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
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
