I think I neglected to send my first reply to the mailing list, and I'd
definitely like it to be saved there.
To extract average timeseries from parcels you don't need to convert from
CIFTI. We have the function:
wb_command -cifti-parcellate that will do this if you use the COLUMN
direction. This would then be a CIFTI parcellated timeseries (Tim will
this work yet?). As for the CIFTI label, since you want FreeSurfer
aparc.a2009s, you can use
${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k/${SubjectID}.aparc
.a2009s.32k_fs_LR.dlabel.nii in the distributed data if you only need the
cortical parcels. If you need the subcortical ROIs as well, you could
recreate the CIFTI label with the subcortical structures like this:
wb_command -cifti-create-label <cifti-label-out> -volume
${StudyFolder}/${SubjectID}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz
${StudyFolder}/${SubjectID}/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz
-left-label
${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k/${SubjectID}.L.apa
rc.a2009s.32k_fs_LR.label.gii -roi-left
${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k/${SubjectID}.L.atl
asroi.32k_fs_LR.shape.gii -right-label
${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k/${SubjectID}.R.apa
rc.a2009s.32k_fs_LR.label.gii -roi-right
${StudyFolder}/${SubjectID}/MNINonLinear/fsaverage_LR32k/${SubjectID}.R.atl
asroi.32k_fs_LR.shape.gii
If you need to get the parcellated timeseries out of CIFTI into some other
format, let me know and we can think of the best way to do that.
Thanks,
Matt.
On 7/12/13 11:14 AM, "[email protected]" <[email protected]>
wrote:
>Thanks Matt!
>
>> I am assuming you just did something like:
>>
>> wb_command -cifti-convert -to-nifti <file.dtseries.nii> <file.nii.gz>?
>
>Yes, exactly!
>
>> What you are doing is converting a CIFTI file to a NIFTI-1 file, which
>>can
>> be helpful when needing to do analyses in packages that do not yet
>>support
>> CIFTI. Because the dimensions of NIFTI-1 do not support indices greater
>> than 32767, it is necessary to wrap the 91282 grayordinates space 3
>>times
>> (dim2) and pad it with zeros at the end. dim4 remains time.
>>
>> It is important to remember that this conversion is designed for you to
>> run element-wise operations in a fake NIFTI volume. Once you have
>> generated your results you can convert them back to CIFTI for
>> visualization. If you need to consider the spatial relationships
>>between
>> the data, you really need to be using a CIFTI aware tool for this kind
>>of
>> thing. Smoothing a CIFTI file is a good example of an operation that
>> considers spatial neighbors, and we have implemented an excellent
>> surface-based gaussian smoothing algorithm in wb_command. If the
>> operation you desire does not yet exist in wb_command, we would be
>> interested to know what it is. You can also split CIFTI files into 2
>> GIFTI surface and 1 NIFTI volume components using wb_command
>> -cifti-separate which you can separately analyze considering spatial
>> relationships in standard surface-based and volume-based analysis
>>streams.
>> At the end you can recombine the results into CIFTI using wb_command
>> -cifti-create-dense-timeseries.
>>
>> The goal of CIFTI is to model the sheet-like cortex as a surface but the
>> globular subcortical nuclei as volumes, as this is more
>>neurobiologically
>> valid than simply analyzing the whole brain as a volume. Also, CIFTI
>> saves a lot of computational space/time by focusing only on the grey
>> matter data of interest.
>>
>> What is it that you need coordinates for? The subcortical volume
>>portion
>> of the CIFTI has voxels defined and a mm transform in the header. The
>> surface data are defined on the vertex indices of our standard 32k mesh
>> and require a 32k mesh surface to get coordinates from (and the
>> coordinates will depend on what surface you use).
>
>In fact, I want to extract averaged time series across freesurfer
>parcellation (aparc.a2009s) to perform connectivity analysis. Maybe you
>have a better way to do this by keeping gifti format?
>
>> Peace,
>>
>> Matt.
>>
>> On 7/12/13 8:55 AM, "[email protected]" <[email protected]>
>> wrote:
>>
>>>Hello,
>>>I'm trying to convert fMRI time-series cifti file to nifti using the
>>>workbench command. I have obtained a 4D nifti file, but I do not
>>>understand its dimensions:
>>>dim1 32767
>>>dim2 3
>>>dim3 1
>>>dim4 1200
>>>The first correspond to grayordinates and the fourth to time points, but
>>>what about the second?
>>>Also, how can I find coordinates of grayordinates?
>>>Thank in advance for your help!
>>>Arnaud
>>>
>>>
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>>>HCP-Users mailing list
>>>[email protected]
>>>http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>>
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