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