So we had a chance to discuss this internally, and this appears to be the
best solution right now:
wb_command -metric-math "(x > 0.5) * (x < 1.5)"
${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.BA1_ROI.32
k_fs_LR.func.gii -var x
${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemispehre}.BA.32k_fs_
LR.label.gii
wb_command -cifti-roi-average
${Subject}/MNINonLinear/Results/${fMRIName}/${fMRIName}_Atlas.dtseries.nii
${Hemisphere}_BA1_Timeseries.txt -left-roi|-right-roi
${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.${Hemisphere}.BA1_ROI.32
k_fs_LR.func.gii
The first command selects label key 1 (which is BA1 in those GIFTI label
files, you can check by opening the file in a text editor and looking at
the label table) from the label file and saves it as a binary ROI. The
second command (run separately for left and right hemispheres) gives you a
timeseries as a text file that is the average timeseries inside the BA1
ROI.
There are a couple of bugs/new features needed this uncovered:
1) The CIFTI files don't have the left and right hemisphere labels
separated (because FreeSurfer calls them the same thing). We'll fix this
in the next version of the pipelines. For now, the CIFTI .dlabel.nii
files probably won't be what you want unless you want an average across
both hemispheres. -cifti-parcellate makes the average timeseries for a
number of CIFTI parcels, but if you wanted that, you'd need to make
.dlabel.nii files with separate left and right hemisphere areas. This
isn't hard to do, so let me know if this is what you want.
2) We'll make a command for selecting specific labels from a label file
and turning them into ROIs (though the math command is fine for this too).
I didn't understand the comments about native space or volume-based
analysis, so hopefully the above will achieve what you want.
Peace,
Matt.
On 9/23/13 9:31 AM, "Harms, Michael" <mha...@wustl.edu> wrote:
>
>I just noticed the -cifti-parcellate command in 'wb_command', which looks
>like it will do the trick.
>
>cheers,
>-MH
>
>--
>Michael Harms, Ph.D.
>
>-----------------------------------------------------------
>Conte Center for the Neuroscience of Mental Disorders
>Washington University School of Medicine
>Department of Psychiatry, Box 8134
>660 South Euclid Ave. Tel: 314-747-6173
>St. Louis, MO 63110 Email: mha...@wustl.edu
>
>
>
>
>On 9/23/13 9:13 AM, "Harms, Michael" <mha...@wustl.edu> wrote:
>
>>
>>Hi Jo,
>>All the preprocessed fMRI data is in HCP-standard volume (MNI152) or
>>grayordinate space.
>>Those are contained in ${subj}/MNINonLinear/Results
>>
>>The subject-specific FreeSurfer labels transferred to this space and at
>>the same surface mesh resolution are contained in
>>${subj}/MNINonLinear/fsaverage_LR32k
>>
>>As for the 'wb_command' option to extract an average timeseries within a
>>specified label, Matt or Jenn will have to chime in with that.
>>
>>cheers,
>>-MH
>>
>>--
>>Michael Harms, Ph.D.
>>
>>-----------------------------------------------------------
>>Conte Center for the Neuroscience of Mental Disorders
>>Washington University School of Medicine
>>Department of Psychiatry, Box 8134
>>660 South Euclid Ave. Tel: 314-747-6173
>>St. Louis, MO 63110 Email: mha...@wustl.edu
>>
>>
>>
>>
>>On 9/21/13 12:37 PM, "J.A. Etzel" <jet...@artsci.wustl.edu> wrote:
>>
>>>I downloaded the T1w and tfMRI_MOTOR preprocessed data via the Q1 data
>>>release web interface for an individual. Using the Connectome Workbench
>>>I can open the native-space anatomy, including cifti labels, and the
>>>MNI-space 4d functional timeseries (e.g. tfMRI_MOTOR_LR.nii.gz) outside
>>>the Workbench.
>>>
>>>I would like to extract the coordinates/grayordinates corresponding to
>>>an anatomical structure included in the cifti label file (e.g. BA1),
>>>then extract the functional timeseries corresponding to those
>>>coordinates/grayordinates. In other words, I would like to use the (e.g.
>>>BA1) label as a native-space mask for the functional data.
>>>
>>>Is this possible with the current release, or do I need to use a ROI
>>>derived from a standard MNI-space atlas? Or convert the cifti labels in
>>>the workbench to a standard MNI-space NIfTI? Is the preprocessed
>>>functional data available in native space?
>>>
>>>thanks!
>>>Jo
>>>
>>>
>>>--
>>>Joset A. Etzel, Ph.D.
>>>Research Analyst
>>>Cognitive Control & Psychopathology Lab
>>>Washington University in St. Louis
>>>http://mvpa.blogspot.com/
>>>_______________________________________________
>>>HCP-Users mailing list
>>>HCP-Users@humanconnectome.org
>>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
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>
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