Hi Bruce, I;d like to take up your offer of sending a subject with the annot file, as I'm quite stuck. Where can I upload it to? I can't seem to find the link on the wiki. Also, I only retained the mri, surf, and label subdirectories, although the tar is still quite big (~125 MB). Are there specific files that you need? Cheers, 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 12:25 PM To: Fornito, Alexander Cc: Greg Harris; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Defining one's own atlas in FreeSurfer yes, sulc represents large scale structure of the folding patterns and preferences deep folds over shallow ones, while curv is a differential measure (mean curvature) and is much noiser. The sulc alignment comes first and aligns the major folds, then the curv alignment moves secondary folds such as the hand area into alignment where they are consistent. Don't know why you can't create a .annot file. I'm waiting for Kevin to respond. You could try sending us the subject with the .annot file and we can take a look, or maybe the .xdebug_tksurfer file has some clue? cheers, Bruce On Fri, 16 Dec 2005, Fornito, Alexander wrote: > 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
