Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

Great that's quick! On Mon, Apr 22, 2019 at 9:09 PM Glasser, Matthew wrote: > A few weeks maybe if you want a pre-release version. > > Matt. > > From: Yizhou Ma > Date: Monday, April 22, 2019 at 9:06 PM > To: Matt Glasser > Cc: "hcp-users@humanconnectome.org" > Subject: Re: [HCP-Users]

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

A few weeks maybe if you want a pre-release version. Matt. From: Yizhou Ma mailto:maxxx...@umn.edu>> Date: Monday, April 22, 2019 at 9:06 PM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org"

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

Thank you Matt. This is really helpful. Any idea when the new classifier you mentioned in 1. will be available? On Mon, Apr 22, 2019 at 8:50 PM Glasser, Matthew wrote: > I guess I haven’t been in the habit of throwing out data like this. > Things I would consider would include: > >1. MR+FIX

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

I guess I haven’t been in the habit of throwing out data like this. Things I would consider would include: 1. MR+FIX classification accuracy (if runs were poorly classified, they won’t be denoised well). I’ll note that we are training an improved MR+FIX classifier using a combination of

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

Thank you Matt. Do you have some suggestions for the metrics to use to determine scan quality after ICA FIX? Thanks, Cherry On Mon, Apr 22, 2019 at 8:15 PM Glasser, Matthew wrote: > I would decide after cleaning with MR ICA+FIX if you actually have to > exclude the scans and run with them all.

Re: [HCP-Users] Multi-run ICA-FIX with excessive movement

I would decide after cleaning with MR ICA+FIX if you actually have to exclude the scans and run with them all. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Yizhou Ma mailto:maxxx...@umn.edu>> Date: Monday, April 22, 2019 at 3:47 PM To:

[HCP-Users] Multi-run ICA-FIX with excessive movement

Dear HCP experts, I am writing for a question with multi-run ICA-FIX for my dataset. I have 4 resting state scans (TR=0.8, length=6.5min each) and 3 task scans (TR=0.8, length=6min each) that I intend to run multi-run ICA-FIX on. We used Euclidean norm values to threshold volumes with excessive

Re: [HCP-Users] unequal length of movement regressors

We have seen this occur on rare occasions, and don’t have an explanation for it. Try just running fMRIVolume again. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine

Re: [HCP-Users] Diffusion Preprocessing Failure

I haven't used eddy, but since it looks like an output file, my first thought is permissions - does that folder exist, and can the user you are running the eddy job as write files to it? Does a file with that name exist, and not have write permissions? Tim On Mon, Apr 22, 2019 at 11:39 AM

[HCP-Users] unequal length of movement regressors

Hi, Is there a reason why movement_regressors.txt might have unequal length of columns (i.e. timepoints)? I have seen this happen (infrequently) in different runs for different subjects for some HCP-style data we collected. Preprocessing was done using v3.27.0 Moataz

Re: [HCP-Users] wb_command -metric-tfce

For the most part, it exists because I was testing a new method for computing the TFCE transform itself (it is an integral containing cluster size which other utilities generally approximate by using many different thresholds). We do not currently do statistical testing within wb_command. Tim

[HCP-Users] Diffusion Preprocessing Failure

Hello, I am attempting to run the diffusion preprocessing with HCP version 3.27.0 with the GPU enabled eddy, however I receive an error that "eddy_unwarped_Neg" could not be opened, see below: START: eddy_postproc JAC resampling has been used. Eddy Output is now combined. Image Exception :

Re: [HCP-Users] DeDriftAndResamplePipeline error

OK, thank you very much. You guys are doing an awesome work! Leah. > On Apr 20, 2019, at 5:18 PM, Harms, Michael wrote: > > > That particular error message can be ignored. We’ll fix the scripts so that > it doesn’t occur in the future. > > Cheers, > -MH > > -- > Michael Harms, Ph.D. >