AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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December 01, 2015 02:53AM
Hi AFNI group:

I was trying to map data from a surface domain to an AFNI volume domain by 3dSurf2Vol, with left hemi and right hemi separately.
But with using 3dcalc to combine the left and right hemi volume together, I realized that there were some overlaping voxels between left and right hemi. I'm not sure where goes wrong.
I have tried different parameters of -map_func, well, it turns out this parameters do have influnce on the results, but it never got perfect separated left and right hemi without overlapping.

Below are commands:

foreach hemi (lh rh)
3dSurf2Vol \
-spec "$spath"/group/Freesurfer/SUMA/subAvg_"$hemi"+tlrc.spec \
-surf_A smoothwm \
-surf_B pial \
-sv "$spath"/group/subAvg_SurfVol_at+tlrc.nii.gz \
-grid_parent "$spath"/sub01/map2sub2g/ts_normalized+tlrc.nii.gz \
-sdata_1D "$hemi"_"$infile"_"$test"_"$thresh".dset \
-map_func mode \
-f_steps 2 \
-f_index voxels \
-prefix "$hemi"_"$infile"_"$test"_"$thresh"_sb
end
## combine left and right hemi together
3dcalc \
-float -prefix "$infile"_"$test"_"$thresh".nii \
-a lh_"$infile"_"$test"_"$thresh"_sb+tlrc. \
-b rh_"$infile"_"$test"_"$thresh"_sb+tlrc. \
-expr '(a+b)'

Thanks !!!
Subject Author Posted

Trouble with 3dSurf2Vol

Liu Mengxing December 01, 2015 02:53AM

Re: Trouble with 3dSurf2Vol

rick reynolds December 01, 2015 12:13PM

Re: Trouble with 3dSurf2Vol

Liu Mengxing December 01, 2015 06:53PM

Re: Trouble with 3dSurf2Vol

rick reynolds December 01, 2015 09:18PM

Re: Trouble with 3dSurf2Vol

Liu Mengxing December 01, 2015 10:20PM

Re: Trouble with 3dSurf2Vol

rick reynolds December 04, 2015 12:11PM

Re: Trouble with 3dSurf2Vol

Liu Mengxing December 04, 2015 07:41PM