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
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