External Email - Use Caution
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 between COR
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 -0.00997 0.01155 -0.43638;
-0.01472 -0.43023 0.90260 22.14351;
0.00403 0.90266 0.43033 34.58801;
0.00000 0.00000 0.00000 1.00000;
-------- 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 between COR
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 -0.00997 0.01155 -0.43638;
-0.01472 -0.43023 0.90260 22.14351;
0.00403 0.90266 0.43033 34.58801;
0.00000 0.00000 0.00000 1.00000;
-------- 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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