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, "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:
>>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" <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=vhD8z9
19
>>>>>MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPA
Yp
>>>>> 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_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
>>> 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=u5j7Df9p95woZ9z0eTo3nv8WhnplQZYwSn-
D2Unh2Fc&s=IYkkOT7fsaJ0JUphfRnuXu7nq8c2fD5YCiJvjFxBDwM&e=
>>_______________________________________________
>>caret-users mailing list
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lman_listinfo_caret-2Dusers&d=AwIF-g&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=vhD8z919MO
RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=u5j7Df9p95woZ9z0eTo3nv8WhnplQZYwSn-D2U
nh2Fc&s=IYkkOT7fsaJ0JUphfRnuXu7nq8c2fD5YCiJvjFxBDwM&e=
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