Dear Free Surfers,
I am analyzing fMRI time series that were reconstructed offline (GRAPPA data that needed some artifact corrections, long story). Unfortunately, the offline reconstructed f.nii do not include proper header info. I think I was able to set the orientations correctly using mri_convert, but now FSFAST preprocessing (specifically, mc-sess) fails because the headers say that the number of TRs (number of full volume acquisitions) in the measurement is 1, whereas in fact the correct value is 316.
I could not find a tool that could change the "nframes" value (mri_convert can adjust many other things but not this one it seems). Any suggestions?
Bests,
Tommi
--- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Hi Tommi, that's going to be a problem because all the tools look at the number of frames to determine how much data to read in (unlike voxel size or direction cosines). I don't know of an easy way around it, though I can think of some hard ones. How hard is it to fix the grappa recon to write out the right number of frames?
doug
On 9/22/10 1:35 AM, raij@nmr.mgh.harvard.edu wrote:
Dear Free Surfers,
I am analyzing fMRI time series that were reconstructed offline (GRAPPA data that needed some artifact corrections, long story). Unfortunately, the offline reconstructed f.nii do not include proper header info. I think I was able to set the orientations correctly using mri_convert, but now FSFAST preprocessing (specifically, mc-sess) fails because the headers say that the number of TRs (number of full volume acquisitions) in the measurement is 1, whereas in fact the correct value is 316.
I could not find a tool that could change the "nframes" value (mri_convert can adjust many other things but not this one it seems). Any suggestions?
Bests,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The 'fsledithd' utility (of FSL) can be used to edit the number of frames (as well as a host of other fields) in a Nifti file.
cheers, -MH
On Wed, 2010-09-22 at 09:02 -0400, Douglas Greve wrote:
Hi Tommi, that's going to be a problem because all the tools look at the number of frames to determine how much data to read in (unlike voxel size or direction cosines). I don't know of an easy way around it, though I can think of some hard ones. How hard is it to fix the grappa recon to write out the right number of frames?
doug
On 9/22/10 1:35 AM, raij@nmr.mgh.harvard.edu wrote:
Dear Free Surfers,
I am analyzing fMRI time series that were reconstructed offline (GRAPPA data that needed some artifact corrections, long story). Unfortunately, the offline reconstructed f.nii do not include proper header info. I think I was able to set the orientations correctly using mri_convert, but now FSFAST preprocessing (specifically, mc-sess) fails because the headers say that the number of TRs (number of full volume acquisitions) in the measurement is 1, whereas in fact the correct value is 316.
I could not find a tool that could change the "nframes" value (mri_convert can adjust many other things but not this one it seems). Any suggestions?
Bests,
Tommi
Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.
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
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-
Douglas Greve -
Michael Harms -
raij＠nmr.mgh.harvard.edu