Hi YSL, Unfortunately, the bold font weight doesn't display in my email reply, because I've got my email client set to text only, rather than HTML. (And I'm not going to change it -- not even for you, YSL.;-)
But here is what I meant by BOLD: http://brainmap.wustl.edu/pub/donna/ETC/bold_not_bold.html login pub password download The bold font just has heavier weighting; it is thicker. If you want to pinpoint the anatomic region of activation, then there are many ways to do this. Some use AAL in MRIcron. Some use the Harvard Oxford Atlas in FSL or Freesurfer. And some use PALS, as you are trying to do. Here are the paint/parcellation/label columns in the Human.PALS_B12.BOTH.COMPOSITE_Areas_Functional_WS.73730.paint paint file: Lobes (PALS atlas) Geography - Colin RIGHT on PALS-B12 AVERAGE-MED-WALL B1-12 RIGHT AVERAGE-MED-WALL B1-12 LEFT Visuotopic - BOTH (from colin RIGHT) - PALS-B12 Brodmann - BOTH (from colin RIGHT) - PALS-B12 OrbitoFrontal BOTH - PALS-B12 (from case Fb LEFT) Visuotopic + OrbitoFrontal - RIGHT - PALS-B12 Modalities - RIGHT - PALS-B12 Modalities - LEFT - PALS-B12 Clusters - Left-right depth asymmetries (Cases B1-24, paired Williams Syndrome folding abnormalities (RIGHT) - PALS-B12 Williams Syndrome folding abnormalities (LEFT) - PALS-B12 Sulcal ID - Colin RIGHT on PALS-B12 Geography - Colin LEFT on PALS-B12 Sulcal ID - Colin LEFT on PALS-B12 Both the Brodmann and Sulcal ID colums are good general use columns. But if your activation is in the visuotopic or orbitofrontal regions, then those columns are likely to give you greater specificity. For some regions, there are probabilistic atlases for the anatomical regions mapped by the Amunts/Zilles et. al. See PALS_B12.BOTH-HEMS.DEMO.73730.spec, scene 10. There are many different columns in the probabilistic atlas metric file loaded in that scene. Finally, if you are getting overwhelmed by too many columns in a paint or metric file, then you can try: Toolbar: spec: paint: open desired paint file select "Erase all existing columns" press Set All Columns to Do Not Load For the single column or two of interest, change Do Not Load to Create New Column This will load just the column of interest, and thereby cut way back the amount of output you get when you click on nodes. Donna On 04/13/2009 09:16 AM, Yune S. Lee wrote: > Hello Donna, > Many thanks for your answer and it did help me understanding on the > previous question. > But below are the parts that I wasn't clear. > > Paint: LOBE.PARIETAL GYRUS ??? ???????? ??? Brodmann.4 ??? ??? > COGNITIVE COGNITIVE minus_cluster_area_424.611_nodes_569 ??? ??? ??? > GYRUS ??? > > The paint name associated with the currently selected paint column is > printed in BOLD, while the paint names associated with all other columns > are not in bold. > -> what do you mean by 'BOLD'? you mean the words with captial such as > LOBE.PARIETAL GYRUS? > it would be great what BOLD / non-bold is about again. > > Basically, I'm trying to figure out the anatomy region of the > activation. Should it be the only way to click areas one by one > and see the results of the identify window or is there any better way > something like AAL map in the MRIcron. > Your help would be again greatly appreciated. > > Thanks, > YSL > > > > Donna Dierker wrote: >> On 04/13/2009 08:23 AM, Yune S. Lee wrote: >> >>> I see. Glad to hear that it has nothing to do with any font failure. >>> By the way, I went to the paint selection page to see what was mapped >>> for the particular column, but I couldn't find it. >>> As is shown in the attached, Average-MED-Wall B1-12 was selected >>> (assume it was the default or automatically selected when I opened up >>> the left template), but I didn't notice any change when I tried some >>> other views (e.g., Modalities-LEFT-PALS-B12). >>> >> When Average-MED-Wall B1-12 column is selected, then only the nodes >> inside the medial wall will have a paint name associated with them. All >> other nodes will have paint name "?????", which in this context means >> "not inside the medial wall". >> >> The Modalities paint column should have a real paint name for almost >> every node. >> >> I think I know what is confusing you, though: When you click on a node >> with the composite paint file loaded, you get a BUNCH of output like this: >> >> >> >> >> >> They are printed in the same sequence as the columns >> are listed in the D/C paint selection menu (or the Overlay/Underlay - >> Surface paint dropdown menu). You will get some ??? output for almost >> every node, since many of the parcellation schemes apply to a restricted >> area (e.g., visuotopic or frontal). All nodes outside those areas will >> get ???? for that column. >> >> >>> It would be appreciated to help me understand your tip. >>> >>> Thanks, >>> YSL >>> >>> >>> >>> David Van Essen wrote: >>> >>>> YSL, >>>> >>>> Basically, '???' means that there was no specific assignment for that >>>> node in that column of the paint file. Use Display Control: Page >>>> Selection: Paint Selection to see what was mapped for that particular >>>> column (e.g., the 4th column is probably visuotopic areas, which only >>>> cover a small fraction of the cortical surface and therefore have >>>> lots of '???' entries. >>>> >>>> DVE >>>> >>>> On Apr 12, 2009, at 4:30 PM, Yune S. Lee wrote: >>>> >>>> >>>>> Hello Caret users, >>>>> >>>>> I'm wondering if a string of '?' means the broken font in the >>>>> paint of the identify window or something meaningless >>>>> For instance, for the node 71770, the identify window shows as below: >>>>> >>>>> *paint: LOBE.PARIETAL SUL ??? ?????????? ??? Broadmann.43 ??? ??? >>>>> SOMATOSENSORY AUDITORY ??? >>>>> >>>>> * I don't have other language package installed any more, but wonder >>>>> if this has something to do with character issue. >>>>> Any help would be appreciated. >>>>> >>>>> Thanks, >>>>> YSL >>>>> >>>>> >>>>> * >>>>> >>>>> * >>>>> _______________________________________________ >>>>> caret-users mailing list >>>>> caret-users@brainvis.wustl.edu <mailto:caret-users@brainvis.wustl.edu> >>>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>>> >>>> ------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> caret-users mailing list >>>> caret-users@brainvis.wustl.edu >>>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>>> >>>> >>> ------------------------------------------------------------------------ >>> >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> http://brainvis.wustl.edu/mailman/listinfo/caret-users >>> >>> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> http://brainvis.wustl.edu/mailman/listinfo/caret-users >> > > ------------------------------------------------------------------------ > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://brainvis.wustl.edu/mailman/listinfo/caret-users > _______________________________________________ caret-users mailing list caret-users@brainvis.wustl.edu http://brainvis.wustl.edu/mailman/listinfo/caret-users
