Hi Marcel,

First, you will find a lot of details about the usage of mri_cvs_register if you use the --help flag in the terminal.

See detailed responses to your questions below:

 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?

The file ddescritions are detailed if you run mri_cvs_register --help. For your purposes you do not need to use the --nocleanup option. The final ransformation that you will need is called final*norm.m3z

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

These comments are wrt to an older version of the code. We do not use the tm3d format any more. I will update the wiki.

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

"template" is always your target (atlas space where you are registering TO) and subject is the moving image that you are registering.

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.

You will need the m3z file from cvs and the rigid registration that you get from BBR.

Lilla


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