sorry, also add -ic 0 0 0 Chris Watson wrote: > Still get an error: > > [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm -iis 1 > -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 "image" > > mri_convert I.001 -it ge -ot spm -iis 1 -ijs 1 -iks 1 -iid 1 0 0 -ijd > 0 1 0 -ikd 0 0 1 image > $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ > reading from I.001... > fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d > zero frames specified in file - setting to 1 > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > i_ras = (1, 0, 0) > j_ras = (0, 1, 0) > k_ras = (0, 0, 1) > Reslicing using trilinear interpolation > MRIresample(): error inverting matrix; determinant is nan, matrix is: > 1.000 0.000 0.000 nan; > 0.000 1.000 0.000 nan; > 0.000 0.000 1.000 nan; > 0.000 0.000 0.000 1.000; > > > Douglas N Greve wrote: >> You can try specifying the input geometry with something like -iis 1 >> -ijs 1 -iks 1 -iid 1 0 0 -ijd 0 1 0 -ikd 0 0 1 >> >> this is undoubtedly wrong, but should allow the command to finish >> >> Chris Watson wrote: >> >>> It got a little further (with "-it ge" and without any --in_type >>> flag), but I get this error: >>> >>> [matl...@occipital new_func]$ mri_convert I.001 -it ge -ot spm "image" >>> mri_convert I.001 -it ge -ot spm image >>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>> reading from I.001... >>> fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d >>> zero frames specified in file - setting to 1 >>> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 >>> i_ras = (nan, nan, nan) >>> j_ras = (nan, nan, nan) >>> k_ras = (nan, nan, nan) >>> Reslicing using trilinear interpolation >>> MRIresample(): error inverting matrix; determinant is nan, matrix is: >>> nan nan nan nan; >>> nan nan nan nan; >>> nan nan nan nan; >>> 0.000 0.000 0.000 1.000; >>> >>> Douglas N Greve wrote: >>> >>>> sorry, it's a little finicky, I think it is looking for a %03d >>>> format, meaning I.001 for slices numbers less than 1000, and I.1001 >>>> for greater >>>> >>>> Chris Watson wrote: >>>> >>>> >>>>> I renamed them all to "I.1, I.2, ..., I.8000" (there are 8000 >>>>> images total), and I got the same error messages. (With the "-it >>>>> ge" option, it is still looking for the old filename, it seems) >>>>> >>>>> [matl...@occipital new_func]$ mri_convert I.1 -it lx -ot spm "image" >>>>> mri_convert I.1 -it lx -ot spm image >>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>> reading from I.1... >>>>> genesisRead(): can't determine file name format for >>>>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 >>>>> >>>>> [matl...@occipital new_func]$ mri_convert I.1 -it ge -ot spm "image" >>>>> mri_convert I.1 -it ge -ot spm image >>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>> reading from I.1... >>>>> fname_format : /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.%03d >>>>> genesisRead(): error opening file >>>>> /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.001 >>>>> >>>>> [matl...@occipital new_func]$ mri_convert I.1 -it dicom -ot spm >>>>> "image" >>>>> mri_convert I.1 -it dicom -ot spm image >>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>> reading from I.1... >>>>> Starting DICOMRead2() >>>>> dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 >>>>> dcmdir = /raid2/fmri5/LDProj/BOSEN/functional/new_func >>>>> ERROR: /raid2/fmri5/LDProj/BOSEN/functional/new_func/I.1 is not a >>>>> dicom file >>>>> >>>>> >>>>> >>>>> Douglas N Greve wrote: >>>>> >>>>>> can you rename your files to remove the .s01? >>>>>> >>>>>> Chris Watson wrote: >>>>>> >>>>>> >>>>>>> Hello, >>>>>>> I'm trying to use mri_convert to convert old (~1999) functional >>>>>>> data that was acquired on a GE LX scanner. However, nothing >>>>>>> seems to work. I'm running version 4.4.0 on RHEL4 x86_64. Here's >>>>>>> my command line: (results are similar if I omit the -in_type flag) >>>>>>> >>>>>>> [matl...@occipital functional]$ mri_convert I.001.s01 -it lx -ot >>>>>>> spm "image" >>>>>>> mri_convert I.001.s01 -it lx -ot spm image >>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>>> reading from I.001.s01... >>>>>>> genesisRead(): can't determine file name format for >>>>>>> /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 >>>>>>> >>>>>>> [matl...@occipital functional]$ mri_convert I.001.s01 -it ge -ot >>>>>>> spm "image" >>>>>>> mri_convert I.001.s01 -it ge -ot spm image >>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>>> reading from I.001.s01... >>>>>>> fname_format : /raid2/fmri5/LDProj/BOSEN/functional/I.%03d >>>>>>> genesisRead(): error opening file >>>>>>> /raid2/fmri5/LDProj/BOSEN/functional/I.001 >>>>>>> >>>>>>> [matl...@occipital functional]$ mri_convert I.001.s01 -it dicom >>>>>>> -ot spm "image" >>>>>>> mri_convert I.001.s01 -it dicom -ot spm image >>>>>>> $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 nicks Exp $ >>>>>>> reading from I.001.s01... >>>>>>> Starting DICOMRead2() >>>>>>> dcmfile = /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 >>>>>>> dcmdir = /raid2/fmri5/LDProj/BOSEN/functional >>>>>>> ERROR: /raid2/fmri5/LDProj/BOSEN/functional/I.001.s01 is not a >>>>>>> dicom file >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Freesurfer mailing list >>>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >> > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
