Hi Sampada
the recon-all script is designed to analyze T1-weighted structural data. Once that has been done, it can be used to facilitate fMRI analysis. Is that what you are trying to do? What are the 8 volumes?
cheers Bruce
On Fri, 9 May 2014, Dr Sampada Sinha wrote:
Hello Freesurfer, Thanks Shantanu I was able to convert the .nii to .mgz files . However, about the recon-all command do I run it separately for each .mgz file or run it one time for all .mgz file(which are eight in numbers)? And what command do I use for recon-all? I have tried many but none is working..
Thanks and regards,
Sampada
On Tue, May 6, 2014 at 11:12 PM, Shantanu Ghosh shantanu@nmr.mgh.harvard.edu wrote: sorry
try: cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.niisampada/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 a directory called /Users/sampada/Desktop/test/org
try something like:
cd Users/sampada/Desktop/ mkdir test cd test mri_covert /Users/sampada/Desktop/d2n119495/s400a1001.nii sampada/Desktop/test/s400a1001.nii
Hth, shantanu
On Tue, May 6, 2014 9:50 pm, Dr Sampada Sinha wrote:
Hello Shantanu,
Many thanks for your reply! This is my exact commandline which I give to free surfer for the 1st of the eight nii files. When i am able to convert this nii to mgz then i will ask how to convert all the eight files 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 <shantanu@nmr.mgh.harvard.edu
wrote:
can you send your exact mri_convert commandline?
On Tue, May 6, 2014 6:11 pm, Dr Sampada Sinha wrote:
*Hello freesurfer*
*Sorry for the personal message Shantanu. *
*I managed to convert my dicom to nifti using mricron software,
though had
to make some changes to the preferences. *
*About the dcmunpack: The user manual on dcmunpack on fs site says
that
the unpackdcmdir is used only to unpack Siemens dicom files. We use
Phillips
infinity for our PET scan.*
*I am very new to Unix, free surfer and neuroimaging, so couldn't understand what nipy would do...*
*My FS is working fine as when I typed tkmedit bert orig.mngz for
volume
view it was displaying image.*
*But the when I tried to convert my .nii files to .mgz format , I get
the
following error:*
Last login: Tue May 6 10:40:32 on ttys000 dhcp020-222-117:~ sampada$ export
FREESURFER_HOME=/Applications/freesurfer
dhcp020-222-117:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni dhcp020-222-117:~ sampada$ mri_convert '/Users/sampada/Desktop/d2n119495/s400a1001.nii' '/Users/sampada/Desktop/test/mri/org/.mgz' mri_convert /Users/sampada/Desktop/d2n119495/s400a1001.nii /Users/sampada/Desktop/test/mri/org/.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/sampada/Desktop/d2n119495/s400a1001.nii... TR=7.10, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0268034, -0.99958, 0.0110098) j_ras = (0.0381548, 0.0120287, 0.999199) k_ras = (0.998912, 0.0263618, -0.0384612) writing to /Users/sampada/Desktop/test/mri/org/.mgz... mghWrite(/Users/sampada/Desktop/test/mri/org/.mgz, -1): could not
open
file
ERROR: failure writing /Users/sampada/Desktop/test/mri/org/.mgz
*Will you please let me know what command I need to use to mri
convert and
recon all of my files? * I* have 8 .nii files (in the order of T1>T2>T1>T2>DTI>T1(resting
stage)>T2
(in the order of the acquisition acquired at the time of
experiment).*
*Thanks and regards,*
*Sampada*
On Tue, Apr 29, 2014 at 12:17 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Have you tried using dcmunpack? You run it twice, once without any output to get a list of runs in the folder. The 2nd with how you
want
the data converted. Run it with --help to get more info doug
On 04/28/2014 06:55 PM, Dr Sampada Sinha wrote: > Hello I have only recently started the fmri data analysis and I > downloaded freesurfer point by point from martinos site and > incorporated the license file as well into the
Applications/freesurfer
> directory. I have run into the first problem and that is of data > conversion. My file is in dcm format and I have 11,000 dcm files
to
> convert. However, before I was using Jamaan Alghamadi created gui
and
> it is not able to convert the mri dcm files. Then I shifted to
UNIX
> and again it is saying error. > > My file is on the desktop and I have given it subject id as Grace.
My
> directory to the dcm file is '/Users/sampada/desktop/Grace. > > My terminal look like this before I proceed with the file
conversion
> > Last login: Mon Apr 28 15:10:13 on ttys001 > > dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer > > dhcp020-223-179:~ sampada$ source
$FREESURFER_HOME/SetUpFreeSurfer.sh
> > -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > FREESURFER_HOME /Applications/freesurfer > > FSFAST_HOME /Applications/freesurfer/fsfast > > FSF_OUTPUT_FORMAT nii.gz > > SUBJECTS_DIR /Applications/freesurfer/subjects > > MNI_DIR /Applications/freesurfer/mni > > > > Will anyone please let me know what I am doing wrong? I will be
very
> grateful for any input. > > > Thanks and regards, > > > Sampada > Senior research support specialist > Molecular and neuroimaging department > Department of Psychiatry > 451, biomedical research building > University at Buffalo (south campus) > Buffalo, NY-14216 > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
-- Shantanu Ghosh, Ph.D. Harvard Medical School & Massachusetts General Hospital Martinos Center for Biomedical Imaging -- Not only is the universe stranger than we think, it is stranger than we can think. -Werner Heisenberg
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