p.s.:
try mris_ca_train --help
On Thu, 15 Dec 2005, Bruce Fischl wrote:
-n 2 tells it to use 2 feature dimensions (sulc and curv) -t <fname> tells it to use the color LUT in <fname> On Fri, 16 Dec 2005, Fornito, Alexander wrote:
Hi, I'm also trying to create my own custom atlas, but can't seem to create an annotation file. I load my files in tksurfer, than click the "Export annotation" option and save the file. When I then try to re-import the annotation, nothing appears, and I get the message:
% surfer: WARNING: no labels imported; annotation was empty
Any help is much appreciated!
PS - Greg, I noticed that you used -n and -t in your command line. What do these flags refer to? I can't seem to get options in the usage.
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne alexander.fornito@wh.org.au
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greg Harris Sent: Thu 15/12/2005 4:21 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Defining one's own atlas in FreeSurfer
By snooping in the log files in scripts/ and considering the instruction to train and then label with commands such as
mris_ca_train -n 2 -t ./iowa_gross_fs_colors.txt rh sphere.reg iowa_gross_hand_parc ${SUBJECT_LIST} ./rh.iowa_gross_cort_parc.gcs
which prepares the way for
mris_ca_label ${SUBJECT} rh sphere.reg /opt/freesurfer/average/rh.iowa_gross_cort_parc.gcs
it becomes evident that the -autorecon3 step applies the MGH standard parcellation atlas from
/opt/freesurfer/average/[lr]h.curvature.buckner40.filled.desikan_killiany.gcs
and thus, the "standard" atlas is known as "curvature.buckner40.filled.desikan_killiany".
When we evaluate our own atlas, we compare hand-traced labels with the labels produced by mris_ca_label.
Now my question: Is there a way we could access the training data for "curvature.buckner40.filled.desikan_killiany", so we can compare how mris_ca_label approximates the MGH atlas's gold standard with how it approximates the Iowa atlas's gold standard?
We are curious how many subjects went into the standard atlas at mris_ca_train, too. Is there a paper (a pdf?) where this is reported?
Greg Harris University of Iowa Psychiatry Brain Imaging Lab
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