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

--

Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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