Dear HCP gurus; I’m writing about step 3 below. I have run some of my own data through the HCP pipelines, and they have worked well when I use RegName=“FS”. However, when I try to use RegName=“MSMSulc” the script can’t find this file: allparameterssulcDRconf I have been unable to find this file anywhere - not in the Pipelines-master directory nor in the MSM_HOCR_v2 directory (downloaded from your link, below). The MSM_HOCR_v2 directory has the following config files: config_MSMsulc_pairwise, configMSMSulc_strain, MSMAll_config_STRAIN, and a file of size 0 named allparameterssulcDRconfStage1to4. Please advise whether I should use one of the alternate files named above, or where I can find allparameterssulcDRconf. Thanks so much, Sally
On Jun 30, 2017, at 3:19 PM, Glasser, Matthew <[email protected]<mailto:[email protected]>> wrote: You can give MSMSulc and MSMAll a try if you wish using the latest version of the HCP pipelines and the MSM binary, which is here: https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v2<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.doc.ic.ac.uk_-7Eecr05_MSM-5FHOCR-5Fv2&d=DwMF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=FnxR7WKbDxh2At2YW0pY1A&m=CzDp4Ukmm8OuwpwAp9eYjkBN0s8CYTBMIoP_fut4qhA&s=x-zvb7DUgSc7Ck0jE53IXlmoNQSeuA5YIMIg6jL5Zb4&e=>/ Here is the recommended order of pipelines: 1. PreFreeSurfer 2. FreeSurfer 3. PostFreeSurfer (using MSMSulc) 4. fMRIVolume 5. fMRISurface 6. ICA+FIX 7. MSMAll (Do MSM Surface Registration) 8. GroupDeDrift (Compute and Group drift, can skip if you don’t want to) 9. DedriftAndResample (Apply MSMAll) 10. *Global Noise Removal* (not available publicly yet, but will handle residual global noise in the data without removing the global signal) 11. Resting state analysis For a resting state analysis, you could do something like dual regression and fslnets to make netmats. You could use the HCP’s multi-modal parcellation to parcellate the MSMAll aligned dense timeseries into a parcellated timeseries, and then use fslnets to estimate functional connectivity (can be either full correlation or partial correlation—which is better if step 10 has not been done). You can also use the MIGP algorithm to combine resting state fMRI data across subjects for group ICA or group dense functional connectivity. You can use wb_command -cifti-correlation to compute functional connectivity. Peace, Matt. From: <[email protected]<mailto:[email protected]>> on behalf of "Fales, Christina L" <[email protected]<mailto:[email protected]>> Date: Friday, June 30, 2017 at 12:30 PM To: "'[email protected]<mailto:'[email protected]>'" <[email protected]<mailto:[email protected]>> Cc: "Fales, Christina L" <[email protected]<mailto:[email protected]>> Subject: [HCP-Users] Resting State processing Hi HCP gurus: I’ve been trying to adapt the HCP pipeline for use in our group, and having trouble with the tools for resting state processing. The pipeline’s Example programs are super helpful for illustrating calls to the minimal preprocessing and the Task-fMRI tools. However the resting-fMRI tools are organized differently, with no example calling program provided. I wonder if I could get a few tips? I am using pipeline version v3.22.0-beta.2, and I have so far successfully run pipeline modules on HCP subjects as well as our own: PreFreesurferPipeline.sh FreesurferPipeline.sh PostFreesurferPipeline.sh GenericfMRIVolumeProcessingPipeline.sh GenericfMRISurfaceProcessingPipeline.sh ICA-FIX I know that after ICA-Fix I could continue with a group analysis using Dual Regression and FSLnets. But how to proceed if one wanted to do a seed-based analysis? I’m not sure I see the purpose of PostFix, ReApplyFix and RestingStateStats. They rely on compiled matlab code, so it is hard to figure out what they are actually doing. Regardless, I tried running RestingStateStats, but it triggered an error when it could not find a file apparently created by MSMSulc. (I assume this is because I ran earlier parts of the pipeline with RegName=”FS”). When I tried to rerun PostFreesurferPipeline.sh with RegName=”MSMSulc”, it seems that our version of the pipeline does not include an MSM binary. I have searched the HCP website but don’t see where this binary is available. Alternatively, if I download the available MSMAll, can it be used with pipeline version 3.22? Unfortunately with all of the excellent documentation on the HCP website, there is a dearth of *high-level* guidance on how to proceed with resting-state processing. I’d be grateful for any insights… Thanks, Christina Fales _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwMF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=FnxR7WKbDxh2At2YW0pY1A&m=CzDp4Ukmm8OuwpwAp9eYjkBN0s8CYTBMIoP_fut4qhA&s=aXr9H0WE1PQNdPvoblg2MhD-gZud-z0TJ6DKaYJBF8U&e=> The information contained in this electronic e-mail transmission and any attachments are intended only for the use of the individual or entity to whom or to which it is addressed, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. 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Receipt by anyone other than the intended recipient is not a waiver of any attorney-client, physician-patient or other privilege. _______________________________________________ HCP-Users mailing list [email protected]<mailto:[email protected]> http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DwQF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=FnxR7WKbDxh2At2YW0pY1A&m=CzDp4Ukmm8OuwpwAp9eYjkBN0s8CYTBMIoP_fut4qhA&s=aXr9H0WE1PQNdPvoblg2MhD-gZud-z0TJ6DKaYJBF8U&e=> Sally Durgerian Neurolab G2415 Medical College of Wisconsin 8701 W. Watertown Plank Rd. Milwaukee WI 53226 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
