Just some background: Many features of caret5/caret_command are being
ported to workbench/wb_command, but not all. I just found out about
wb_command -show-scene yesterday, which made my week. But I searched
the output of wb_command -all-commands-help for "to-volume" and found
nothing, possibly because workbench tends to use CIFTI rather than
volume/NIFTI outputs.
But in your case, you want a volume/NIFTI output, which caret_command
can give you. Trouble is, the caret_command feature you want needs old
style coord/topo pairs. You can make them like so:
caret_command -file-convert -sc -is GS
$SUBJECT.$HEM.midthickness.32k_fs_LR.surf.gii -os CARET
$SUBJECT.$HEM.midthickness.32k_fs_LR.coord
$SUBJECT.$HEM.midthickness.32k_fs_LR.topo CLOSED FIDUCIAL
Then feed the .coord/.topo outputs to the subsequent commands.
The $SUBJECT.$HEM.BA.164k_fs_LR.label.gii is serving the
input-metric-paint-or-shape-file-name argument.
To find out the column argument, do this (your output will be 32k -- not
164k, and subject ID will vary):
wb_command -file-information 545345.L.BA.164k_fs_LR.label.gii
Name: 545345.L.BA.164k_fs_LR.label.gii
Type: Label
Structure: CortexLeft
Maps to Surface: true
Maps to Volume: false
Maps with LabelTable: true
Maps with Palette: false
Number of Maps: 1
Number of Vertices: 163842
Map Map Name
1 545345_L_BA ### <== I recommend using the index number under
the Map column, but Map Name might work, too. Where they have spaces,
this can confound your command line, but this one doesn't. This is your
input-metric-paint-or-shape-column argument.
Label table for ALL maps
KEY NAME RED GREEN BLUE ALPHA
0 ??? 0.000 0.000 0.000 0.000
1 BA1 0.000 0.361 0.090 1.000
2 BA2 0.514 0.580 1.000 1.000
3 BA3a 0.000 0.000 1.000 1.000
4 BA3b 1.000 0.400 0.200 1.000
5 BA4a 0.769 1.000 0.078 1.000
6 BA4p 1.000 0.200 0.800 1.000
7 BA6 0.004 0.149 0.600 1.000
8 BA44 0.600 0.000 0.149 1.000
9 BA45 0.451 0.600 0.000 1.000
10 V1 0.600 0.059 0.000 1.000
11 V2 0.000 0.839 0.506 1.000
12 MT 0.608 0.000 0.600 1.000
13 perirhinal 0.129 0.588 0.980 1.000
On 12/11/2013 08:03 AM, Long wrote:
Hi Donna,
Thank you for the reply! Could you mind to give more details about
these files: <input-coordinate-file-name>
<input-topology-file-name>
<input-metric-paint-or-shape-file-name>
and <input-metric-paint-or-shape-column>?
where are these in the 'fsaverage_LR32k' folder?
Best,
Xiangyu
On Tue, Dec 10, 2013 at 8:59 PM, Donna Dierker
<[email protected] <mailto:[email protected]>> wrote:
I'm not sure how to do this with workbench/wb_command, but it can
be done with caret5:
http://brainvis.wustl.edu/wiki/index.php/Caret:Download
You would find the midthickness 32k surf.gii that corresponds to
the label.gii and use commands like this:
caret_command -surface-region-of-interest-selection
<input-coord-file-name>
<input-topology-file-name>
<input-region-of-interest-file-name.roi>
<output-region-of-interest-file-name.roi>
[-paint paint-file-name column paint-name NORMAL
caret_command -surface-to-volume
<input-coordinate-file-name>
<input-topology-file-name>
<input-metric-paint-or-shape-file-name>
<input-metric-paint-or-shape-column>
<output-volume-file-name>
[-inner inner-boundary]
[-outer outer-boundary]
[-step intersection-step]
Intersect a surface with a volume and assign the specified
column's data of the metric, paint, or shape file to the
volume.
The output volume file must exist and it must be in the
same stereotaxic space as the surface. A volume file may
be created by using the "-volume-create" or
"-volume-create-in-stereotaxic-space" commands.
The default inner boundary, outer boundar, and step size
are -1.5, 1.5, and 0.5 respectively.
The metric, paint, or shape file column is either the
number of the column, which starts at one, or the name of
the column. If a name contains spaces, it must be
enclosed in double quotes. Name has priority over number.
There might be an easier way, but this is what comes to mind.
On Dec 9, 2013, at 10:11 AM, Long <[email protected]
<mailto:[email protected]>> wrote:
> Dear all,
>
> I'm trying to use the BAs from the well parcellated file
BA.32k_fs_LR.label.gii as the ROI, so how could I extract the
specific BAs, i.e., BA 4 from this file and convert it to the
volumetric nifti image? Thank you for your time!
>
> Best,
> Xiangyu
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