Re: [HCP-Users] ICA+FIX error

sity School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave.Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: on behalf of Marta Moreno > > Date: Sunday, March 31, 2019 at 6:44 PM > To

Re: [HCP-Users] ICA+FIX error

South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of Marta Moreno Date: Sunday, March 31, 2019 at 6:44 PM To: HCP Users Subject: [HCP-Users] ICA+FIX error Dear Experts, I am running hip_fix

Re: [HCP-Users] ICA+FIX error

> Subject: [HCP-Users] ICA+FIX error Dear Experts, I am running hip_fix and getting the following error with just one of my subjects, please see below. It seams the script stoped at the end, in section "Rename some files (relative to the default names coded in fix_3_clean)”, first

[HCP-Users] ICA+FIX error

Dear Experts, I am running hip_fix and getting the following error with just one of my subjects, please see below. It seams the script stoped at the end, in section "Rename some files (relative to the default names coded in fix_3_clean)”, first line: "$FSLDIR/bin/immv

[HCP-Users] ICA+FIX not running

Dear Experts, I downloaded the ICAFIX HCPpipelines v4.0.0 and installed fsl 6.0.1. I am running the hcp_fix_multi_run option and getting the following message (see below). What am I doing wrong? bash-3.2$ hcp_fix_multi_run RS_fMRI_1/RS_fMRI_1.nii.gz@RS_fMRI_2/RS_fMRI_2.nii.gz RS_fMRI_MR

Re: [HCP-Users] ICA FIX output missing

, Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ICA FIX output missing Dear Tim, True, it had not been added to the path. Now I added

Re: [HCP-Users] ICA FIX output missing

<mailto:lto...@stanford.edu> | (650) 5615738 From: Timothy Coalson Date: Tuesday, February 26, 2019 at 4:38 PM To: Leonardo Tozzi Cc: "Harms, Michael" , "Glasser, Matthew" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] ICA FIX output missing

Re: [HCP-Users] ICA FIX output missing

Email: mha...@wustl.edu From: "Glasser, Matthew" Date: Tuesday, February 26, 2019 at 8:19 PM To: NEUROSCIENCE tim , Leonardo Tozzi Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] ICA FIX output missing Regarding task analysis,

Re: [HCP-Users] ICA FIX output missing

rs@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ICA FIX output missing That is saying that you don't have the matlab gifti library installed (or it isn't on your matlab path). Tim On Tue, Feb 26, 2019 at 6:09 PM

Re: [HCP-Users] ICA FIX output missing

| Postdoctoral Fellow > > Stanford University | 401 Quarry Rd > > lto...@stanford.edu | (650) 5615738 > > > > > > *From: *"Harms, Michael" > *Date: *Tuesday, February 26, 2019 at 7:37 AM > *To: *"Glasser, Matthew" , Leonardo Tozzi < > l

Re: [HCP-Users] ICA FIX output missing

...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" Date: Tuesday, February 26, 2019 at 7:37 AM To: "Glasser, Matthew" , Leonardo Tozzi , "hcp-users@humanconnectome.org" Cc: "Burgess, Gregory" Subject: Re: [HCP-Users] ICA FIX o

Re: [HCP-Users] ICA FIX output missing

.edu From: "Glasser, Matthew" Date: Monday, February 25, 2019 at 6:53 PM To: Leonardo Tozzi , "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] ICA FIX output missing You’ll want to be using wb_command 1.3.2. I am not aware of any modificatio

Re: [HCP-Users] ICA FIX output missing

to:lto...@stanford.edu>> Date: Monday, February 25, 2019 at 5:09 PM To: "Harms, Michael" mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users

Re: [HCP-Users] ICA FIX output missing

2019 at 9:59 AM To: Leonardo Tozzi , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] ICA FIX output missing Hi, The log files for ICA FIX are a bit scattered. In the .ica directory check: .fix_2b_predict.log (from the prediction – i.e,. R code) and .fix.log (from the cleaning s

Re: [HCP-Users] ICA FIX output missing

users@humanconnectome.org" Subject: [HCP-Users] ICA FIX output missing Dear Experts, I have been trying to use ICA FIX to denoise task data of a large number of subjects from the HYA release. I have managed to make it run with no errors on our local HPC cluster, but I still have one problem. In the vas

