Lilla,
Thanks very much for your answers--they're very helpful!
I have one quick follow-up question, and then an additional question from our first attempt at running mri_cvs_register.
First the follow-up question: We are interested specifically in multi-modal integration with CVS. In particular, we are curious about functional data in specific sub-cortical regions. Would applyMorph be able to morph a functional overlay volume (.nii file?)
Second, we have been testing mri_cvs_register and have received the same error in all of our attempts. I've reproduced a lot of the last lines from the error message below, as well as attached the log. Do these indicate an error I can easily correct? Thanks again for all of the help!
Joakim
************************************************************************ **** before reading annotation /home/decharms/data/freesurfer/round4/9033b/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/free surfer/average/colortable_desikan_killiany.txt) trying to write annotation /usr/local/freesurfer/bin /home/decharms/data/freesurfer/cvs_test perl /usr/local/freesurfer//bin/elastic_registration_CVS.pl --fixed 9032b --moving 903 3b --settings /usr/local/freesurfer//bin/mri_cvs_register.settings.txt --exe surf2vol --pial ===================== settings: /home/decharms/data/freesurfer/round4 ======================== ===================== settings: aparc.annot ======================== ===================== settings: norm ======================== ===================== processing brain 9033b ======================== ===================== template brain 9032b ======================== trying to execute elastic registration -> cmd line = surf2vol -fixed_mri /home/decharms/data/freesurfer/round4/9032b/mri/norm.mgz -moving _mri /home/decharms/data/freesurfer/round4/9033b/mri/norm.mgz -fixed_surf /home/decha rms/data/freesurfer/round4/9032b/surf/lh.white -moving_surf /home/decharms/data/free surfer/round4/9033b/cvs/lh.resample.white -fixed_surf_2 /home/decharms/data/freesurfer /round4/9032b/surf/rh.white -moving_surf_2 /home/decharms/data/freesurfer/round4/9033b /cvs/rh.resample.white -fixed_surf_3 /home/decharms/data/freesurfer/round4/9032b/sur f/lh.pial -moving_surf_3 /home/decharms/data/freesurfer/round4/9033b/cvs/lh.resample.p ial -fixed_surf_4 /home/decharms/data/freesurfer/round4/9032b/surf/rh.pial -moving_su rf_4 /home/decharms/data/freesurfer/round4/9033b/cvs/rh.resample.pial -aparc /home/d echarms/data/freesurfer/round4/9032b/label/lh.aparc.annot -aparc_2 /home/decharms/data /freesurfer/round4/9032b/label/rh.aparc.annot -aparc_3 /home/decharms/data/freesurfer/ round4/9032b/label/lh.aparc.annot -aparc_4 /home/decharms/data/freesurfer/round4/9032b /label/rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -cache_transform /home/decharms/dat a/freesurfer/round4/9033b/cvs/transform.txt -penalty_weight 1000 -fem_steps 17 -elt_vo l_range 5.0,10.0 -log_summary -poisson .3 -topology_old -compress -pc_type none -ksp_t ype preonly -pc_type jacobi -ksp_type cg -ksp_view -ksp_converged_reason -out /home/de charms/data/freesurfer/round4/9033b/cvs/el_reg_to9032b.mgz -out_surf /home/decharms/da ta/freesurfer/round4/9033b/cvs/surf-mfc_to9032b -out_mesh /home/decharms/data/freesurf er/round4/9033b/cvs/el_reg_to9032b &> /home/decharms/data/freesurfer/round4/9033b/cvs/ trace_el_reg_to9032b_9033b.txt error executing surf2vol at /usr/local/freesurfer//bin/elastic_registration_CVS.pl lin e 162.
-----Original Message----- From: Lilla Zollei [mailto:lzollei@nmr.mgh.harvard.edu] Sent: Friday, November 12, 2010 12:25 PM To: Joakim Vinberg Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] More information about mri_cvs_register
Hi Joakim,
I had a couple of questions regarding mri_cvs_register (which looks terrific), and couldn't find any answers after a quick search. If I missed an important page or pages, please don't hesitate to send me there.
We are interested in using mri_cvs_register on a large body of
subjects.
Specifically, I am curious if we should choose a single subject to be the template for this analysis, or whether we can use the fsaverage brain as the template?
You will not be able to use fsaverage as a template as it does not have a corresponding surface and volumetric atlas. We are in the process of building and releasing a CVS atlas, but it is not ready yet, so for now the best thing to do would be to register all your subjects to a randomly selected one.
Second, approximately how long can we expect mri_cvs_register to take for a single CVS alignment? We're running a quad-core Athlon Phenom
with
4GB total; mri_cvs_register is getting a single core (ish) in this
case?
The longest step at the moment is the volumetric registration which might take about 15 hrs. The rest is about 2 hours.
Yes, it is going to get a single core except when it is reading in and writing the non-linear registration warp. Then it might go up to even 2.
I am working on changing this as it causes a bit of a bottleneck.
Finally, what does the output of this function look like? Can we use
it
with the typical transform processes, or are their dedicated functions to use after the alignment?
"mri_cvs_register --help" gives you the full list of out put files. basically, you will end up with some registered volumes and a set of non-linear warps. The full CVS warp is currently not saved as it takes up a lot of memory. If you want to construct it and apply it to a new volume, you would need to call two functions:
(1) createMorph --out fullCVSmorph.tm3d --template template.mgz \ --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d
(2) applyMorph --template template.mgz --transform fullCVSmorph.tm3d \ vol movingvol.mgz outputvol.mgz linear
I will add these and more details to the wiki, but please let me know if
you have any more questions.
--Lilla
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