Hi Lilla et al,
I am preparing to CVS register 30+ subjects to improve FSL probabilistic
tractography alignment across subjects. First, thanks for a really cool
tool! Then, I have some questions:
1. mri_cvs_register step1 is spherical registration. However, I have
already run FS5.3 recon-all -all for all subjects, which includes
spherical registration. Are the recon-all and mri_cvs_register spherical
registrations identical? If so, will mri_cvs_register be able to use the
previously computed spherical registration (with flags --step2 --step3),
or will it need to compute a new spherical registration? Will
mri_cvs_register overwrite any of my earlier recon-all results?
2. What are the pros and cons for using one of the following as templates,
and which one would you recommend:
-Randomly selected individual subject
-CVS35
-CVS35_inMNI152
3. When using MNI152_1mm as template, I guess this is a 1 mm resolution
image (as $FREESURFER_HOME/subjects/cvs_avg35_inMNI152/mri/T1.mgz seems to
be in 1 mm resolution)? Technically, is this the cvs_avg35 image that has
been CVS-registered with the MNI152_1mm image? Or is this a FLIRT-type 3D
registration from cvs_avg35 to MNI152_1mm without surface information (I
guess extracting the surface from MNI152 would be difficult)?
4. I run into the following error in FS stable 5.3 (source
/usr/local/freesurfer/nmr-stable53-env):
mri_cvs_check --mov $SUBJECT
Using the CVS template as registration target.
The following files are missing:
/usr/local/freesurfer/stable5_3_0/bin/mri_cvs_register.settings.txt
You need to find these files or run reconall on the data in order to run
mri_cvs_register.
Is this file required, or is this a bogus error?
5. Are there parallel processing versions that could be run on the cluster?
Thanks!
Tommi
---
Tommi Raij, MD, PhD
TM Core Director
MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
Bldg 149, 13th St
Charlestown, MA 02129
U.S.A.