, then
Hi Stefano - The alignment here doesn't look good but it's hard to tell by
looking at it this way. Search in the file scripts/trac-all.log for these
2 lines:
bbregister Done
To check results, run:
Immediately below these lines, there's a tkregister2 command line that you
can run to check
I have encountered this error in the past, and I think it was because I was
not
sourcing SetUpFreeSurfer.sh correctly. That is the the script
that sets up the MNI_DIR I think.
echo $MNI_DIR or whatever it is called and it should show you
if it is being setup properly. It may be pointing to the
Thank you Michael!
LT
On Mon, Mar 11, 2013 at 8:54 AM, Michael Harms mha...@conte.wustl.eduwrote:
Hi Laura,
If you're looking for another reference that has used this approach, you
could see our 2010 paper:
http://www.ncbi.nlm.nih.gov/pubmed/20118463
cheers,
-MH
--
Michael Harms,
Thanks Doug,
I've seen the page, but I understand that everything is within the same
subject. I want to find the equivalencies between subjects. I mean, the
plane y = 30 in fsaverage, will correspond to a plane with a bigger Y for a
larger head (could be defined anatomically, the most outer point
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