Thanks so much!!! -Daniel On 8/21/15, 1:06 PM, "[email protected] on behalf of [email protected]" <[email protected] on behalf of [email protected]> wrote:
>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_sum >>>s_ >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.ed >>>>>>u_ >ma >>>>>>ilman_listinfo_caret-2Dusers&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8 >>>>>>z9 >19 >>>>>>MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnl >>>>>>PA >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=vhD8z9 >>>>>19 >MO >>>>>RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAY >>>>>pW >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_m >>>ai >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] >> >>https://urldefense.proofpoint.com/v2/url?u=http-3A__brainvis.wustl.edu_ma >>ilman_listinfo_caret-2Dusers&d=AwIFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919 >>MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=u_QlfkpE2DytwSV9WPScS1V4gZWLtZAPKNV >>8Oh94jPk&s=Aw-GpmqeqT0NuTjvfTnT5ic7dKEUWVe6ihqeNKLvrBs&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=AwIFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MO >RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=u_QlfkpE2DytwSV9WPScS1V4gZWLtZAPKNV8Oh >94jPk&s=Aw-GpmqeqT0NuTjvfTnT5ic7dKEUWVe6ihqeNKLvrBs&e= _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
