It depends on how critical it is the $metric_filename have zeroes in the medial wall, rather than just look gray when you view/capture it. For display/capture purposes, you can use the existing PALS paint file:
Human.PALS_B12.BOTH.COMPOSITE_Areas_Functional_WS.73730.paint … which has these columns: AVERAGE-MED-WALL B1-12 RIGHT AVERAGE-MED-WALL B1-12 LEFT Then adjust your D/C: Surface Overlay/Underlay settings as shown here: http://brainmap.wustl.edu/pub/donna/US/CT/YALE/medial_wall_gray.png login pub password download That paint file is included in this archive: CARET_TUTORIAL_SEPT06.zip http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6595030 If you are doing analysis with $metric_filename that needs the medial wall to be zeroed out, you can create an inverted mask like this: caret_command -surface-region-of-interest-selection my.coord my.topo "" cortical_mask_outside_medial_wall.roi -paint medial.wall.paint column-number MEDIAL.WALL NORMAL -invert-selection But then what you do next depends on your analysis, and I suspect you care more about the display. On Aug 20, 2015, at 8:27 AM, "Yang, Daniel" <daniel.yj.y...@yale.edu> wrote: > Dear Donna, > > Thanks! I am trying to map the functional volume in MNI152 (SPM99) space > to the surface space (PALS) as metric. It is like the following: > > caret_command -volume-map-to-surface-pals \ > "" \ > $metric_filename \ > SPM99 \ > $hemisphere \ > METRIC_AVERAGE_NODES \ > $fMRI_vol_filename \ > -metric-afm > > > Could you please provide an example to use “select” in caret_command to > select the medial wall paint column as an overlay on top of the functional > overlay? > > Many thanks!!! > Daniel > > On 8/19/15, 6:38 PM, "caret-users-boun...@brainvis.wustl.edu on behalf of > Donna Dierker" <caret-users-boun...@brainvis.wustl.edu on behalf of > do...@brainvis.wustl.edu> wrote: > >> Could you elaborate on how you are using caret_command? >> >> The Enable Medial Wall Override affects display, which is not applicable >> using caret_command, unless you are using -show-scenes, in which case you >> would select the medial wall paint column as an overlay on top of your >> functional overlay, in order to gray out the medial wall. It gets more >> complicated if you want to exclude the medial wall from processing, but >> isn't too hard (search for "select" in the caret_command full help >> output). >> >> >> On Aug 19, 2015, at 3:13 PM, "Yang, Daniel" <daniel.yj.y...@yale.edu> >> wrote: >> >>> Dear Caret Experts, >>> >>> In Paint Main, I can check “Enable Medial Wall Override” to gray out >>> medial wall. Is it possible to do so via caret_command? >>> >>> Many thanks! >>> Daniel >>> _______________________________________________ >>> caret-users mailing list >>> caret-users@brainvis.wustl.edu >>> >>> https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_ma >>> ilman_listinfo_caret-2Dusers&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919 >>> MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAYp >>> WTcIsjmI&s=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZY&e= >> >> >> _______________________________________________ >> caret-users mailing list >> caret-users@brainvis.wustl.edu >> https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_mai >> lman_listinfo_caret-2Dusers&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MO >> RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAYpWTc >> IsjmI&s=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZY&e= > > > _______________________________________________ > 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
