3dskullstrip command is ran but showimg the warning(text in red color). Other skull stripping algorithms are not showing such warning for the same input. Can you please help me in this.
I did not get the BRIK extension as well.


bibl04@BIBL04:~/abin$ ./3dSkullStrip -input a.nii -prefix ss_mask.nii -mask_vol
oo Warning 3dSkullStrip (SUMA_3dSkullStrip.c:1537):
Input dataset has a very low value range.
If stripping fails, try scaling it by 1000
with:
3dcalc -a a.nii -expr 'a*1000' -prefix PPP
and try stripping again with new volume.
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 84, avoid_vent -1
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 96, avoid_vent -1
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 108, avoid_vent -1
Warning 3dSkullStrip:****************
Surface self intersecting! trying again:
smoothing of 120, avoid_vent -1
Warning 3dSkullStrip: Stubborn intersection remaining at smoothing of 120. Ignoring it.The output dataset is a mask reflecting where voxels in the
input dataset lie in the brain.
To obtain a masked version of the input with identical values inside
the brain, you can either use 3dSkullStrip's -orig_vol option
or run the following command:
3dcalc -a a.nii -b ss_mask.nii+orig -expr 'a*step(b)' \
-prefix ss_mask.nii_orig_vol
to generate a new masked version of the input.
bibl04@BIBL04:~/abin$ 3dcalc -a a.nii -expr 'a*1000' -prefix PPP
3dcalc: command not found
bibl04@BIBL04:~/abin$ ./3dcalc -a a.nii -expr 'a*1000' -prefix PPP
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Nov 8 2014) [64-bit]
++ Authored by: A cast of thousands
++ Output dataset ./PPP+orig.BRIK