Dear Surfers, I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel size 1 mm iso)using the below command:
mris_fwhm --s <SBJ_NAME>--hemi rh --smooth-only --i fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask /masks/brain.self.rh.nii.gz
When I apply this command, it works without any error. The message on screen is as below:
<SBJ_NAME> rh white Number of vertices 160391 Number of faces 320778 Total area 102725.085938 GroupSurface 0 AvgVtxArea 0.640467 AvgVtxDist 0.875515 StdVtxDist 0.253406 Loading mask masks/brain.self.rh.nii.gz Found 36045 voxels in mask Not Polynomial detrending Smoothing input by fwhm=0.660000, gstd=0.280276, niters=0 Only smoothing, so saving and exiting now
But the outcome is the same as input. I think it is expected based on (niters=0). When I use the same command with fwhm =1, then i see the difference and niters=1.
My question is, why is fwhm = 0.66 not acceptable? How can i solve this issue.
Regards
_____________________________________
Shahin Nasr
Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129
The smoothing works through iterative nearest neighbor smoothing, so the fwhm is essentially discretized because you can't have fractions of an iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 iteration, so it chooses 0.
On 12/21/18 11:23 AM, shahin@nmr.mgh.harvard.edu wrote:
Dear Surfers, I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel size 1 mm iso)using the below command:
mris_fwhm --s <SBJ_NAME>--hemi rh --smooth-only --i fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask /masks/brain.self.rh.nii.gz
When I apply this command, it works without any error. The message on screen is as below:
<SBJ_NAME> rh white Number of vertices 160391 Number of faces 320778 Total area 102725.085938 GroupSurface 0 AvgVtxArea 0.640467 AvgVtxDist 0.875515 StdVtxDist 0.253406 Loading mask masks/brain.self.rh.nii.gz Found 36045 voxels in mask Not Polynomial detrending Smoothing input by fwhm=0.660000, gstd=0.280276, niters=0 Only smoothing, so saving and exiting now
But the outcome is the same as input. I think it is expected based on(niters=0). When I use the same command with fwhm =1, then i see the difference and niters=1.
My question is, why is fwhm = 0.66 not acceptable? How can i solve this issue.
Regards
Shahin Nasr
Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
So, is there anyway around this issue?
The smoothing works through iterative nearest neighbor smoothing, so the fwhm is essentially discretized because you can't have fractions of an iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 iteration, so it chooses 0.
On 12/21/18 11:23 AM, shahin@nmr.mgh.harvard.edu wrote:
Dear Surfers, I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel size 1 mm iso)using the below command:
mris_fwhm --s <SBJ_NAME>--hemi rh --smooth-only --i fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask /masks/brain.self.rh.nii.gz
When I apply this command, it works without any error. The message on screen is as below:
<SBJ_NAME> rh white Number of vertices 160391 Number of faces 320778 Total area 102725.085938 GroupSurface 0 AvgVtxArea 0.640467 AvgVtxDist 0.875515 StdVtxDist 0.253406 Loading mask masks/brain.self.rh.nii.gz Found 36045 voxels in mask Not Polynomial detrending Smoothing input by fwhm=0.660000, gstd=0.280276, niters=0 Only smoothing, so saving and exiting now
But the outcome is the same as input. I think it is expected basedon (niters=0). When I use the same command with fwhm =1, then i see the difference and niters=1.
My question is, why is fwhm = 0.66 not acceptable? How can i solve this issue.
Regards
Shahin Nasr
Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129
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
_____________________________________
Shahin Nasr
Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129
No, not in the current framework. Even if there were, fwhm=.66 would not give you much smoothing. The intervertex distance is about 1mm, at fwhm=.66mm, the nearest vertex would be about 3 standard deviations away, meaning that the smoothing would be minimal.
On 12/21/18 12:12 PM, shahin@nmr.mgh.harvard.edu wrote:
So, is there anyway around this issue?
The smoothing works through iterative nearest neighbor smoothing, so the fwhm is essentially discretized because you can't have fractions of an iteration. It looks like fwhm=0.66 is closer to 0 iterations than 1 iteration, so it chooses 0.
On 12/21/18 11:23 AM, shahin@nmr.mgh.harvard.edu wrote:
Dear Surfers, I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel size 1 mm iso)using the below command:
mris_fwhm --s <SBJ_NAME>--hemi rh --smooth-only --i fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask /masks/brain.self.rh.nii.gz
When I apply this command, it works without any error. The message on screen is as below:
<SBJ_NAME> rh white Number of vertices 160391 Number of faces 320778 Total area 102725.085938 GroupSurface 0 AvgVtxArea 0.640467 AvgVtxDist 0.875515 StdVtxDist 0.253406 Loading mask masks/brain.self.rh.nii.gz Found 36045 voxels in mask Not Polynomial detrending Smoothing input by fwhm=0.660000, gstd=0.280276, niters=0 Only smoothing, so saving and exiting now
But the outcome is the same as input. I think it is expected basedon (niters=0). When I use the same command with fwhm =1, then i see the difference and niters=1.
My question is, why is fwhm = 0.66 not acceptable? How can i solve this issue.
Regards
Shahin Nasr
Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129
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
Shahin Nasr
Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129
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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Greve, Douglas N.,Ph.D. -
shahin＠nmr.mgh.harvard.edu