[RESOLVED] Resting state networks for concatenated bold runs (ICAFix+MSMAll)

Use Questions
1

Hi! I have another use question related to the ICA+Fix and MSMAll steps of the HCP pipeline.

I’m interested in getting the MSMAll aligned resting state networks (RSNs) from my bold runs. I am able to run the HCP preprocessing steps, and also hcp_icafix and hcp_msmall without any errors.

I did not supply hcp_icafix_bolds to hcp_icafix. I also did not supply hcp_icafix_bolds or hcp_msmall_bolds to hcp_msmall. Based on the documentation, my understanding is that this should lead to all bold runs getting concatenated into fMRI_CONCAT_ALL. I don’t have any task-BOLD runs, just 2 rest state runs.

This results in two .dscalar.nii files in MNINonLinear/fsaverage_LR32k

  • 100307_3T.individual_RSNs_d40_MSMAll_InitialReg_1_d40_WRN.32k_fs_LR.dscalar.nii
  • 100307_3T.individual_RSNs_d40_MSMAll_InitialReg_2_d40_WRN.32k_fs_LR.dscalar.nii

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image800×236 28.7 KB

If I’m interpreting this correctly, these are the RSNs from the two bold runs separately (1,2), but not the concatenated fMRI_CONCAT_ALL.

  1. Am I interpreting this correctly
  2. How can I get the RSNs from the concatenated bold runs? Should I specify hcp_icafix_bolds or hcp_msmall_bolds differently?

Attaching the log files and my batch file here:

batch.txt (5.8 KB)
done_hcp_msmall_fMRI_CONCAT_ALL_100307_3T_2025-04-03_02.13.36.540632.log (1.9 MB)
done_hcp_icafix_fMRI_CONCAT_ALL_100307_3T_2025-04-02_17.30.34.092709.log (30.1 KB)

Thanks for the support!

All the best,
Dustin

2

Hi Dustin,

I am not 100% sure, but I think your assumptions are correct. It seems like RSN outputs are not generated for the concatenated results, which can be found in the MNINonLinear/Results subfolder. In there you have the fMRI_CONCAT_ALL for all BOLDs and fMRI_REST for rest bolds, since you have only rest data this is irrelevant for you.

I never used RSNs in my analyses so I cannot really help you out here. Maybe you can ask on the HCP Users Group since these question is more down their alley. Maybe simply averaging the two RNSs for your BOLDs is what you are looking for and gives the “same” result as getting RSNs from a concatenated BOLD?

I regularly use fMRI_CONCAT_ALL and fMRI_REST outputs though, for example to parcellaate and then create functional resting-state connectomes.

Best, Jure

3

Makes sense, thank you. Do you know if the input to MSMAll takes the individual or concatenated BOLDs?

4

I would say both, as you get MSMAll results/outputs both for individual BOLDs and for the concatenated fMRI_CONCAT_All. Also there are two input parameters to the HCP MSMAll one for the ICAFix concat name and the other for used BOLDs.

Best, Jure

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