Re: [Freesurfer] mri_convert with old GE-LX data
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert with old GE-LX data
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
Re: [Freesurfer] mri_convert with old GE-LX data
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_convert with old GE-LX data
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
Re: [Freesurfer] mri_convert with old GE-LX data
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
Re: [Freesurfer] mri_convert with old GE-LX data
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
Re: [Freesurfer] mri_convert with old GE-LX data
It completed but it's only giving me 1 .img file, and when I loaded it into mricro, it thinks the z dimension is 8000 (the number of slices total). It should give me 400 volumes (20 slices each). So I want image001.img, 002.img, and so on. How can I do this? Do I have to rename the files differently? Douglas N Greve wrote: 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()
Re: [Freesurfer] mri_convert with old GE-LX data
Sorry, I don't know how to make our tools do this. It's a one-off on an old data set on a file format that we don't really support anymore, so I'm afraid that you're on your own on this one. doug Chris Watson wrote: It completed but it's only giving me 1 .img file, and when I loaded it into mricro, it thinks the z dimension is 8000 (the number of slices total). It should give me 400 volumes (20 slices each). So I want image001.img, 002.img, and so on. How can I do this? Do I have to rename the files differently? Douglas N Greve wrote: 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
