Hi Bruce, MIPAV did allow me to save it in other formats like Nifti and Analyze, but it only created corrupted files.
Thanks. 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 6:14 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>wrote: > 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. >>> >>> >>> >>
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