In the stable3 version of mri_vol2surf, there is an option listed "projfac-avg". I can't tell if it is working or not. In the output messages, it says that ProjFrac = 0.5 (or whatever value is given with -projfrac) but there is no mention of the projfrac-avg min and max. Is the program doing what it is supposed to and not giving any relevant messages, or is the lack of messages an indicator that it is just doing the basic projfrac without averaging along the normal?
What's your cmd line? What's the output?
On Wed, 10 May 2006, Don Hagler wrote:
In the stable3 version of mri_vol2surf, there is an option listed "projfac-avg". I can't tell if it is working or not. In the output messages, it says that ProjFrac = 0.5 (or whatever value is given with -projfrac) but there is no mention of the projfrac-avg min and max. Is the program doing what it is supposed to and not giving any relevant messages, or is the lack of messages an indicator that it is just doing the basic projfrac without averaging along the normal?
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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
freesurfer@nmr.mgh.harvard.edu
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Don Hagler -
Doug Greve