Dear Donna,
Thank you so much for your help, these details are very useful to me.
I tried your method, the 'caret_command -file-convert' part works fine, but
there is no '-file-information' option for the wb_command, and my workbench
version is beta 0.84.
I try to run the following command:
caret_command -surface-to-volume \
100408.L.midthickness.32k_fs_LR.coord \
100408.L.midthickness.32k_fs_LR.topo \
100408.L.BA.32k_fs_LR.label.gii \
1 \
100408LBA.nii
then an error pop up:
SURFACE TO VOLUME ERROR: Metric/Paint/Shape file extension not valid.
I think the 100408.L.BA.32k_fs_LR.label.gii need to be converted as well?
Best,
Xiangyu
On Wed, Dec 11, 2013 at 3:33 PM, Donna Dierker <[email protected]>wrote:
> 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]>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]> 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
>> > _______________________________________________
>> > HCP-Users mailing list
>> > [email protected]
>> > http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> >
>>
>>
>
>
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