HCP 7T preprocessed data - how to apply head motion correction and censoring?

Dear all,

I am currently working with the HCP 7T minimally preprocessed dataset. Initially, I tried to preprocess the raw data (which the HCP also provides). However, I face too many problems in preprocessing their raw data with AFNI. The HCP information also states that their raw data is a bit special and requires more elaborated preprocessing methods. Since my knowledge is not sufficient to deal with all these problems inherent in their raw data, I went back to the minimally preprocessed data.

The HCP preprocessed data did not apply motion censoring thatI wanted to apply beside some further preprocessing steps in AFNI proc (such as bandpassing).
However, their functional runs are already aligned to MNI, hence I have to drop the volreg block in AFNI proc.
But the volreg block is required for head motion censoring, since the software needs to estimate head motion in the first place.

One can provide head motion data directly to


but HCP provides no head motion data.

The question now is: what can I do to apply head motion censoring in the preprocessed HCP data? Is there any option?

Hi Philipp,

Pass the motion file using -regress_motion_file.

  • rick

Hi Rick,

the problem is that they did not supply any head motion estimations for the 7T data at all.
However, after checking the data more, it looks as if their so-called minimally preprocessed data already included a perfect motion correction.
When I run through the single volumes, the brain looks almost perfectly static, i.e., there is almost zero motion.

This is what they state in their manual:

I just didn’t expect that their motion correction would be so good. Maybe after all motion correction or even censoring in AFNI is not required.

If motion registration has already been done, you certainly don’t want to ask AFNI to do it a second time. But still include the motion parameters in the regression, and censoring as may be appropriate. It would be pretty bad if they performed motion correction but did not provide any estimates with the output data. It should be available somewhere.

  • rick