Thanks so much!!! -Daniel

On 8/21/15, 1:06 PM, "caret-users-boun...@brainvis.wustl.edu on behalf of
do...@brainvis.wustl.edu" <caret-users-boun...@brainvis.wustl.edu on
behalf of do...@brainvis.wustl.edu> 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, "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_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" <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
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>>>>>>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=
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