can you use MIPAV to convert it to nifti?

On Mon, 13 Dec 2010, Lisa F. Akiyama wrote:

Hi Bruce,

No, I was not able to successfully converting it to a different format using
mri_convert.
A similar error appeared.

When I read the tag information using MIPAV, it seems like it contains
plenty of information (listed in dicom tag format)
to know the orientation/positioning of the subject.
Attached is the tag information listed in a text file. (I've deleted
subject's personal info)

Thank you.


Best,
Lisa

______________________________
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington


P Please consider the environment before printing this e-mail.



On Mon, Dec 13, 2010 at 3:12 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu>wrote:

Hi Lisa,

can you convert it to one of our supported formats? But even then, how will
you know left from right?

Bruce

On Mon, 13 Dec 2010, Lisa F. Akiyama wrote:

 Hello FreeSurfer experts,

I am trying to run recon-all on old (back from late 1990's) raw MRI data.
Each slice is in a raw format.
When I try to execute recon-all, I get the error shown below:

todd:~$ recon-all -subjid A_H -i

$SUBJECTS_DIR/adults_jp/A_H/slices/HA970313a1997031316500756

Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects

Actual FREESURFER_HOME /usr/local/freesurfer

Linux neptune-ubuntu 2.6.35-23-generic #41-Ubuntu SMP Wed Nov 24 11:55:36

UTC 2010 x86_64 GNU/Linux

/usr/local/freesurfer/subjects/A_H


 mri_convert

/usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756
/usr/local/freesurfer/subjects/A_H/mri/orig/001.mgz

 mri_convert

/usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756
/usr/local/freesurfer/subjects/A_H/mri/orig/001.mgz

$Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $

reading from

/usr/local/freesurfer/subjects/adults_jp/A_H/slices/HA970313a1997031316500756...

Getting Series No

INFO: Found 136 files in
/usr/local/freesurfer/subjects/adults_jp/A_H/slices

INFO: Scanning for Series Number 32664

Scanning Directory

INFO: found 0 files in series

ERROR: could not find any files (SeriesList==NULL)

Linux neptune-ubuntu 2.6.35-23-generic #41-Ubuntu SMP Wed Nov 24 11:55:36

UTC 2010 x86_64 GNU/Linux

 recon-all -s A_H exited with ERRORS at Mon Dec 13 14:34:21 PST 2010

Does anyone know how to resolve this issue?


Thank you.


Best,
Lisa
______________________________
Lisa F. Akiyama
Research Study Assistant
Institute for Learning & Brain Sciences (I-LABS)
University of Washington
E-mail: lrisa87@uw.edu

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