Hi Bruce, Is there a reason why use sulc and curv together would be better than one alone? Also, any ideas as to why I can't create my annotations? Thanks again for your help, Alex
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology The University of Melbourne [EMAIL PROTECTED] -----Original Message----- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 16/12/2005 11:34 AM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer -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 > [EMAIL PROTECTED] > > > > -----Original Message----- > From: [EMAIL PROTECTED] 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
