Use these commands: caret_command -spec-file-add my.spec paint_file Human.PALS_B12.BOTH.COMPOSITE_Areas_Functional_WS.73730.paint caret_command -spec-file-add my.spec area_color_file Human.Cerebral.COMPOSITE_OrbFrontDistinct_WS_MWblack.areacolor
Are you using scenes, Daniel? There's a good chance you'll find it worth the learning curve. Then you can use a script to swap out what changes and generate captures. Quicker and less error prone. > Dear Donna, > Thanks so much! Very helpful! Yes, I do want to primarily display the blacked-out medial wall, rather than analyze it. > Could you please show how I can use caret_command to add/select > AVERAGE-MED-WALL B1-12 RIGHT as the Display Column from the Paint file as > a secondary overlay to an existing spec? > I would like to avoid clicking in the caret UI if possible. > Many thanks! > Daniel > On 8/20/15, 11:02 AM, "[email protected] on behalf of > Donna Dierker" <[email protected] on behalf of [email protected]> wrote: >>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: https://urldefense.proofpoint.com/v2/url?u=http-3A__brainmap.wustl.edu_pub _donna_US_CT_YALE_medial-5Fwall-5Fgray.png&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sd qw&r=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=u5j7Df9p95woZ9z0eTo3nv8 WhnplQZYwSn-D2Unh2Fc&s=0ubFqD2d6iE4otxojW-Jv3VgMJLlcUYIOpV6mXdrNS0&e= login pub >>password download >>That paint file is included in this archive: >>CARET_TUTORIAL_SEPT06.zip >>https://urldefense.proofpoint.com/v2/url?u=http-3A__sumsdb.wustl.edu_sums_ archivelist.do-3Farchive-5Fid-3D6595030&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw& r=vhD8z919MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=u5j7Df9p95woZ9z0eTo3nv8Whn plQZYwSn-D2Unh2Fc&s=8OClUz8TulQVknEPxf1ukRvEn-YtXtwpKga-vaZ-wlc&e= 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" <[email protected]> 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 âselectâ 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, "[email protected] on behalf >>>of >>> Donna Dierker" <[email protected] on behalf of [email protected]> 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" <[email protected]> wrote: >>>>> Dear Caret Experts, >>>>> In Paint Main, I can check âEnable Medial Wall Overrideâ to gray out >>>>> medial wall. Is it possible to do so via caret_command? >>>>> Many thanks! >>>>> Daniel >>>>> _______________________________________________ >>>>> caret-users mailing list >>>>> [email protected] >>>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_ ma >>>>>ilman_listinfo_caret-2Dusers&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z9 19 >>>>>MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPA Yp >>>>> WTcIsjmI&s=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZY&e= >>>> _______________________________________________ >>>> caret-users mailing list >>>> [email protected] >>>>https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_m ai >>>>lman_listinfo_caret-2Dusers&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919 MO >>>>RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAYpW Tc >>>> IsjmI&s=K1vKNA8KK-hNQ2Za8ncWGM47HbBDDXZwfOaGXikwyZY&e= >>> _______________________________________________ >>> caret-users mailing list >>> [email protected] >>>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=u5j7Df9p95woZ9z0eTo3nv8WhnplQZYwSn- D2Unh2Fc&s=IYkkOT7fsaJ0JUphfRnuXu7nq8c2fD5YCiJvjFxBDwM&e= >>_______________________________________________ >>caret-users mailing list >>[email protected] >>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=u5j7Df9p95woZ9z0eTo3nv8WhnplQZYwSn-D2U nh2Fc&s=IYkkOT7fsaJ0JUphfRnuXu7nq8c2fD5YCiJvjFxBDwM&e= > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
