Level3 .fsf pipelines

[KevinAquino]

Hi all,

I was wondering if the level 3 .fsf pipelines will be released in this repo? I would like to replicate some of the HCP findings, particularly the task related results in "Using temporal ICA to selectively remove global noise while preserving global signal in functional MRI data."

I have found https://github.com/Washington-University/HCPpipelines/blob/e60eb03aa106cc4cb57da8cbb78fc178889583a8/TaskfMRIAnalysis/TaskfMRILevel3.sh within the repo, but its 6 years old and I imagine a lot has changed since then!

[coalsont]

I don't know the definitive state of this, but apparently the script got moved to a different branch of the repo for whatever reason:

https://github.com/Washington-University/HCPpipelines/tree/level3-task-fmri-analysis/TaskfMRIAnalysis

[KevinAquino]

Cool! thanks Tim!

[mharms]

Hi, Yes, our internal version has definitely changed, but needs some work to be appropriate for public distribution. Plus, we mostly recommend using PALM for Level3 (group) analyses anyway.

Cheers, -MH

-- Michael Harms, Ph.D.

Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms@wustl.edu

From: Kevin M Aquino notifications@github.com Reply-To: Washington-University/HCPpipelines reply@reply.github.com Date: Wednesday, August 21, 2019 at 6:32 PM To: Washington-University/HCPpipelines HCPpipelines@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [Washington-University/HCPpipelines] Level3 .fsf pipelines (#127)

Hi all,

I was wondering if the level 3 .fsf pipelines will be released in this repo? I would like to replicate some of the HCP findings, particularly the task related results in "Using temporal ICA to selectively remove global noise while preserving global signal in functional MRI data."

I have found https://github.com/Washington-University/HCPpipelines/blob/e60eb03aa106cc4cb57da8cbb78fc178889583a8/TaskfMRIAnalysis/TaskfMRILevel3.sh within the repo, but its 6 years old and I imagine a lot has changed since then!

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHubhttps://github.com/Washington-University/HCPpipelines/issues/127?email_source=notifications&email_token=AA5TABROX7FB2C3ZZ7TLSI3QFXGAVA5CNFSM4IOPINDKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HGUUSCA, or mute the threadhttps://github.com/notifications/unsubscribe-auth/AA5TABS4HASE6SU4MYS3WLTQFXGAVANCNFSM4IOPINDA.

---

The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

[KevinAquino]

Great!

I had a look at: https://store.humanconnectome.org/courses/2018/exploring-the-human-connectome.php and the tutorial seems to explain the steps quite nicely! (really great write up in the pdf!)

Out of interest while I have both of you - in the manuscript (tICA) the analysis of the task fMRI at group level looks like it is using PALM for group analysis. However there is no explanation if any covariates were taken into account (when taking 100 subsets with 28 subjects), is this true or have I missed something! thanks!

[glasserm]

We did not use PALM for this analysis, but rather a version of this level 3 script.

[KevinAquino]

Great thanks @glasserm ! Is there anything special about the level3 design template? Although I can find the templates for the level 3 analysis, the .fsf files are not in repository thanks!

[glasserm]

design_template449.txt

You have to manually edit it to the correct number of subjects.

[KevinAquino]

Great thank you for that!