I am out of the office until Wednesday 11/09/2005. Any computer related help should be directed to [EMAIL PROTECTED]
-Matt >>> caret-users 10/26/05 12:51 >>> Mike, In addition to Donna's helpful comments regarding mapping of regional volume data to average fiducial surfaces, there are a couple of other ways to adjust colors that might prove useful. One is the Attributes: Metric: Convert Metric to RGB paint file option. Another is Surface: ROI: Operations: Assign paint attributes to selected nodes. Since this dialog now contains various items that may be of interest to others, I am copying this to the caret-users list. David On Oct 26, 2005, at 11:08 AM, Donna Hanlon wrote: > Hi Mike, > > If nothing else, you could make sure your visualization spec has the > appropriate average fiducial surface in it; load the spec file and > make sure that fiducial was selected; and use the Map to Caret vs the > Map to Caret with Atlas option. (In fact, if you think you'll almost > always be using AFM vs MFM, then there's no advantage to the Map to > Caret with Atlas over the Map to Caret option, assuming you have the > correct average fiducial loaded.) Just remember to save the resulting > metric/paint, since I believe the Map to Caret function doesn't > generate an output file; it just loads the mapping in memory as a > metric/paint column, but disappears if you exit Caret without saving > as a metric/paint. > > If you go the paint route, the areacolor file (Attributes: Area Color, > http://brainmap.wustl.edu/caret/html/file_formats/ > file_formats.html#areaColor) controls the color mapping. If you go the > metric route, the palette file > (http://brainmap.wustl.edu/caret/html/file_formats/ > file_formats.html#paletteFile) controls the color mapping. > > Donna > > On 10/26/2005 10:57 AM, Mike Fox wrote: > >> Is there a way to map regional data to the average fiducial map? When >> I map functional data I appear to have this option, but not when I >> map regional data (with which AFM would be most useful). >> >> Alternatively, If I map regional data as functional data (ie data >> with discreet integer values) using AFM, is there a way to specify >> the color of each region. I'm currently using this approach and plan >> to try and change the colors of each region later using photoshop, >> but I figure there must be a way to do it in caret. >> >> Thanks, >> >> Mike >> >> Michael Fox >> >> Laboratory of Dr. Marcus Raichle >> >> Mallinckrodt Institute of Radiology >> >> Washington University in St. Louis >> >> Medical Scientist Training Program >> >> (314) 747-3073 >> >> ---------------------------------------------------------------------- >> -- >> >> *From:* David Van Essen [mailto:[EMAIL PROTECTED] >> *Sent:* Friday, October 21, 2005 9:36 PM >> *To:* Mike Fox >> *Cc:* Donna Hanlon; David Van Essen >> *Subject:* Re: visualization specs; MFM vs AFM >> >> Mike, >> >> On Oct 21, 2005, at 10:48 AM, Mike Fox wrote: >> >> Dr. Van Essen, >> >> Thanks for the spec files. I was having a tremendous amount of >> difficulty finding them on sums without your links. >> >> We are working to enhance our search capabilities, but obviously have >> quite a ways to go on this. >> >> The question I had concerned the validity of mapping to 12 >> individuals, then averaging those results, as compared to mapping >> just once to the average anatomy of the 12 individuals (a new >> function of caret). The two do not always give the same result, >> and I was wondering if you felt one was superior to the other and >> why. I know that volume space atlas registration has adopted the >> second approach (ie data is warped to a single atlas which is the >> average of multiple subjects anatomy), but this does not >> necessarily make it superior. >> >> For starters, it's useful to review what I said about this topic in >> the Discussion of the PALS paper: >> >> In order to interpret the results of MFM, it is important to consider >> several underlying assumptions. Without access to the individual >> structural and fMRI data in any given study, it is impossible to work >> backwards from volume-averaged group data to determine what the >> actual pattern would be in any individual. Hence, the activations >> seen on any of the individual PALS-B12 surfaces do not reflect a >> pattern in fact attributable to any of the actual fMRI subjects. Nor >> do they necessarily reflect the pattern that would have arisen in the >> 12 subjects whose structural data contributed to the atlas if they >> had been tested using the same fMRI paradigm. MFM does provide an >> objective strategy for estimating both the region of most likely >> activation and a plausible upper bound on the total extent of >> activation. This constitutes an important advance over the common >> current practice of mapping volume-averaged results onto a >> single-subject atlas. >> >> In many situations, it is appropriate to map group-average data using >> both AFM and MFM. The two mapping methods yield similar but not >> identical spatial patterns and are inherently complementary. AFM is >> conceptually simpler and allows readout of values at each surface >> node that correspond to a particular voxel value. MFM provides a more >> objective assessment of the most likely spatial distribution on the >> atlas surface. >> >> ----- >> >> In short, I contend that MFM is a superior way to estimate the most >> likely spatial location of regions likely to have been modulated in >> any given paradigm. AFM can give significant biases in spatial >> localization, depending on the nature and location of the data. >> >> However, a price is paid in terms of relating the surface node values >> in an MFM map to the voxel values in the volume. In some situations >> that's pretty important, but in others it may be largely irrelevant. >> >> These issues are truly complex, as they are intimately linked to the >> nature of structural and functional variability and what is really >> meant by corresponding locations in different individual hemispheres. >> >> I hope this is helpful. If you have further comments, questions, or >> discussion points, let me know. >> >> David >> _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://pulvinar.wustl.edu/mailman/listinfo/caret-users
