Hello,

I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps:

1. recon-all on anatomical data (obvious)

2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject)

I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject -> template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file?

In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used:

createMorph --out fullCVSmorph.tm3d --template template.mgz \

--subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d

However, there is no single *.tm3d file in my cvs directory... Here are the files that are present:

el_reg_tocvs_avg35_inMNI152.affine.mgz
el_reg_tocvs_avg35_inMNI152_aseg.mgz
el_reg_tocvs_avg35_inMNI152.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
final_CVSmorph_tocvs_avg35_inMNI152.m3z
lh.dbg_surf.pial
lh.dbg_surf.white
lh.resample.aparc.annot
lh.resample.pial
lh.resample.white
nlalign-afteraseg-norm.mgz
nlalign-aseg.mgz
rh.dbg_surf.pial
rh.dbg_surf.white
rh.resample.aparc.annot
rh.resample.pial
rh.resample.white
step1_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz
step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz
summary.AC1004_to_cvs_avg35_inMNI152.mri_cvs_register.1308031447.log
transform.txt

In my particular case, which images should be entered as arguments to --template and --subject ?

3. standard EPI pre-processing, which results in motion-correction parameters and realigned images

4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI -> anatomical

I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration.

Sorry for the lenghty post, but I'm quite new to freesurfer and I'm a bit confused:)

Best regards,

Marcel