Donna, Thanks again for the advice.
AAL and the SPM Anatomy toolboxes are both (yes you guessed it) SPM toolboxes. They both use the Colin brain (or more formally the ICBM high-resolution single subject template). AAL labels 45 areas in each hemisphere and the SPM Anatomy toolbox has the Amunts/Zilles cyto data. If you are going the SPM route then Marsbar adds some more SPM integration to AAL but it is still all MATLAB. I would prefer to use Caret to get the same info if I can. I don't know what might be comparable to AAL in Caret but since Colin is already registered to PALS you can add the labels from: http://www.cyceron.fr/freeware/ So in my case single-subject case you would recommend a volumetric registration and then a segmentation and surface registration to PALS. Is the volumetric registration just for AC-PC? For a project related reason I am trying to use AFNI to set manual Talairach markers to get into "true" Talairach coordinates. Would that be good enough for pre-segmentation alignment? If that suffices (and I still haven't gotten AFNI to work right yet:), is the 4.6 segmentation tutorial the next step? Thanks again for any advice. I will try and get in touch with Johannes too. Cheers, -Morgan On Thu, 2005-09-22 at 08:04 -0500, Donna Hanlon wrote: > Hi Morgan, > > See comments below. > > Also, have you met Johannes Klein, who also works in the FMRIB? He has > extensive experience with Caret registration. > > Donna > > On 09/22/2005 06:49 AM, Morgan Hough wrote: > > >Donna, > > > >Thanks for your email. I was just following the instructions at the top > >of this page: > > > >http://brainmap.wustl.edu/help/mapper.html > > > > > It's on my do-list to update this page (along with several others), but > was there a page that linked to here? If so, I think I'll remove that > link, because this page is so out-of-date (although still helpful for > those that are still using colin and/or older versions of Caret). > > >which solicits nominations. The email is set to [EMAIL PROTECTED] which > >I guess gets forwarded to the list. > > > > > Yeah, John got tired of the spam, so we aliased that address to the > list, which allows only member posts. > > >That said, I am very interested in using caret to visualize results and > >look at the correspondence to probabilistic cyto maps, etc. These data > >are 99 FMRI sessions across three tasks collected from a single subject. > >It is rather complicated but I am only just getting into caret and your > >email is very helpful. So if I am doing all my analysis with FSL tools > >and I have a high-resolution structural image for this single subject I > >should still FLIRT to MNI 152? > > > There are some good reasons to spatially normalize before segmenting, > but they typically apply to inter-subject analyses. > > One reason that applies to single subject analysis is that it eases > drawing of borders by ensuring AC-PC alignment. Just making sure the > subject is well aligned to AC-PC makes it easier to draw borders during > flattening, because the template frontal cut almost always intersects > the medial wall border posterior to the olfactory sulcus. Also, when > drawing the registration borders, you don't need to rotate the surface > to approximate AC-PC alignment (e.g., when figuring out the starting > point for the aSTG landmark). > > >Since I only have one subject I can take > >the time to do a better fit if a better fit is possible. Maybe Colin is > >not the best approach (although it was tempting because I would like to > >look at the AAL correspondence as well). > > > What is AAL? > > >Should I take a surface based > >approach for this single subject to get the "best" fit. Thanks again for > >your time. > > > > > What you're doing is definitely not the mainstream (inter-subject) > registration application, so in some ways I'm tempted to say go ahead > and use Colin. Most of the partitioning schemes available in the > PALS_B12 atlas were actually registered via colin, so they're more > "upstream" in the colin atlas. That said, the colin atlas doesn't have > the Amunt/Zilles cyto areas fMRI mapped, whereas PALS does (see PALS > tutorial -- Caret version, not webcaret at > http://sumsdb.wustl.edu:8081/sums/directory.do?dir_id=6332260&dir_name=PALS_ATLAS_TUTORIAL). > > Also, David often fixes 'nits' he comes across in paint, border, and > coord files, and the PALS_B12 datasets get much more of his attention > than the colin atlas does. > > >BTW, the PALS paper hit NeuroImage early views. I don't have the link > >handy but it is there as well. > > > >Cheers, > > > >-Morgan > > > >On Tue, 2005-09-20 at 08:59 -0500, Donna Hanlon wrote: > > > > > >>Hi Morgan, > >> > >>Many of our best users are FSL users, so we want to make life as easy as > >>possible for them. While we don't have Colin in FSL (what we're calling > >>"flirt") grid, we do have the PALS_B12 surfaces that way: > >> > >>http://brainvis.wustl.edu/help/pals_volume_normalization/ > >> > >>We're recommending users move from Colin to PALS_B12 -- not only for > >>multi-fiducial mapping (MFM) of fMRI data, but *especially* for > >>registration purposes > >>(http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html). > >>See David's PALS paper for many important details: > >> > >>http://brainmap.wustl.edu/resources/-PALS_ATLAS_June14_05.pdf > >> > >>We're shooing people away from Colin and steering them to PALS_B12. > >>There might be some specific applications for which it makes sense to > >>use Colin, but I'd like to have a better understanding of them before > >>adding more Colin grids. Please elaborate a bit more on the requirement. > >> > >>Space-dependent grids (more accurately in our context, volume > >>registration method dependent fiducial surfaces) generally have been > >>used to support fMRI mapping of group results to a visualization atlas > >>brain (e.g., Colin or PALS_B12). For registration, we never had > >>grid-dependent target datasets. This is because registration operates > >>on the sphere. It does matter what fiducial or average fiducial you use > >>when you visualize/project your registration results. Again -- there is > >>a flirt version of the PALS_B12 average fiducial in > >>CARET_HOME/data_files/fmri_mapping_files. > >> > >>I realize this is probably somewhat confusing, so please let me know > >>where I need to be more clear. > >> > >>Donna > >> > >>On 09/20/2005 07:37 AM, Morgan Hough wrote: > >> > >> > >> > >>>I just wanted to nominate FSL output for grid support. I would be happy > >>>to help supply any information but I believe you are already familiar > >>>with the FSL tools. Please let me know if there is anything we can do to > >>>make supporting FSL easier (such as for instance supplying Colin so that > >>>people can register to that). > >>> > >>>Thanks in advance for your time. > >>> > >>>Cheers, > >>> > >>>-Morgan > >>> > >>> > >>> > >>> > >>> > >>_______________________________________________ > >>caret-users mailing list > >>caret-users@brainvis.wustl.edu > >>http://pulvinar.wustl.edu/mailman/listinfo/caret-users > >> > >> > > > >_______________________________________________ > >caret-users mailing list > >caret-users@brainvis.wustl.edu > >http://pulvinar.wustl.edu/mailman/listinfo/caret-users > > > > > > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users
