Thanks Donna, everything seems to work now, so Im happy :) About the surfaces, I saw something in the archive, is it a white brain, or deflated pial: http://sumsdb.wustl.edu:8081/sums/search.do?category_id=6 and then click the first option with a brain icon on it that is possible to view in the web browser.
There are 12 versions of each hemisphere so I presume that it is an individual brain. Do you think is ok to use one of them, or do you happen to have an average surface? I think you are right, inflated brains may be best suited for visualizing purposes, however, just in case some stubborn SPM guy would like once in a while see hes activation the way he is used to . I think Freesurfer has a pial surface. Maybe it works to import that somehow? Also, it would be nice to have the option to see the whole brain at once (the non-split way) even inflated, but I guess thats not yet possible . Cheers, Julian > On 03/07/2007 10:27 AM, Julianm Macoveanu wrote: >> Yes, I use the CARET_TUTORIAL_SEPT06/MAPPNING_PROCEDURES files, and load >> the >> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec file. >> >> I think I got the hang of it. The break through was, after creating the >> metric file load one of the predefined scenes before trying to open my >> metric file. In this way it didn't complain anymore about different >> number >> of nodes. >> >> If I understand it right if I want now to see the activation on a pial >> surface I should just open the coord file and add it to my template spec >> file. Do you know where I could find this? I think it should also be >> something between pial and fiducial. >> > The PALS_B12 atlas (and the colin atlas before it) has no pial > surfaces. One can generate pseudo-pial surfaces by using Surface: > Geometry: Expand or Shrink surface to expand a fiducial surface, but > I've never tried this with an average fiducial surface, and I don't > really recommend it. We prefer the inflated surface for visualization, > unless you have activity in the operculum or insula that is difficult to > see; in such cases, we then use the Very Inflated surface. Activity in > buried sulci isn't visible when viewed on a pial or a regular fiducial > (less so with an average fiducial). > > I realize some people still prefer looking at a highly structured pial > surface, but considering this is group data you're mapping, the > structure of any one individual is not really representative of the > "group" structure of your subjects. We believe mapping to PALS_B12 and > viewing the results on the inflated surface is a more faithful > representation of your results than viewing them on, say, colin27's pial > surface. Slowly, we're hoping to win you over. ;-) > >> Also, L and R are overlaid wrong, what SPM reports as left, I see it on >> the >> right hemisphere in Caret. How can this be changed? >> > Use File: Open Data File: volume functional file and check the Volume is > an SPM2 Volume with Right on Left checkbox. >> Thanks, >> Julian >> >> -----Original Message----- >> From: [EMAIL PROTECTED] >> [mailto:[EMAIL PROTECTED] On Behalf Of Donna >> Dierker >> Sent: Wednesday, March 07, 2007 4:05 PM >> To: Caret, SureFit, and SuMS software users >> Subject: [BULK] Re: [caret-users] Map SPM volume >> Importance: Low >> >> Hi Julian, >> >> When mapping to atlas, are you selecting a spec file created from this >> dataset: >> >> CARET_TUTORIAL_SEPT-06 >> http://sumsdb.wustl.edu/sums/directory.do?id=6585200 >> >> ... using steps as described in Section 5.1 of this tutorial: >> >> Caret_Tutorial_Oct06.pdf >> http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6602379 >> >> It's tough to see how you could get this error under those >> circumstances, since the files in that spec file (or derivative thereof) >> all have the same 73730 standard mesh. >> >> While this spec won't have a pial surface, it will have left and right >> versions of the following configurations: >> >> PALS_B12 average fiducial >> inflated >> very inflated >> flat >> >> Since you're using SPM2, I'd suggest replacing the average fiducial >> coord files with these files: >> >> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord >> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord >> >> To do so, after opening >> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec, select File: >> Open Data File: and select >> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. Repeat >> for Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_SPM2.clean.73730.coord. >> Then, select Toolbar: Spec and use the X buttons to delete these >> versions, which are similar but not as optimal as the SPM2 versions in >> your case: >> >> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord >> Human.PALS_B12.RIGHT_AVG_B1-12.FIDUCIAL_FLIRT.clean.73730.coord >> >> Both the SPM2 and FLIRT versions are in mni152 space, but the >> contributing PALS_B12 anatomicals were normalized using SPM2 for the >> SPM2 versions, while FSL's flirt (affine only) was used to normalize the >> FLIRT versions. >> >> Donna >> >> On 03/07/2007 08:33 AM, Julianm Macoveanu wrote: >> >>> Hi guys, >>> >>> I need some help with basic stuff. I just want to use Caret to >>> visualize my SPM2 activations on inflated/Fiducial surfaces. So I have >>> the normalized volume file to start with. >>> >>> >>> >>> I have opened a spec file from the Caret tutorial, use the map volume >>> to surface function, choose my volume, then Map to spec file with >>> atlas (and without). I have also tried not to open any spec file to >>> begin with, and then just open the one I chose as output during the >>> mapping procedure >>> >>> >>> >>> As space I tried the SPM2, as this is the kind of volume I have (but >>> also 711-sc). >>> >>> >>> >>> After the metric file is generated, I just try to open it, but I get >>> the error that my metric file contains different number of nodes. >>> >>> >>> >>> What I would like to have is a spec file that have all different >>> surfaces (including pial and multi-fiducial which I could not find in >>> any examples of spec files) and then just create metric files from my >>> SPM volumes in order to visualize the activations. >>> >>> >>> >>> Cheers, >>> >>> Julian >>> >>> >>> >>> >> >> _______________________________________________ >> caret-users mailing list >> firstname.lastname@example.org >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users >> >> _______________________________________________ >> caret-users mailing list >> email@example.com >> http://pulvinar.wustl.edu/mailman/listinfo/caret-users >> >> > > > -- > Donna L. Dierker > (Formerly Donna Hanlon; no change in marital status -- see > http://home.att.net/~donna.hanlon for details.) > > _______________________________________________ > caret-users mailing list > firstname.lastname@example.org > http://pulvinar.wustl.edu/mailman/listinfo/caret-users >