[HCP-Users] ICA FIX output missing

Dear Experts, I have been trying to use ICA FIX to denoise task data of a large number of subjects from the HYA release. I have managed to make it run with no errors on our local HPC cluster, but I still have one problem. In the vast majority of subjects, even if FIX works and produces a file

Re: [HCP-Users] ICA-FIX

5 AM To: Megan Ní Bhroin <nibhr...@tcd.ie<mailto:nibhr...@tcd.ie>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ICA-FIX Hi - I would th

Re: [HCP-Users] ICA-FIX

Hi - I would think the easiest and best thing to do would be just to apply more aggressive high-pass filtering to the already FIX-cleaned data. Was there a reason you didn't want to do that? It's not at all a problem that the less aggressive HP filter had already been applied before original

[HCP-Users] ICA-FIX

Hi there, I'm very new to Neuroimaging but wondering if you could help me with some issues I am having. I want to run the ICA FIX pipeline on HCP resting state data. I wish to do this as I would like to apply a more aggressive temporal filtering than is already in place. Do you have any

Re: [HCP-Users] ICA+FIX cleanup scripts

gt; > Date: Sunday, October 29, 2017 at 12:03 PM > To: Matt Glasser <glass...@wustl.edu <mailto:glass...@wustl.edu>> > Cc: HCP Users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: Re: [HCP-Users] ICA+FIX cleanup scripts > &g

Re: [HCP-Users] ICA+FIX cleanup scripts

ectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] ICA+FIX cleanup scripts Thanks for your answer. I just want to use the “hcp_fix" script for clean up of resting state data after HCP pipelines. I only need to know if I just need to run the “hcp_fix" on data

Re: [HCP-Users] ICA+FIX cleanup scripts

alf of Marta Moreno > <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> > Date: Sunday, October 29, 2017 at 9:11 AM > To: HCP Users <hcp-users@humanconnectome.org > <mailto:hcp-users@humanconnectome.org>> > Subject: [HCP-Users] ICA+FIX cleanup scripts

Re: [HCP-Users] ICA+FIX cleanup scripts

ectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] ICA+FIX cleanup scripts Dear experts, I would like to use ICA+FIX cleanup after HCP minimal preprocessing pipelines on high quality resting-state data acquired with a GE scanner. HCP minimal preprocessing is workin

[HCP-Users] ICA+FIX cleanup scripts

Dear experts, I would like to use ICA+FIX cleanup after HCP minimal preprocessing pipelines on high quality resting-state data acquired with a GE scanner. HCP minimal preprocessing is working fine and installed locally. I have downloaded now the tar file with ICA+FIX cleanup scripts. Could

Re: [HCP-Users] ICA+FIX set up to run

..@loni.usc.edu<mailto:joey.contre...@loni.usc.edu>> Date: Friday, October 27, 2017 at 2:14 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] ICA+FIX s

[HCP-Users] ICA+FIX set up to run

Hello I am trying to run ICA+FIX on my data (thats already been preprocessed using structural and functional HCP pipelines). I wanted to clarify that if you already have a matlab license with the signal toolbox you do not need MATLAB Runtime Component or to install Octave (per my understanding

Re: [HCP-Users] ICA-FIX HP200 training data

Great, thank you! From: Stephen Smith [st...@fmrib.ox.ac.uk] Sent: Monday, November 07, 2016 2:36 PM To: Ely, Benjamin Cc: HCP-Users@humanconnectome.org Subject: Re: [HCP-Users] ICA-FIX HP200 training data Hi - try the following: www.fmrib.ox.ac.uk/~steve/ftp

Re: [HCP-Users] ICA-FIX HP200 training data

Hi - try the following: www.fmrib.ox.ac.uk/~steve/ftp/HCP20_hp200.RData Cheers > On 7 Nov 2016, at 17:45, Ely, Benjamin wrote: > > Hi HCP team, > > I'm interested in comparing the performance of ICA-FIX using a 200s vs. 2000s > highpass filter cutoff for some

[HCP-Users] ICA-FIX HP200 training data

Hi HCP team, I'm interested in comparing the performance of ICA-FIX using a 200s vs. 2000s highpass filter cutoff for some locally-acquired HCP-like resting-state data, as suggested in a previous thread. The HCP wrapper for ICA-FIX includes a reference to a 200s training file, HCP_hp200.RData,