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
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>>>ai
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>>>MO
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>>>RXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=h5-YV_ETDHGYBcqGmBeefwlj-rjDZnlPAYpW
>>>Tc
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>> 
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>>MORXy6GkKdTAw3V58rxzUZGOKpGXPDgqUHY&m=u5j7Df9p95woZ9z0eTo3nv8WhnplQZYwSn-
>>D2Unh2Fc&s=IYkkOT7fsaJ0JUphfRnuXu7nq8c2fD5YCiJvjFxBDwM&e=
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