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 “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, "[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 “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 >>>> [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
