unpack the non Siemens DICOMs?
Thanks,
Moahmad
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streamline
INFO: Step is 5 voxels
WARN: Turning off FA check for center streamline
INFO: Step is 5 voxels
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into tracula or vice versa?
a.y
On Mon, 21 Jul 2014, Shantanu Ghosh wrote:
Hi FS experts,
Is the DtiMap software (www.kennedykrieger.org) compatible with
Freesurfer/Tracula?
Thanks
Shantanu
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Hi FS experts,
Is the DtiMap software (www.kennedykrieger.org) compatible with
Freesurfer/Tracula?
Thanks
Shantanu
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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.
Shantanu
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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Tracula version from here: http://ftp.nmr.mgh.harvard.edu/fswiki/Tracula ?
Thank you,
Trang
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,
Martijn
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thanks.
On Fri, June 13, 2014 12:30 pm, Anastasia Yendiki wrote:
The right one to source is /usr/local/freesurfer/nmr-dev-env
On Fri, 13 Jun 2014, Shantanu Ghosh wrote:
Hi Anastasia,
Thanks for the reply.
After I edit my .tcshrc file to source the dev, I still get an error
message
don't need to
download anything.
a.y
On Mon, 2 Jun 2014, Shantanu Ghosh wrote:
Dear Anastasia and Freesurfer experts,
I am trying to set up an analysis of motion parameters using the flag
-q
from a set of DTI Dicoms located on the Martinos cluster, but I am facing
problems -- it says ERROR
not recognize the -qa flag. What am I doing wrong?
Attached is the log file, and an updated config file.
Any help is highly appreciated.
Thanks.
Shantanu
Original Message
Subject: TRACULA: ERROR in -qa Flag
From:Shantanu Ghosh shant
] trac-all -qa -s 008801 -c
/autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt
ERROR: flag -qa unrecognized
-qa -s 008801 -c
/autofs/space/glia_001/users/shantanu/dtistudy/dticonfigfile.txt
glia:shantanu[122]
Thanks in advance for all help.
Shantanu
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is /Users/sampada/Desktop/Vaibhav2
Actual FREESURFER_HOME /Applications/freesurfer
/Users/sampada/Desktop/Vaibhav2/s600a1001.mgz: Not a directory.
Will you please let me know where I am going wrong?
Thanks and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh
shant
and regards,
Sampada
On Wed, May 14, 2014 at 8:45 PM, Shantanu Ghosh
shant...@nmr.mgh.harvard.edu wrote:
You should set your SUBJECTS_DIR variable to the directory with all
the
subjects. Edit the .bashrc/.tcshrc/.cshrc by replacing the current
one
with
SUBJECTS_DIR /User
directory of mri/orig, its still not
recognising the command and shows an error.
Thanks and regards,
Sampada
On Fri, May 9, 2014 at 8:00 PM, Shantanu Ghosh
shant...@nmr.mgh.harvard.edu
wrote:
You should try to run recon_all command with -all flag to run on the
structural T1 dataset. After
the sender and
properly
dispose of the e-mail.
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at one
go.
mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii'
'/Users/sampada/Desktop/test/mri/org/.mgz'
Regards,
Sampada
On Tue, May 6, 2014 at 6:43 PM, Shantanu Ghosh
shant...@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014
sorry
try:
cd Users/sampada/Desktop/
mkdir test
cd test
mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii
sampada/Desktop/test/s400a1001.mgz
Hth,
shantanu
On Tue, May 6, 2014 11:10 pm, Shantanu Ghosh wrote:
You don't need the quotation marks in your path
also, it seems you don't have
Dear Freesurfers,
Pardon me for a very basic question.
If I wanted to extract the hemisphere-wise GM and WM values for multiple
subjects using a single command, what is the best way to do it?
Thanks in advance.
Shantanu
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Harvard Medical School Massachusetts General
You could also try the nipy version. works real well with Snow Leopard OS
shantanu
On Mon, April 28, 2014 9:09 pm, Shantanu Ghosh wrote:
Hi Sampada,
Please cc the freesurfer list when answering/asking questions so others
can answer too. And also people with similar issues will benefit from
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
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can think. -Werner
and regards,
Sampada
On Mon, Apr 28, 2014 at 7:00 PM, Shantanu Ghosh
shant...@nmr.mgh.harvard.edu wrote:
You can convert Dicom using MRICroN with the dcm2nii utility
shantanu
On Mon, April 28, 2014 6:55 pm, Dr Sampada Sinha wrote:
Hello I have only recently started the fmri data analysis
in error
but does not contain patient information, please contact the sender
and
properly
dispose of the e-mail.
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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/listinfo/freesurfer
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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can think. -Werner Heisenberg
clarification or suggestions would be greatly appreciated!
Thanks,
Alex
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mailing list
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information, please contact the sender and
properly
dispose of the e-mail.
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Harvard Medical School
Ghosh, Ph.D.
Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
--
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Harvard Medical School Massachusetts
@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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, Shantanu Ghosh shant...@nmr.mgh.harvard.edu
wrote:
ok try editing qdec.table.dat by just pressing Enter after the subject
with the error and the last line
hth. shantanu
On Wed, March 6, 2013 12:12 pm, Varghese Chikku wrote:
no luck Shantanu
This comes up
Loading data table
/Users
.
