Hi Lisa, unless you can get the data into a format we support I'm not sure there's much we can do. Have you tried reading it into matlab and writing it out using our matlab functions (e.g. MRIwrite or save_mgh)?
cheers Bruce On Fri, 17 Dec 2010, Lisa F. Akiyama wrote: > 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. >>>> >>>> >>>> >>> > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
