[Freesurfer] analyses of single trials
Hi, Is it possible, with existing software, to extract signal changes at vertices, voxels, or ROIs for single trials, rather than across trials? This would allow an examination of intra-subject variability in BOLD response, habituation effects, etc... Something like this was done by: Yamaguchi S, Hale LA, D'Esposito M, Knight RT (2004): Rapid prefrontal-hippocampal habituation to novel events. J Neurosci 24:5356-5363. thanks, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 2608 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] procedural question about FDR correction
Hi, FDR correction for multiple comparisons gives you different p-values for the left and right hemispheres. It seems really weird to report in a paper: a) that you've corrected for the right and left hemispheres separately and b) that the p-value that gave rise to a corrected probability of .05 was different for each. How do people deal with this issue? Take the most stringent p-value and use it for both hemispheres? Just report that FDR adjusted the p- value to .05? Also, correcting for right and left hemispheres separately assumes that they are independent observations. Unless you're studying callosotomy patients (and maybe even if you are) this doesn't seem justified. Are we supposed to be adjusting p-values accordingly? Thanks, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 2608 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] anatomical weirdness?
Greetings, Is the subcollosal gyrus included in the ACC label from the cortical parcellation of Fischl, 2004? We are using the ACC label to constrain Monte Carlo simulations to the ACC. A max vertex for an ACC cluster has the annotation G_subcollosal, but is listed in the ROI-constrained surfcluster as being in the ACC. We are using average7 to display our data, if that makes any difference. Is the subcollosal gyrus part of ACC -- I didn't think it was. Is the ACC label too generous if it is including it? thanks for the clarification, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 2608 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] annotation file and labels for fsaverage
Greetings, We are using fsaverage as the template for overlaying our group fMRI data. Which annotation file should we use for designating ROIs? There seem to be two options: lh.aparc.a2005s.annot and lh.aparc.annot. And which atlas is each annotation file derived from? Thank you, Dara Dara S. Manoach, Ph.D. Psychiatric Neuroimaging Massachusetts General Hospital Charlestown Navy Yard 149 13th Street, Room 2608 Charlestown, MA 02129 email: [EMAIL PROTECTED] phone: 617-724-6148 fax: 617-726-4078 http://nmr.mgh.harvard.edu/manoachlab ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] annotation file and labels for fsaverage
Thanks very much for the detailed info Karl (and Doug and Bruce)! My primary ROI is ACC, so we'll probably use Aparc with the cingulate divisions. I'll have to review the paper to see if the anatomic bases of the divisions are described. I'm surprised, though, that there is not an insula label, and I'm wondering why it would not be possible to use ROI labels from the two annotation schemes to examine activation in group data (i.e., ACC labels from aparc and insula from aparc2005). best, dara On Sep 8, 2008, at 8:18 PM, Bruce Fischl wrote: for what it's worth we label the cc now explicitly in the aseg, which is certainly more accurate than the aparc used to be. Thanks for the detailed answer though Carl! Bruce On Mon, 8 Sep 2008 [EMAIL PROTECTED] wrote: Hi Dara, You can certainly use either one as Doug says, but depending on your purposes, one or the other may have some virtues. 2005 consists of discrete sulcal and gyral labels with traditional anatomical names so there are a lot more labels (which is why Doug describes it as very detailed), whereas aparc in general collapses these into summary regions. But it is not a a simple case of lumper vs splitterFor instance it seems that Aparc divides the cingulate into rostral anterior, caudal anterior, posterior cingulate whereas in aparc 2005 it is lumped into one cingulate label Aparc shows the corpus c. nicely (I think there may even be a subparcellation available in development) whereas the cc is lost in the medial wall in 2005. Aparc differentiates the pars orbitalis nicely on the orbital surface from the rest of the ofc, aparc 2005 does not — possibly of interest to someone who is looking at ventrolateral pfc and its neighbors Aparc includes in its lateral ofc label everything lateral to the rectus gyrus, including the central ofc and the (unlabeled) transverse sulcus neither of which would be understood as being in the lateral ofc as that term is typically used today. Aparc 2005 shows a view that nicely differentiates the rectus gyrus on sagital section from the adjoining, whereas aparc lumps a broad territory into “medial OFC” Aparc 2005 includes parcellation of the Insula, aparc does not and it is lost in the unknown medial wall (there has been talk of fixing this but is this real, Bruce or Doug?) Perhaps what we need is a “best of aparc and aparc 2005”. For surfing purposes you can also “fool” tksurfer into showing you the names of the (typically more more detailed) 2005 parcellations while viewing the brain labeled with the aparc labels which at times have more detail — though I have never asked Doug if this will always work correctly. If others have discovered pros and cons in other regions, please share. Best, Carl Carl E. Schwartz, M.D. Harvard Medical School Director, Developmental Neuroimaging & Psychopathology Laboratory Psychiatric Neuroscience Program Massachusetts General Hospital tel 617-726-8965 fax 617-726-4078 ___ 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
