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.