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)
[matlab7@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
[matlab7@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
[matlab7@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
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)
[matlab7@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
[matlab7@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
[matlab7@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
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)
[matlab7@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
[matlab7@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
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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
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)
[matlab7@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
[matlab7@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
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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
It got a little further (with "-it ge" and without any --in_type flag), but I get this error:
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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
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:
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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
Still get an error:
[matlab7@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:
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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
sorry, also add -ic 0 0 0
Chris Watson wrote:
Still get an error:
[matlab7@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:
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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) > > [matlab7@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 > > [matlab7@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 > > [matlab7@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 > > >
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:
[matlab7@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:
[matlab7@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)
[matlab7@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
[matlab7@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
[matlab7@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) >> >> [matlab7@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 >> >> [matlab7@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 >> >> [matlab7@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 >> >> >> >> > >
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:
[matlab7@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:
[matlab7@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) > > [matlab7@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 > > [matlab7@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 > > [matlab7@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) >>> >>> [matlab7@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 >>> >>> [matlab7@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 >>> >>> [matlab7@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@nmr.mgh.harvard.edu
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Chris Watson -
Douglas N Greve