hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid.
There are two things you can do,
mri_concat spm_*.img --o 4d.img
you can also do it with mri_convert, but I don't think it buys you anything over using mri_concat.
doug
Siddharth Srivastava wrote:
hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid.
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Hi Doug, Thanks for the reply. I tried mri_concat as you suggested, and got the following:
WARNING: analyzeRead(): matfile <usual path to>spmfile1-0003.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find <usual path to>spmfile1-0003.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in <usual path to>spmfile1-0003.mat file -----------------------------------------------------------------
These files are the outputs from spm_reslice command, and i looked at the contents of the mat files: they have 2 entries: "M" and "mat", and store the same matrix. Do you think mri_concat may be getting confused by 2 entries in the mat file? Is there any flag i can use (eg --it analyze ) to make it run? I would also be interested in using the mri_convert option as an alternative. can you (or anyone) help me with the command line flags?
regards, sid.
On Mon, Dec 15, 2008 at 12:11 PM, Doug Greve greve@nmr.mgh.harvard.eduwrote:
There are two things you can do,
mri_concat spm_*.img --o 4d.img
you can also do it with mri_convert, but I don't think it buys you anything over using mri_concat.
doug
Siddharth Srivastava wrote:
hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid.
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
mri_convert will fail in the same way. But it should have worked. Can you point me to the dir and give me read perms?
Siddharth Srivastava wrote:
Hi Doug, Thanks for the reply. I tried mri_concat as you suggested, and got the following:
WARNING: analyzeRead(): matfile <usual path to>spmfile1-0003.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it.
INFO: could not find <usual path to>spmfile1-0003.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in <usual path to>spmfile1-0003.mat file
These files are the outputs from spm_reslice command, and i looked at the contents of the mat files: they have 2 entries: "M" and "mat", and store the same matrix. Do you think mri_concat may be getting confused by 2 entries in the mat file? Is there any flag i can use (eg --it analyze ) to make it run? I would also be interested in using the mri_convert option as an alternative. can you (or anyone) help me with the command line flags?
regards, sid.
On Mon, Dec 15, 2008 at 12:11 PM, Doug Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
There are two things you can do, mri_concat spm_*.img --o 4d.img you can also do it with mri_convert, but I don't think it buys you anything over using mri_concat. doug Siddharth Srivastava wrote:hi everyone, is it possible to combine, using mri_convert, a set of 3D spm/analyze files into a 4D analyze file ? can anyone help me out with the syntax, if possible? thanks, sid.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@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 http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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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Doug Greve -
Siddharth Srivastava