What's your cmd line? What's the output?
I've pasted the script I used and the output below. You can see that there
is no mention of projfract-avg in the output.
By the way, it seems that it is ignoring the voxel resolution in the
registration file and instead using the (erroneous) resolution in the source
volume. That is, all of the activation is painted onto the midbrain. I
assume that it is related to this warning:
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)
The bfloats and hdrs were generated with fourier, so there is no .bhdr file.
Anyway, it seems to me that it would be better to trust the voxel
resolution in the registration file.
CMD LINE:
#! /bin/csh
source /space/monkeys/1/pubsw/packages/freesurfer/UCSDsurferenv-R302.csh
set curdir = `pwd`
set datadir = "/usr1"
set datadir = "/space/monkeys/1/home/dhagler/data"
set fspace = "$datadir/fspace"
set subj = xxxx
set reg = register.dat
set pf_min = 0.1
set pf_max = 0.9
set pf_delta = 0.1
set session = 060312XX
set indir = avg-pol
set instem = pol-dfix-ccw-vreg-unwarp_fmri+orig
set newstem = test-polret
foreach hemi (rh lh)
foreach infix (_r _i)
set srcpath = "$fspace/$session/image/$indir/$instem$infix"
set srcreg = "$fspace/$session/image/$indir/$reg"
set outpath = $curdir/$newstem-mgh$infix-$hemi.w
mri_vol2surf \
--srcfmt bfloat --srcvol $srcpath --srcreg $srcreg \
--srcoldreg --float2int tkreg \
--hemi $hemi --surf white \
--projfrac-avg $pf_min $pf_max $pf_delta \
--trgsubject $subj \
--o $outpath --ofmt paint
end
end
OUTPUT:
CPU is x86_64
OS is RH4-x86_64-R302
afni,fsl,imagej and spm5b are now available.
Make sure you set SUBJECTS_DIR points to the subjects directory
-----------------------------------------------------------------
Could not find the direction cosine information.
Will use the CORONAL orientation.
If not suitable, please provide the information in
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_r.bhdr
file
-----------------------------------------------------------------
INFO: output format is paint
srcvol =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_r
srctype = bfloat
srcreg =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/register.dat
srcregold = 1
srcwarp unspecified
surf = white
hemi = rh
trgsubject = xxxx
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
interp = nearest
float2int = tkreg
INFO: float2int code = 2
INFO: bvolumeRead: min = -33.9456, max = 35.5154
Done loading volume
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)
Reading surface /home/dhagler/data/subjects/xxxx/surf/rh.white
Done reading source surface
Reading thickness /home/dhagler/data/subjects/xxxx/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.1 0.1 0.9
vol2surf_linear: nhits = 6675/127873
2 0.2 0.1 0.9
vol2surf_linear: nhits = 6602/127873
3 0.3 0.1 0.9
vol2surf_linear: nhits = 6551/127873
4 0.4 0.1 0.9
vol2surf_linear: nhits = 6534/127873
5 0.5 0.1 0.9
vol2surf_linear: nhits = 6483/127873
6 0.6 0.1 0.9
vol2surf_linear: nhits = 6435/127873
7 0.7 0.1 0.9
vol2surf_linear: nhits = 6419/127873
8 0.8 0.1 0.9
vol2surf_linear: nhits = 6353/127873
Done mapping volume to surface
Number of source voxels hit = 3362
avg = -0.601, stdev = 2.468, min = -29.056, max = 9.192
-----------------------------------------------------------------
Could not find the direction cosine information.
Will use the CORONAL orientation.
