I recently received some questions about the NYU cocaine dataste and wanted to post them here in case the answers are of help to anyone else.

 1.The rest-state fmri data have already  transformed into MNI152 3mm standard space by non-linear transformation  as well as linear. Were those fmri data directly transformed into MNI space, or “linear registration of functional to structural images (with intermediate registration to a low-resolution image and b0 unwarping); nonlinear registration of structural images to the MNI152 template” （Kelly et al, 2010）？

Answer. Yes, the data have been transformed to MNI152 space using the methods outlined in Kelly et al., 2010: 


2."The 23 youngest male and 2 female cocaine-dependent participants are group-matched ......" As there are 3 female cocaine-dependent participants, which 2 female are group-matched?


Answer. I will have to check on this and post again later. By group-matched, we mean that there are no differences between the two groups in terms of sex and other demographic variables - individuals participants were not matched to one another.

3. The  INDI cocaine dataset has already been preprocessed and transformed into standard space. Without motion parameters, regression of nuisance covariates would be incomplete. Will the 6 motion parameters obtained during motion correction step be available in the future?

Answer. Motion correction has not been performed. The only preprocessing steps performed on the data were:
 

• Removal of the first 4 timepoints
• Slice-timing correction (for ascending interleaved acquisition)
• Reorientation to RPI
• Registration to T2-style image and b0 unwarping
• Linear and non-linear transformation to MNI152 3mm space

Hope that helps!
Clare

Thanks indeed.

1> so, which one using the methods outlined in Kelly et al., 2010, NYU_Cocaine.FLIRT.LiteNIFTI or NYU_Cocaine.FNIRT.LiteNIFTI?

3>As data have already been transformed into standard space, it is impossible to perform motion correction. Thus, we cannot get 6 motion parameters.
May you provide the 6 motion parameters so that we can perform regression of nuisances?

Hi Ci-long,

Sorry, I meant to give more complete details about the registration.

We performed a linear registration of the functional to structural images (with intermediate registration to a low-resolution t2-like image and b0 unwarping). For registration of structural to MNI152 template, the data included in the FLIRT directory was registered using a 12 degrees of freedom linear affine transformation. For the data included in the FNIRT directory, this linear registration was further refined wth nonlinear registration (FNIRT). The functional data were transformed to MNI152 space using a concatenation of the functional-to-structural and structural-to-MNI transforms.

Regarding the motion correction, we hadn't previously appreciated the effect of normalization on motion - we will rectify this situation soon, probably by uploading the motion parameters.

Finally, regarding the number of males and females, it appears that I made a mistake in the counts - there are indeed 3 females in the cocaine group. But, as I mentioned, the groups are group-matched on demographics, and, given that there are 4 females in the control group, this only means that the groups are better matched than we thought!

Cheers,
Clare

Thanks for your answer and data sharing.

We are looking forward to those motion parameters