Hi Paul,
Thanks for your reply. I previously had been using the resting state file as the master when I was resampling. But I was able to fix this issue by eroding the mask first and then resampling to lpi:
3dmask_tool -input fs_ap_latvent.nii -dilate_input -1 -prefix fs_ap_latvent_erode.nii.gz
3dresample -orient lpi -prefix fs_ap_latvent_erode_lpi.nii.gz -input fs_ap_latvent_erode.nii.gz
I did notice another problem though when I was checking the overlay of the masks. It appears that some of my original T1 images are oblique, which results in the masks not overlaying in the proper anatomical position.
There are a few potential issues with my data and it would be great to hear your opinion on whether the following steps I took to solve those issues are necessary. For context, my processing pipeline consists of dcm2niix, SSwarper, reconall/@SUMA_Make_Spec_FS to create WM/CSF masks, and proc.py (very similar to example 11b).
Potential issues/solutions:
1. The anatomical data (LPI), EPI data (RPI), freesurfer masks (RSP), and atlas (LPI) which I'll be using for time course extraction are in different orientations. Prior to preprocessing I reoriented the EPI and freesurfer masks to be in LPI space. I did this because in the end I will be extracting time courses from an atlas which is in LPI orientation and I wanted to be sure that when I was extracting the time course form the left PFC, for example, that it truly was the left PFC and not the right. Is it necessary to change the orientation of the EPI/freesurfer files prior to submission to proc.py? Or is the orientation difference taken care of during the align block, since the -master flag is used in many of the commands and the master anat is in LPI orientation?
2. Some of my T1 images are oblique. Should I cardinalize these images using 3dWarp -deoblique and resubmit the deoblique images to SSWarper, reconall, and @SUMA_Make_Spec_FS steps? The major problem here is that when the original data are used, in oblique format, the resulting Ventricle/WM masks are not aligned to the anatomy and thus signal is being regressed from the wrong portion of the image during preprocessing.
Thank you for your help!
Jenna
