Hi Freesurfer experts,
We are analyzing data for a simultaneous PET-MRI study, and are having trouble
registering individual subject BPnd maps to fsaverage space. I attached a photo
of a post-registration subject (the left side is cut off). I had previously
registered each individual BPnd volume map to the subject's volume space using
bbregister (naming the reg file register{subject}.dat), and then transformed
them into a new volume file using the mri_vol2vol command, and referencing the
file generated by bbregister.
This is the command I used:
mri_vol2vol --mov
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd.nii
(**this is the original volume file**) --fstarg --reg register0045.dat --o
$SUBJECTS_DIR/NNC_PMOD_LoganRef_BPnd/fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii
When I visualize this file using tkmedit, the map looks fine (and is not cut
off).
However, after transforming this file into fsaverage space, it becomes cut off.
First I copied each individual volume file into each subject's mri folder. Then
I used this command to transform the individual files into mni305 space:
mri_vol2vol --mov fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg.nii --targ
$FREESURFER_HOME/average/mni305.cor.subfov2.mgz --xfm transforms/talairach.xfm
--o fs_NNC112_0045_RBV_MC_s10v3_LoganRef_BPnd_reg_mni305.subfov2.mgz
Do you know why some of the volume maps are being cut off after transforming
them into fsaverage space?
Thanks for your help,
Anais
_______________________________________________
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.
