Hello Donna, thank you very much for your fast and detailed reply. Unfortunately our servers were down on friday (due to an ac-malfunction) so that I couldn`t access my data. Meanwhile they are up again and I uploaded one of the spmT-maps along with a jpg of the the SPM-results and my resulting AFM-picture when feeding the data into Caret. The file is named: RH_FSU_spmT.
When mapping activations of a t-test to the AFM (with a threshold derived from my t-Test SPM), large, correctly located activations are still present with small activations and strange foci gone (even though the range of T-values is different from those of my SPMs). Thank you very much for hinting me to the AFM. Anyway, it would be great If you could take a look at the spmT-image (map) I sent (just to hear that everything is fine). Thank you very much Raphael Am 19.08.2010 17:00, schrieb Donna Dierker: > Mathijs& Raphael, > > See inline comments below. > > Donna > > > On 08/19/2010 08:53 AM, Raemaekers-2, M. wrote: >> Dear Rafael, >> >> Not sure of this, but the results that you describe may be the result of a >> misalignment between your statistical map and your surface. >> >> It somehow seems that SPM and CARET are not using the niftii positioning >> information exactly the same, > Any details you can provide would be appreciated. >> but for me it works when I coregister&reslice a statistical map to the >> T1-image (as put in Talairach orientation before segmentation), and then map >> the resliced statistical image to the surface. > Mathijs' comments here suggest, to me, that he is generating his own surfaces > and mapping individual maps to the individual's surface. this differs from > what Raphael is doing, which is mapping group results to the PALS atlas, at > least as I understand it. > > But in both cases, your statistical maps do need to align with the target > surface. In Mathijs individual case, the map must align with the T1 used to > generate the segmentation and resulting surface. In Raphael's case, it must > be in MNI space (i.e., spatially normalized to the standard templates in the > SPM distribution). Now on to Raphael's comments below... > >> Hope this helps. >> >> Regards, >> Mathijs >> >> ________________________________ >> >> Van:[email protected] namens Raphael Hilgenstock >> Verzonden: do 19-8-2010 13:56 >> Aan:[email protected] >> Onderwerp: [caret-users] SPM8 - Mapping Functionals to Volume problem >> >> >> >> Dear List, >> >> I`ve got a problem mapping SPM8 t- and F-contrasts to Caret surfaces. >> Unfortunately I even don`t know if it is possible to map SPM8 images to >> Caret as haven`t found any informationen on the compatibility of both >> programs (even on the list). Is there a difference between SPM5- and >> SPM8-space that has to be accounted for when projecting activations?! >> > We haven't yet generated SPM8 surfaces for the PALS atlas, but we should > do so. Odds are, John Ashburner made significant improvements to the > spatial normalization between the SPM5 and SPM8 revisions. Still, using > SPM5 is an acceptable substitute. I can tell you that when I compared > the SPM2 and SPM5 surfaces, differences were modest. I would just > specify which PALS_B12 target you used in your methods. >> I`m asking because I ran across the following problem: >> >> I processed data to map activations using the Tutorial_Sept_06 (provided >> on the Sumsdb site) click by click with the >> Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec-file (is this >> approach still the standard of mapping functional files to volumes?). >> > Yes. >> When I mapped an F-contrast (spm_F.hdr and .nii) on an inflated brain >> there where more spots (and some spots in strange locations) on my >> MFM-image than on my SPM. > This is not unusual with MFM, which maps your volume to each of the 12 > PALS subjects' surfaces, and then averages the resulting 12 maps. The > tutorial talks about the pros and cons of the MFM and AFM methods. > David feels the MFM method is more representative, but in practice many > WUSTL researchers use the AFM method, because it appears more > conservative. There is a way to constrain the display to an extent > equal to the average supra-threshold area in the contributing subjects. > The tutorial talks about that, too. >> When I mapped a t-contrast (spm_T.hdr and >> .nii) all activations were gone! When lowering the threshold also this >> (T-)map is showing activations that can be expected from my SPM but also >> "new" acitavtions. > I am confused about this. If all activity disappeared (using the same > contrast that gave positive F results) on your t-map, then I start > doubting the volume -- either it really is all zeroes, or the origin is > way off and/or not specified -- something like that. Upload your > spm_T.hdr and .img and/or .nii here: > > http://pulvinar.wustl.edu/cgi-bin/upload.cgi >> The MFMs were thresholded with my SPM t/F-treshold >> and the treshold type in Caret set to "column" (does this acutally mean >> that just the information (t/F-values) form the the spm_T/F image is >> read without any changes to the threshold by Caret? I infered that from >> posts I read but I´m not yet definitively sure). > This gets confusing, but relates to what I mentioned earlier about the > MFM threshold that keeps the supra-threshold area equal to the mean > supra-threshold area of the 12 PALS subjects. If you select this option > and enter a threshold when you map, then Caret computes the threshold > needed to hold the area at this level, and it stores it in the user > threshold, I believe. You over-ride this with your own column threshold. >> As suggested in another >> post I also used different algorithms (e.g. Metric-Gaussian). However >> the result is still the same. I´m most concerned about strange >> activation foci that I won`t find in my SPMs. >> > This is a normal consequence of MFM mapping -- a reflection of normal > anatomical variability. It might go away with proper thresholding. But > first, try AFM mapping and see if your concerns disappear. >> Is there anything I did wrong?! > Don't know. The disappearing t activations puzzle me, which is why I > want to see your volume. >> Any hint or help would be greatly >> appreciated. >> >> Thanks& best regards >> Raphael >> > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users > ___________________________________________________________ Der frühe Vogel fängt den Wurm. Hier gelangen Sie zum neuen Yahoo! Mail: http://mail.yahoo.de _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
