Thanks so much!!! -Daniel

On 8/21/15, 1:06 PM, " on behalf of" < on
behalf of> wrote:

>Use these commands:
>caret_command -spec-file-add my.spec paint_file
>caret_command -spec-file-add my.spec area_color_file
>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
>> 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, " on behalf
>> Donna Dierker" < on behalf of
>> 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:
>>>… which has these columns:
>>>Then adjust your D/C: Surface Overlay/Underlay settings as shown here:
>login pub
>>>password download
>>>That paint file is included in this archive:
>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" <>
>>>> Dear Donna,
>>>> Thanks! I am trying to map the functional volume in MNI152 (SPM99)
>>>> 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
>>>> overlay?
>>>> Many thanks!!!
>>>> Daniel
>>>> On 8/19/15, 6:38 PM, " on behalf
>>>> Donna Dierker" < on behalf of
>> wrote:
>>>>> Could you elaborate on how you are using caret_command?
>>>>> The Enable Medial Wall Override affects display, which is not
>>>>> using caret_command, unless you are using -show-scenes, in which case
>>>>> would select the medial wall paint column as an overlay on top of
>>>>> functional overlay, in order to gray out the medial wall.  It gets
>>>>> complicated if you want to exclude the medial wall from processing,
>>>>> isn't too hard (search for "select" in the caret_command full help
>>>>> On Aug 19, 2015, at 3:13 PM, "Yang, Daniel" <>
>>>>>> Dear Caret Experts,
>>>>>> In Paint Main, I can check “Enable Medial Wall Override” to gray
>>>>>> medial wall. Is it possible to do so via caret_command?
>>>>>> Many thanks!
>>>>>> Daniel
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