And what is the voxel resolution of the input to mri_vol2surf?
On 05/02/2018 03:35 PM, Rachel Bencic wrote:
>
>
> Hello,
>
> The voxel resolution of the unwarped mov volume used in bbregister was:
>
> voxel sizes: 3.750000, 3.750000, 5.000000
>
> So the reported values in the warning appear correct.
>
> Rachel
>
>
>
> On 05/02/2018, Douglas Greve wrote:
>
> When you ran bbregister, what was the voxel resolution of the mov volume?
> On 05/02/2018 01:28 PM, Rachel Bencic wrote:
> >
> >
> > Hello FreeSurfer Developers,
> >
> > I'm attempting to resample beta weights generated from AFNI’s
> > 3dDeconvolve command to individual subjects’ cortical surfaces. Prior
> > to running 3dDeconvolve, I ran bbregister to coregister subjects’
> > (unwarped) functional data to their T1 anatomical scans and to
> > generate a registration file to be used in the mri_vol2surf command.
> >
> > However, I get the following warning when I run the mri_vol2surf command:
> >
> > WARNING: the voxel resolution in the source volume (3.75, 3.75, 3.75)
> > differs from that listed in the registration file (3.75, 3.75, 5)
> >
> > I've searched the list and came across a potentially similar case from
> > Apr. 26, 2011 (SUBJECT: (no subject), AUTHOR: Kevin Bickart), which
> > included the following advice:
> >
> > Hi Kevin, you can ignore that warning. The values in the registration
> >
> > file are not correct.
> >
> > doug
> >
> > I thought I would reach out to inquire as to whether this is still the
> > case (i.e., that this warning can be ignored) or if it might be a more
> > serious issue? I will add that mri_vol2surf did appear to run
> > successfully (i.e., it did not error out) and provided a .mgh file as
> > output.
> >
> > In case it is helpful, as a next step I plan to convert the .mgh file
> > to an ASCII file to extract the time series. Ultimately, I plan to run
> > graph analyses on the time series data.
> >
> > Any feedback you have would be greatly appreciated.
> >
> > Rachel
> >
> > 1) FreeSurfer version: freesurfer_6.0_x86_64
> >
> > 2) Platform: OSX High Sierra
> >
> > Here is my command:
> >
> > mri_vol2surf --mov ../betaEPI/Betas_EPIpreproc.nii--srcreg
> > ../bbregistration.dat --hemi lh --projfrac 0.5 --o ./lh.1.mgh
> >
> > mris_convert -c ./lh.1.mgh $parc_dir/${1}/surf/lh.white
> > ../lh_ascii/lh.1.asc
> >
> > And the full output:
> >
> > srcvol = ../betaEPI/Betas_EPIpreproc.nii
> >
> > srcreg = ../bbregistration.dat
> >
> > srcregold = 0
> >
> > srcwarp unspecified
> >
> > surf = white
> >
> > hemi = lh
> >
> > ProjFrac = 0.5
> >
> > thickness = thickness
> >
> > reshape = 0
> >
> > interp = nearest
> >
> > float2int = round
> >
> > GetProjMax = 0
> >
> > INFO: float2int code = 0
> >
> > Done loading volume
> >
> > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR
> > types with c_(r,a,s) = 0.
> >
> > Input reg is register.dat
> >
> > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75)
> > differs
> >
> > from that listed in the registration file (3.75,3.75,5)
> >
> > -------- original matrix -----------
> >
> > 0.99988-0.009970.01155-0.43638;
> >
> > -0.01472-0.430230.9026022.14351;
> >
> > 0.004030.902660.4303334.58801;
> >
> > 0.000000.000000.000001.00000;
> >
> > -------- original matrix -----------
> >
> > Reading surface
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.white
> >
> > Done reading source surface
> >
> > Reading thickness
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/lh.thickness
> >
> > Done
> >
> > Mapping Source Volume onto Source Subject Surface
> >
> > 1 0.5 0.5 0.5
> >
> > using old
> >
> > Done mapping volume to surface
> >
> > Number of source voxels hit = 8657
> >
> > Writing to ./lh.1.mgh
> >
> > Dim: 146930 1 1
> >
> > srcvol = ../betaEPI/Betas_EPIpreproc.nii
> >
> > srcreg = ../bbregistration.dat
> >
> > srcregold = 0
> >
> > srcwarp unspecified
> >
> > surf = white
> >
> > hemi = rh
> >
> > ProjFrac = 0.5
> >
> > thickness = thickness
> >
> > reshape = 0
> >
> > interp = nearest
> >
> > float2int = round
> >
> > GetProjMax = 0
> >
> > INFO: float2int code = 0
> >
> > Done loading volume
> >
> > INFO: This REGISTER_DAT transform is valid only for volumes betweenCOR
> > types with c_(r,a,s) = 0.
> >
> > Input reg is register.dat
> >
> > WARNING: the voxel resolution in the source volume (3.75,3.75,3.75)
> > differs
> >
> > from that listed in the registration file (3.75,3.75,5)
> >
> > -------- original matrix -----------
> >
> > 0.99988-0.009970.01155-0.43638;
> >
> > -0.01472-0.430230.9026022.14351;
> >
> > 0.004030.902660.4303334.58801;
> >
> > 0.000000.000000.000001.00000;
> >
> > -------- original matrix -----------
> >
> > Reading surface
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.white
> >
> > Done reading source surface
> >
> > Reading thickness
> > /Volumes/Vol3/Hamilton/preproc/Parcelled//003/surf/rh.thickness
> >
> > Done
> >
> > Mapping Source Volume onto Source Subject Surface
> >
> > 1 0.5 0.5 0.5
> >
> > using old
> >
> > Done mapping volume to surface
> >
> > Number of source voxels hit = 8681
> >
> > Writing to ./rh.1.mgh
> >
> > Dim: 148618 1 1
>
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