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 > <fis...@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: lris...@uw.edu >>> >>> P Please consider the environment before printing this e-mail. >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
