Re: [HCP-Users] PALM Viewing results

Thank you Tim. I agree about effect size maps being better, but reviewers always want to know what is significant (they are set in their ways!!) So maybe we can do both; an effect size map and then .95-1 in the corr p map? On Mar 16, 2018, at 4:59 PM, Timothy Coalson

Re: [HCP-Users] PALM Viewing results

You can do whatever you need to to satisfy your reviewers, of course. Showing both in one panel was the idea behind turning the significant regions into label outlines. Take a look at page 5 here: https://wustl.app.box.com/s/ti46uqqlukqnh4u97aw74r53r7p8xu3c In this case, the very large group

Re: [HCP-Users] Fw:

Load both of the volumes into wb_view (high-res mask and low-res fMRI - you may want to separate out a single frame from the fMRI to keep memory usage down) and see if they align with each other (if they don't display correctly, turn on oblique volume drawing mode). If they do align, the answer

Re: [HCP-Users] PALM Viewing results

Since the extent that passes significance tests is dependent on number of subjects and other statistical power considerations, we instead recommend viewing the effect size (beta) map. You can overlay outlines of what passed the significance threshold by making that into a label file with

Re: [HCP-Users] Fw:

Perhaps if this were done with wb_command -volume-resample it would work better, but Tim would have to comment on this. Matt. From: HERACLES PANAGIOTIDES > Date: Friday, March 16, 2018 at 12:11 PM To: Matt Glasser >

[HCP-Users] index.txt file truncated before run_eddy

To Whom it may concern, I am attempting to run the diffusion processing pipeline, by using the scripts from the Washington University github. In particular, I am using the DiffusionPreprocessingBatch.sh script, from the Examples folder. We successfully managed to run the structural

Re: [HCP-Users] HCP Pipeline without T2w

Thanks for the recommendation Matt! Pedro, the ciftify toolbox link is here (https://edickie.github.io/ciftify). The toolbox started with exactly with what you are suggesting (modifying the .sh files to make them run without T2w images). Over time we ended up translating the key parts to python

[HCP-Users] PALM Viewing results

Hi, In documentation for randomise, when viewing the 1-p results in FSLView the min/max display range should be set to 0.95/1.0 so that values less than 0.95 (equivalent to p>0.05) are not shown. If these are corrected values (i.e. corrp) then the visible areas correspond to the statistically

[HCP-Users] MEG processing pipelines

Dear HCP experts, In the context of my PhD thesis (using HCP data), I had some questions about MEG processing pipelines. In my research, I somehow need the MEG data during motor task, in the source space (i.e. after beamforming), for each trial and each individual separately. It seems that the

Re: [HCP-Users] Is surface myelin map the same as the volume T1w/T2 map?

We don’t have such a method at this time. Peace, Matt. From: Xavier Guell Paradis > Date: Thursday, March 15, 2018 at 6:50 PM To: Matt Glasser >,

Re: [HCP-Users] HCP Pipeline without T2w

I would recommend the ciftify toolbox if your data do not meet HCP Pipelines acquisition requirements (lacking highres T2w scan and or Fieldmap). The ciftify toolbox is currently beta, but should be fully available in the very near future (Erin Dickie the author is CCed and can give more

Re: [HCP-Users] Fw:

Why can’t you use an MNI space accumbens mask? Peace, Matt. From: > on behalf of HERACLES PANAGIOTIDES > Date: Friday, March 16, 2018 at 8:04 AM To: HCP

[HCP-Users] HCP Pipeline without T2w

Dear all, I have a dataset that I wish to use with the HCP pipeline scripts from the repository in https://github.com/Washington-University/Pipelines, but I don't have the T2w images for the subjects. Is it possible (perhaps with some modification on the .sh files) to use pipeline without the