Make sure you have the latest version of the HCP Pipelines and then this should work.
Peace, Matt. On 11/29/17, 1:11 PM, "[email protected] on behalf of Durgerian, Sally" <[email protected] on behalf of [email protected]> wrote: >Dear HCP gurus; >I¹m 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=³FS². >However, when I try to use RegName=³MSMSulc² the script can¹t 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=C >zDp4Ukmm8OuwpwAp9eYjkBN0s8CYTBMIoP_fut4qhA&s=x-zvb7DUgSc7Ck0jE53IXlmoNQSeu >A5YIMIg6jL5Zb4&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 don¹t 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 HCP¹s 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:hcp-users-bounces@humanconne >ctome.org>> 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: >I¹ve been trying to adapt the HCP pipeline for use in our group, and >having trouble with the tools for resting state processing. The >pipeline¹s 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? I¹m 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=²FS²). >When I tried to rerun PostFreesurferPipeline.sh with RegName=²MSMSulc², >it seems that our version of the pipeline does not include an MSM binary. >I have searched the HCP website but don¹t 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. I¹d be grateful for any insightsŠ >Thanks, >Christina Fales > >_______________________________________________ >HCP-Users mailing list >[email protected]<mailto:[email protected]> >http://lists.humanconnectome.org/mailman/listinfo/hcp-users<https://urldef >ense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_li >stinfo_hcp-2Dusers&d=DwMF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y& >r=FnxR7WKbDxh2At2YW0pY1A&m=CzDp4Ukmm8OuwpwAp9eYjkBN0s8CYTBMIoP_fut4qhA&s=a >Xr9H0WE1PQNdPvoblg2MhD-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. >If the reader of this communication is not the intended recipient, or the >employee or agent responsible for delivering this communication to the >intended recipient, you are hereby notified that any dissemination, >distribution, copying or disclosure of this communication and any >attachment is strictly prohibited. If you have received this transmission >in error, please notify the sender immediately by telephone and >electronic mail, and delete the original communication and any attachment >from any computer, server or other electronic recording or storage device >or medium. 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://urldef >ense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_li >stinfo_hcp-2Dusers&d=DwQF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y& >r=FnxR7WKbDxh2At2YW0pY1A&m=CzDp4Ukmm8OuwpwAp9eYjkBN0s8CYTBMIoP_fut4qhA&s=a >Xr9H0WE1PQNdPvoblg2MhD-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 _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
