Hi Greg,
it's:
mris_ca_train lh sphere.reg my_annot_file <subject 1> ... lh.my_annot_atlas.gcs.
-autorecon3 won't pick it up, you'll have to specify it by hand I think, but Doug would know.
cheers, Bruce
On Fri, 28 Oct 2005, Greg Harris wrote:
Hi Bruce.
mris_sample_parc seems straightforward enough, but I'll need a few hints about mris_ca_train. I get this usage line:
usage: mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> <subject 2> ... <output file>
Apparently, none of the options is '--help' or '-h', so I have no list of options. Is <canon surf> a standard component of the freesurfer distribution? Is <annot file> a table of names, labels and colors? If so, where is the file that drives the generation of the file label/aparc_annot.ctab in each subject? What do I want for <output file>? Presumably this is a special file name that will be picked up in -autorecon3.
Greg
Bruce Fischl wrote:
Hi Greg,
I'll let someone else answer the download question, as I don't offhand remember which site it is.
As for your own atlas, I assume you mean cortical? This shouldn't be a problem. We distribute a binary called mris_sample_aparc that will sample them onto a surface. You can then use mris_ca_train to build your own atlas.
As for the subcortical, this is a tougher question. Note that we are still working on it, and it has some sequence dependence. That said though, our manually labeled thalamus does extend to caudate, and it also goes pretty far lateral where there are some very low contrast thalamic nuclei. I'm not really qualified to comment on this - we'll need to get the neuroanatomists together.
cheers, Bruce
On Fri, 28 Oct 2005, Greg Harris wrote:
Hi Bruce.
I need to watch for the source tarball on the website when it appears. Is the correct url for the website something like https://surfer.nmr.mgh.harvard.edu/fswiki/Download i.e., the FreeSurfer Wiki? Or will I need to search for a tarball at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ ?
We will need instructions on how to define our own atlas, or how to vary the existing atlas that is used to produce -autorecon3. We have extensive traces of 50 or more brains to base this on. We want to subdivide the STG-planum area. We also want the Insula, which I can sort of get by clipping the 'unknown' ribbon with a probabilistic talairach mask after mapping the 'aparc' information back into brains2.
We have concerns about the 'aseg' information; for example, your Thalamus-Proper is much larger than our gross thalamus, and our thalamus roi does not touch our caudate roi. Do the control points have to make the subcortical neighborhood pretty much of uniform intensity of 110 for the white matter spine to develop into a sphere?
Greg Harris University of Iowa Psychiatry Brain Imaging Lab
Bruce Fischl wrote:
We will be posting a "read-only" tarball on the website in the next couple of weeks, and anyone is free to download it and look at it. We will *not* be supporting a make/configure type env for people to download and build, as we simply aren't ready to do so. We plan to implement such a procedure, but it will be a while. Instead of waiting until that was ready, I thought people would like to have access to the source to at least see what things are doing, and be able to see file formats and such.
cheers, Bruce
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