If not suitable, please provide the information in
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_i.bhdr
file
-----------------------------------------------------------------
INFO: output format is paint
srcvol =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_i
srctype = bfloat
srcreg =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/register.dat
srcregold = 1
srcwarp unspecified
surf = white
hemi = rh
trgsubject = xxxx
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
interp = nearest
float2int = tkreg
INFO: float2int code = 2
INFO: bvolumeRead: min = -35.8874, max = 34.6494
Done loading volume
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)
Reading surface /home/dhagler/data/subjects/xxxx/surf/rh.white
Done reading source surface
Reading thickness /home/dhagler/data/subjects/xxxx/surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.1 0.1 0.9
vol2surf_linear: nhits = 6675/127873
2 0.2 0.1 0.9
vol2surf_linear: nhits = 6602/127873
3 0.3 0.1 0.9
vol2surf_linear: nhits = 6551/127873
4 0.4 0.1 0.9
vol2surf_linear: nhits = 6534/127873
5 0.5 0.1 0.9
vol2surf_linear: nhits = 6483/127873
6 0.6 0.1 0.9
vol2surf_linear: nhits = 6435/127873
7 0.7 0.1 0.9
vol2surf_linear: nhits = 6419/127873
8 0.8 0.1 0.9
vol2surf_linear: nhits = 6353/127873
Done mapping volume to surface
Number of source voxels hit = 3362
avg = -0.044, stdev = 1.867, min = -21.658, max = 26.265
-----------------------------------------------------------------
Could not find the direction cosine information.
Will use the CORONAL orientation.
If not suitable, please provide the information in
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_r.bhdr
file
-----------------------------------------------------------------
INFO: output format is paint
srcvol =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_r
srctype = bfloat
srcreg =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/register.dat
srcregold = 1
srcwarp unspecified
surf = white
hemi = lh
trgsubject = xxxx
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
interp = nearest
float2int = tkreg
INFO: float2int code = 2
INFO: bvolumeRead: min = -33.9456, max = 35.5154
Done loading volume
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)
Reading surface /home/dhagler/data/subjects/xxxx/surf/lh.white
Done reading source surface
Reading thickness /home/dhagler/data/subjects/xxxx/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.1 0.1 0.9
vol2surf_linear: nhits = 10440/129282
2 0.2 0.1 0.9
vol2surf_linear: nhits = 10402/129282
3 0.3 0.1 0.9
vol2surf_linear: nhits = 10382/129282
4 0.4 0.1 0.9
vol2surf_linear: nhits = 10330/129282
5 0.5 0.1 0.9
vol2surf_linear: nhits = 10318/129282
6 0.6 0.1 0.9
vol2surf_linear: nhits = 10290/129282
7 0.7 0.1 0.9
vol2surf_linear: nhits = 10259/129282
8 0.8 0.1 0.9
vol2surf_linear: nhits = 10243/129282
Done mapping volume to surface
Number of source voxels hit = 5063
avg = -0.031, stdev = 2.079, min = -28.601, max = 27.890
-----------------------------------------------------------------
Could not find the direction cosine information.
Will use the CORONAL orientation.
If not suitable, please provide the information in
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_i.bhdr
file
-----------------------------------------------------------------
INFO: output format is paint
srcvol =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_i
srctype = bfloat
srcreg =
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/register.dat
srcregold = 1
srcwarp unspecified
surf = white
hemi = lh
trgsubject = xxxx
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
interp = nearest
float2int = tkreg
INFO: float2int code = 2
INFO: bvolumeRead: min = -35.8874, max = 34.6494
Done loading volume
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)
Reading surface /home/dhagler/data/subjects/xxxx/surf/lh.white
Done reading source surface
Reading thickness /home/dhagler/data/subjects/xxxx/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.1 0.1 0.9
vol2surf_linear: nhits = 10440/129282
2 0.2 0.1 0.9
vol2surf_linear: nhits = 10402/129282
3 0.3 0.1 0.9
vol2surf_linear: nhits = 10382/129282
4 0.4 0.1 0.9
vol2surf_linear: nhits = 10330/129282
5 0.5 0.1 0.9
vol2surf_linear: nhits = 10318/129282
6 0.6 0.1 0.9
vol2surf_linear: nhits = 10290/129282
7 0.7 0.1 0.9
vol2surf_linear: nhits = 10259/129282
8 0.8 0.1 0.9
vol2surf_linear: nhits = 10243/129282
Done mapping volume to surface
Number of source voxels hit = 5063
avg = 0.022, stdev = 1.960, min = -29.752, max = 25.854
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