Well, I would also recommend rerunning fMRIVolume if you have spin echo field maps as there are some improvements there too. PreFreeSurfer and FreeSurfer would not need to be rerun.
Peace, Matt. On 11/29/17, 4:35 PM, "[email protected] on behalf of Durgerian, Sally" <[email protected] on behalf of [email protected]> wrote: >Thanks, Matt, >Sorry I hadn’t upgraded to the latest version. Does that mean I have to >re-run all 300 subjects through everything, or can I just re-run the >scripts that involve surfaces? >Sally >On Nov 29, 2017, at 3:37 PM, Glasser, Matthew ><[email protected]<mailto:[email protected]>> wrote: > >ATTENTION: This email originated from a sender outside of MCW. Use >caution when clicking on links or opening attachments. >________________________________ > >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]<mailto:hcp-users-bounces@humanconne >ctome.org> on behalf of >Durgerian, Sally" ><[email protected]<mailto:hcp-users-bounces@humanconne >ctome.org> on behalf of >[email protected]<mailto:[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]><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://urldefense.proofpoint.com/v2/url?u=https-3A__www.doc.ic.ac.uk_-7Ee >cr05_MSM-5FHOCR-5Fv2&d=DwIF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4 >Y&r=FnxR7WKbDxh2At2YW0pY1A&m=9fmlyIS3PcRe7TOic3TTMGglw<http://urldefense.p >roofpoint.com/v2/url?u=https-3A__www.doc.ic.ac.uk_-7Eecr05_MSM-5FHOCR-5Fv2 >&d=DwIF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFYPQkjgspw4Y&r=FnxR7WKbDxh2At2Y >W0pY1A&m=9fmlyIS3PcRe7TOic3TTMGglw>-C41dx0mYnTTsDqRf4&s=OH0o-RNDBVy8LMyJZ7 >Nbpa_62JFY9Igxtm_qcy4SPOk&e=<https://urldefense.proofpoint.com/v2/url?u=ht >tps-3A__urldefense.proofpoint&d=DwIF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4pVFY >PQkjgspw4Y&r=FnxR7WKbDxh2At2YW0pY1A&m=9fmlyIS3PcRe7TOic3TTMGglw-C41dx0mYnT >TsDqRf4&s=0ZARc0ymFOXHlxm7p5sVpIimNSONJkJgS58FZ4kruNA&e=. >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><mailto:hcp-users-bounces@humanconne >ctome.org<http://ctome.org>>> on behalf of "Fales, Christina L" ><[email protected]<mailto:[email protected]><mailto:Cfales@northwell >.edu>> >Date: Friday, June 30, 2017 at 12:30 PM >To: >"'[email protected]<mailto:[email protected]><mail >to:'[email protected]<mailto:[email protected]>>'" ><[email protected]<mailto:[email protected]><mailt >o:[email protected]>> >Cc: "Fales, Christina L" ><[email protected]<mailto:[email protected]><mailto:Cfales@northwell >.edu>> >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. 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Watertown Plank Rd. >Milwaukee WI 53226 > > > > > > > > >_______________________________________________ >HCP-Users mailing list >[email protected] >https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome. >org_mailman_listinfo_hcp-2Dusers&d=DwIF-g&c=aFamLAsxMIDYjNglYHTMV0iqFn3z4p >VFYPQkjgspw4Y&r=FnxR7WKbDxh2At2YW0pY1A&m=9fmlyIS3PcRe7TOic3TTMGglw-C41dx0m >YnTTsDqRf4&s=g5OTqq9odNsxUIlC6J6xBy3xqiuFOnrpw5Q9c12m6uA&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
