Hello FreeSurfer experts,
I just ran smoothing on a single 2D EPI image with a binary mask (that excludes NaN vertices), but it didn't seem work out well as the output image (e.g., test.mgh) contains zero values throughout vertices.
Also, I've got two warning messages (see below): while one of which seems harmless (5311 NaNs), the other (ar=0 <=0) may be critical.
If anyone has any idea/ suggestions, please help. -Glen
mris_fwhm --hemi lh --s fsaverage_sym --mask mask.mgh --fwhm 4 --i rabold4_0065_sym_L.mgh --o test.mgh fsaverage_sym lh white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 GroupSurface 85910.812500 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 WARNING: 5311 NaNs found in volume rabold4_0065_sym_L.mgh...
Loading mask mask.mgh Found 158531 voxels in mask Polynomial detrending, order = 0 Smoothing input by fwhm=4.000000, gstd=1.698644, niters=11 Computing spatial AR1 ar1mn = 0, ar1std = 0, ar1max = 0 avg vertex dist 0.693419 WARNING: ar1 = 0 <= 0. Setting fwhm to 0. avg vertex dist 0.693419 fwhm = 0.000000
The second error just means that it cannot compute the fwhm. This will go away if you add --smoooth-only.
On 05/23/2013 01:31 PM, Glen Lee wrote:
Hello FreeSurfer experts,
I just ran smoothing on a single 2D EPI image with a binary mask (that excludes NaN vertices), but it didn't seem work out well as the output image (e.g., test.mgh) contains zero values throughout vertices. Also, I've got two warning messages (see below): while one of which seems harmless (5311 NaNs), the other (ar=0 <=0) may be critical.
If anyone has any idea/ suggestions, please help. -Glen
mris_fwhm --hemi lh --s fsaverage_sym --mask mask.mgh --fwhm 4 --i rabold4_0065_sym_L.mgh --o test.mgh fsaverage_sym lh white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 GroupSurface 85910.812500 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 WARNING: 5311 NaNs found in volume rabold4_0065_sym_L.mgh...
Loading mask mask.mgh Found 158531 voxels in mask Polynomial detrending, order = 0 Smoothing input by fwhm=4.000000, gstd=1.698644, niters=11 Computing spatial AR1 ar1mn = 0, ar1std = 0, ar1max = 0 avg vertex dist 0.693419 WARNING: ar1 = 0 <= 0. Setting fwhm to 0. avg vertex dist 0.693419 fwhm = 0.000000
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Thanks Doug. Yes, it works well now! -Glen
On Thu, May 23, 2013 at 1:50 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
The second error just means that it cannot compute the fwhm. This will go away if you add --smoooth-only.
On 05/23/2013 01:31 PM, Glen Lee wrote:
Hello FreeSurfer experts,
I just ran smoothing on a single 2D EPI image with a binary mask (that excludes NaN vertices), but it didn't seem work out well as the output image (e.g., test.mgh) contains zero values throughout vertices. Also, I've got two warning messages (see below): while one of which seems harmless (5311 NaNs), the other (ar=0 <=0) may be critical.
If anyone has any idea/ suggestions, please help. -Glen
mris_fwhm --hemi lh --s fsaverage_sym --mask mask.mgh --fwhm 4 --i rabold4_0065_sym_L.mgh --o test.mgh fsaverage_sym lh white Number of vertices 163842 Number of faces 327680 Total area 61972.710938 GroupSurface 85910.812500 AvgVtxArea 0.378247 AvgVtxDist 0.693419 StdVtxDist 0.190498 WARNING: 5311 NaNs found in volume rabold4_0065_sym_L.mgh...
Loading mask mask.mgh Found 158531 voxels in mask Polynomial detrending, order = 0 Smoothing input by fwhm=4.000000, gstd=1.698644, niters=11 Computing spatial AR1 ar1mn = 0, ar1std = 0, ar1max = 0 avg vertex dist 0.693419 WARNING: ar1 = 0 <= 0. Setting fwhm to 0. avg vertex dist 0.693419 fwhm = 0.000000
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