HI! I need to subsample my original 4D .nii files (the f.nii or the fmc.nii after motion correction) from 2.5 2.5 2.75 to 2 2 2 mm, in each orignial 4D nii are 200 volumes: After subsampling with mri_convert -vs 2 2 2 001/fmc.nii 001/fmc.nii -oi -ii
the output info tells me that the inputstructure changed from nframe 200 to nframe 1 (in outputstructure)
as a consequence my subsequent analysis of the estimation of the statistics (-selxavg3-sess, not important I guess) cannot be performed.
if I do the same for the f.nii files, the same happens, and -preproc-sess enters with an ERROR ('cannot perform mc')
How can I keep my 200 frames in the 4D nii and subsample my voxels at the same time, to then continue my statistics?
I would be extremely greatful I someone can help!
Natalie xxx
Hi Natalie,
I am not sure why, because this command is working for me. Which version of freesurfer are you using. Also I am not sure if it helps, but instead of overwriting the input file, can you try a different name for the output and see if that works.
Sita.
On Fri, 4 Jun 2010, caspari@clipper.ens.fr wrote:
HI! I need to subsample my original 4D .nii files (the f.nii or the fmc.nii after motion correction) from 2.5 2.5 2.75 to 2 2 2 mm, in each orignial 4D nii are 200 volumes: After subsampling with mri_convert -vs 2 2 2 001/fmc.nii 001/fmc.nii -oi -ii
the output info tells me that the inputstructure changed from nframe 200 to nframe 1 (in outputstructure)
as a consequence my subsequent analysis of the estimation of the statistics (-selxavg3-sess, not important I guess) cannot be performed.
if I do the same for the f.nii files, the same happens, and -preproc-sess enters with an ERROR ('cannot perform mc')
How can I keep my 200 frames in the 4D nii and subsample my voxels at the same time, to then continue my statistics?
I would be extremely greatful I someone can help!
Natalie xxx
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Natalie,
Please ignore my previous e-mail. Doug suggested this work-around. You can use the output from your mri_convert for the --targ flag in the following command.
mri_vol2vol --mov original.nii --targ mriconvertoutput.nii --regheader --o orig.new.nii
Thanks, Sita.
On Fri, 4 Jun 2010, caspari@clipper.ens.fr wrote:
HI! I need to subsample my original 4D .nii files (the f.nii or the fmc.nii after motion correction) from 2.5 2.5 2.75 to 2 2 2 mm, in each orignial 4D nii are 200 volumes: After subsampling with mri_convert -vs 2 2 2 001/fmc.nii 001/fmc.nii -oi -ii
the output info tells me that the inputstructure changed from nframe 200 to nframe 1 (in outputstructure)
as a consequence my subsequent analysis of the estimation of the statistics (-selxavg3-sess, not important I guess) cannot be performed.
if I do the same for the f.nii files, the same happens, and -preproc-sess enters with an ERROR ('cannot perform mc')
How can I keep my 200 frames in the 4D nii and subsample my voxels at the same time, to then continue my statistics?
I would be extremely greatful I someone can help!
Natalie xxx
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
freesurfer@nmr.mgh.harvard.edu
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caspari＠clipper.ens.fr -
Sita Kakunoori