Hi all,
I used freesurfer to process my anatomical scans, followed by BBregister
to align my resting state scan to the anatomical and finally afni to
process the resting state fmri scans. After recon-all I used bbregister:
*bbregister -s ${sub}_FS --mov ${sub}.RS.nii --reg $sub_RS_register.dat
--init-header --bold --frame $LAST --nearest --template-out
$sub.RS.template.nii*
I used the following for manual adjustments (although none were needed!)
*tkregister2 --mov $sub.RS.template.nii --reg $sub_RS_register.dat --surf*
The plan is to apply the reg file to the entire resting state timeseries
($sub.RS.nii).
My question is the following:
1) Does bbregister already move the last timepoint in $sub.RS.nii as well
as $sub.RS.template.nii or does it just store the rigid transformation in
the reg file (this is what I assume)? This is the reason I assume we
supply reg into tkregister2 as I assume the transform is not applied to the
nifti file header itself.
2) Assuming the transformations are not applied to the file itself, how
would I go about doing this? I used the following based on previous posts:
*mri_vol2vol --mov $sub.RS.nii --reg $sub_RS_register.dat --fstarg --interp
nearest --o $sub.RS.align.nii --precision short --no-resample *
I used no-resample as I do not want to put the data into orig space. The
plan is to align all of my timepoints to the last time point (same as
$sub.RS.template.nii).
----Is --fstarg the best option (default orig.mgz vs --fstarg rawavg.mgz)?
----Is the transform stored in the header of $sub.RS.align.nii and not in
the $sub.RS.template.nii file or $sub.RS.nii?
3) Using @SUMA_Make_Spec_FS did not correctly convert brain.mgz and
aseg.mgz correctly when overlaid with the original $sub.SPGR.FS.mgz as well
as $sub.RS.align.nii or $sub.RS.nii so I just used the following instead
/mri directory:
*mri_convert -ot nii brain.mgz brain.nii*
*mri_convert -ot nii aseg.mgz aseg.nii*
*4) Following relates to viewing images created in AFNI correctly if anyone
knows: *
When I tried to use AFNI to view the original anatomical scan
$sub.SPGR.FS.mgz and $sub.RS.align.nii it was not aligned (assume
anatomical is similar to rawavg.mgz).
When I load brain.nii and $sub.RS.align.nii into afni they are not
overlapped perfectly as in tkregister2. Additionally I get an error about
deobliquing the $sub.RS.align.nii file. Interestingly enough I do not get
this error with the $sub.RS.template.nii so I am not sure if there is an
error in applying the transform or if the template file has no transform
info stored while the aligned file does. How would I apply the reg file to
all timepoints without getting the oblique error or should I use the
following command and is this correct:
*3dWarp -deoblique -gridset $sub.RS.nii -prefix $sub.RS.align.deobl.nii
$sub.RS.align.nii*
Would i deoblique using the gridset of the original $sub.RS.nii, the
aligned file $sub.RS.align.nii or just the template file (or does it not
matter since the voxel dimensions are the same even though centers are
different).
Sorry for the long email but thanks in advance for any advice /
explanations.
Sincerely,
Ajay
_______________________________________________
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.