Many Thanks
chikku
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Harvard Medical School Massachusetts General Hospital
Martinos Center
://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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https
Thirteenth Street, Suite 2301
Charlestown, Massachusetts 2129
U.S.A.
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Harvard Medical School
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
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, Shantanu Ghosh wrote:
Hi Josh,
you can modify the SetUpFreeSurfer.sh to source the correct version.
Hth, Shantanu
On Thu, February 21, 2013 12:55 pm, Joshua Lee wrote:
If I want to install the new Freesurfer version but retain the older
Freesurfer install as well, what issues might I face
version, let me know and I'd be happy to help!
All the best,
Anderson
2013/2/15 Shantanu Ghosh shant...@nmr.mgh.harvard.edu
Hello FreeSurfer experts,
Has algorithm described in Winkler et al. (2012) Neuroimage paper for
computation of surface area been incorporated in v5.1, or is it part
Hello FreeSurfer experts,
Has algorithm described in Winkler et al. (2012) Neuroimage paper for
computation of surface area been incorporated in v5.1, or is it part of
the 5.2b implementation?
Thanks for your help.
Shantanu
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Harvard Medical School Massachusetts
/freesurfer
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sorry the files are in the surf directory
On Thu, February 14, 2013 9:53 am, Shantanu Ghosh wrote:
Hi Christine,
If you cd to the subject directory you can locate the ?h.white surface and
use mris_expand command to do this.
Hth,
Shantanu
On Thu, February 14, 2013 5:39 am, Ecker, Christine
.
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Martinos Center for Biomedical Imaging
Hi Freesurfers,
Can you point out the correct paper that I can cite for the clusterwise
correction for multiple comparisons computed by mri_glmfit-sim in v5.0 ?
Thanks,
Shantanu
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical
, -1): could not open file
ERROR: could not read /volstat/AC066-rh-volume.mgh as type 3
Thanks for all the help.
Shantanu
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Harvard Medical School Massachusetts General Hospital
Martinos Center for Biomedical Imaging
Original Message
Subject: Re: [Freesurfer] Error with mri_vol2surf
From:Shantanu Ghosh shant...@nmr.mgh.harvard.edu
Date:Wed, January 16, 2013 2:05 pm
To: Douglas N Greve gr...@nmr.mgh.harvard.edu
Dear Freesurfers,
I posted the questions yesterday but received no answer so far. I really
need help with this. Posting thsi again.
Thanks in advance, and sorry for the double posting.
S
On Sat, January 12, 2013 2:02 pm, Shantanu Ghosh wrote:
Dear freesurfer experts,
I have .sig maps
) with the warpfield from the registration
form step 2) above. Or is there something I am missing here?
Also, for 3a) how do I get the correct set of triangles for each vertex?
Thanks in advance,
Shantanu
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Harvard Medical School Massachusetts General Hospital
Martinos
Research Institute (NHGRI), National
Institutes of Health (NIH), Bethesda, Maryland 20892, USA
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have at least two levels.
Error loading the data table.
although there are two levels in the .levels filehow is that possible?
2012/11/19 pietro de rossi deross...@gmail.com
thanks...I'll try... and let you know...
2012/11/19 Shantanu Ghosh shant...@nmr.mgh.harvard.edu
Is
886
)
Cannot allocate memory
Thanks in advance,
Shantanu
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Martinos Center for Biomedical Imaging
Harvard-MIT Program in Health Sciences Technology
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https
ink mri_register is what you
want. Possibly mris_register instead (note the s)?
Cheers
Bruce
On Jun 15, 2012, at 8:32 PM, Shantanu Ghosh
shant...@nmr.mgh.harvard.edu wrote:
Hi Freesurfer experts,
I am receiving an error message while processing registration to
fsaverage
using
,
Shantanu
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Harvard-MIT Program in Health Sciences Technology
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tksurfer fsaverage lh inflated -overlay z.mgh
On 06/13/2012 11:26 AM, Shantanu Ghosh wrote:
Hi FS experts,
Sorry if this is a newbie question.
I want to display how an individual patient's crtical thickness varies
from the normal group average, vertex-by-vertex. What is the commandline
to do
:38 PM, Shantanu Ghosh wrote:
hi doug,
i notice slight differences in numbers when using fscalc vs. fscalc.fsl
for calculating the z-score map\ I am just curious why it may happen
thanks in advance,
shantanu
On Wed, June 13, 2012 3:31 pm, Douglas N Greve wrote:
Use mris_preproc to collect
Hello Freesurfer experts,
How can I specify multiple contrasts for my thickness study with two
groups AA and BB, having different number of subjects in each group? My
variables are tract-wise FA values, age and IQ.
Thanks in advance,
Shantanu
--
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Martinos Center
Hello Freesurfer experts,
How can I specify multiple contrasts for my thickness study with two
groups AA and BB, having different number of subjects in each group? My
variables are tract-wise FA values, age and IQ.
Thanks in advance,
Shantanu
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Martinos Center
Hi freesurfers,
I tried to download the tutorial dataset for inspection of fs output, but
receive this error message repeatedly, even with the -c flag:
glia:shantanu[30] wget -c
ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz
--2012-04-20 15:27:05--
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