Conversion from NIFTI (.nii.gz) to CIFTI (dtseries.nii)

[Việt Lương Hoàng]

Hi all, 

Thank you for your work with wb_command. I am currently working on converting resting-state fMRI data from NIfTI format (.nii.gz) to .dtseries.nii. I tried doing this using my own script, but after conversion I noticed that some columns in the output (with shape T × D, where T is the number of time steps and D = 91,282) contain only zeros.

I’ve attached my script here. If there is a straightforward way to adjust it, that would be very helpful. Also, do I need a T1w file for this conversion, or is the resting-state fMRI NIfTI alone sufficient to generate the .dtseries.nii file?

[Glasser, Matthew]

This is the purpose of the HCP fMRI Pipelines.  Why are you trying to do this outside of them?

Matt.

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[Việt Lương Hoàng]

Hi Mattew, 

Because I want to run a script or command the terminal without download lots of external package (FSL, FreeSurfer). If it is not possible then I guess I might install everything and redo the conversion. 

Vào lúc 17:05:32 UTC-5 ngày Thứ Năm, 18 tháng 9, 2025, glas...@wustl.edu đã viết:

[Tim Coalson]

Cifti files are designed to represent cortical data using surface vertices.  To accurately map volume data to the surface, you need to have surface files for that subject.  We use freesurfer to generate these necessary surfaces (and the way we use freesurfer is our pipelines, which also use FSL, and MSM to register them, etc).

If you want your data properly converted to 91k grayordinates space, the HCP pipelines are the recommended way to get there (you need freesurfer plus additional pipeline code of some kind).

Tim

To view this discussion visit https://groups.google.com/a/humanconnectome.org/d/msgid/hcp-users/99c3f624-f486-4da2-9f29-e5f69c806356n%40humanconnectome.org.

[Glasser, Matthew]

Is this HCP data or your data?  If you don’t want to deal with setting up the HCP Pipelines environment, we recommend using the QuNex container: https://qunex.yale.edu.

 

Matt.

[Việt Lương Hoàng]

I want to do the conversion other datas not only HCP Data

Vào lúc 19:12:58 UTC-5 ngày Thứ Năm, 18 tháng 9, 2025, glas...@wustl.edu đã viết:

[Glasser, Matthew]

Using the HCP Pipelines in QuNex is your best bet then.  If you want advice on that, post the specs of your data.