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fmriPrep seems to ignore the single band image. #3350
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Single-band references will not be used in motion correction, since the contrast may differ strongly from the multiband BOLD. The single-band references are used for coregistration with other images (fieldmaps and T1w images). |
Thank you for your timely response. That's to say, the approach fMRIPrep uses is different from that of the HCP Pipelines. By the way, I have another important question maybe crucial for my own analysis. In my running command, I specified |
Yes. See https://neurostars.org/t/mcflirt-related-behavour-fmriprep-strange-motion-estimations-in-confounds-timeseries-tsv-lots-of-zeros/18037 for an investigation that led to this divergence.
The subcortical data is resampled to MNI152NLin6Asym, and the cortical data is sampled to the subject's surface and then mapped to fsLR using MSMsulc. This should very closely align with HCP. |
Thanks again~
Thanks. I think I still have some confusion, please help me correct if there is any mistake. Here is my understanding about how the cortical and subcortical data of .dtseries.nii is derived: |
Yes, that's right. As a minor clarification, the MNI resampling happens in a single interpolation from the original BOLD data. It's effectively the same as resampling BOLD to T1w and then the result to MNI, but with less opportunity for numerical error. |
Thank you very much for your reply and my confusion was addressed! |
What do you mean source space? You mean use targets other than fsLR and MNI152NLin6Asym? |
I'm sorry for the ambiguous description. What I mean is that specifying the generation of cortical and subcortical data in .dtseries.nii files. For example, cortical data could be derived from fMRI volume that aligned with the MNI space (like the HCP Pipelines do), or subcortical data could come from the individual’s native fMRI volume space. I think that there are various combinations of cortical and subcortical data. |
What happened?
I'm using fMRIPrep to process HCP-YA data, which includes single band reference (SBRef) images. However, I've noticed that the SBRef images were not utilized during the motion correction process.
Below is the input data I used.
What command did you use?
What version of fMRIPrep are you running?
24.0.0
How are you running fMRIPrep?
Docker
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
Here is the actual command that was executed (monitored by ps command). mcflirt -in /data/sub-100307/func/sub-100307_task-rest_dir-RL_run-1_bold.nii.gz \ -out /work/fmriprep_24_0_wf/sub_100307_wf/bold_task_rest_dir_RL_run_1_wf/bold_fit_wf/bold_hmc_wf/mcflirt/sub-100307_task-rest_dir-RL_run-1_bold_mcf.nii.gz \ -reffile /work/fmriprep_24_0_wf/sub_100307_wf/bold_task_rest_dir_RL_run_1_wf/bold_fit_wf/hmc_boldref_wf/gen_avg/sub-100307_task-rest_dir-RL_run-1_bold_average.nii.gz \ -mats -plots -rmsabs -rmsrel
Additional information / screenshots
Here I post some of the methods report generated by fmriprep. I think the message suggests that the sbref.nii.gz image was not used during motion correction.
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