Thanks for your response, Michael. The issue with single ICA+ FIX is solved
after running fMRISurface again.
The problem is now with MR ICA+FIX. I am copying the error below for your
convenience. Matt said is probably related to the fact that I am using a MAC.
bash-3.2$ hcp_fix_multi_run
RS_fM
Check RS_fMRI_2_hp2000.ica/.fix.log for clues. Also, what’s in the stderr
output from the run?
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 S
Did you update to the latest version of FIX from FSL’s website?
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Marta Moreno
mailto:mmorenoort...@icloud.com>>
Date: Sunday, March 31, 2019 at 6:44 PM
To: HCP Users
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Use
, 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
lto...@stanford.edu<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 FI
mailto:tsc...@mst.edu>>, Leonardo Tozzi
mailto:lto...@stanford.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA FIX output missing
a) It may give the same
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, I do
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 a
Tozzi, MD, PhD
>
> Williams PanLab | 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, Ma
University | 401 Quarry Rd
lto...@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"
Subj
.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
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] IC
ary 25, 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
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 stage).
And in the .ica/fix directory, check logMatlab.txt (I believe that is from the
feature extraction stage).
Note that ou
ers@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: 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 t
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 FI
sser mailto:glass...@wustl.edu>>
> Cc: HCP Users <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
Yes that is what we do.
Peace,
Matt.
From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Sunday, October 29, 2017 at 12:03 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: HCP Users
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA+FIX cleanup s
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 already preprocessed with HCP pipelines, after which
I get my clean dtseries.nii ready for FC analyses.
Much ap
I think there is a readme with instructions on set up. If you have specific
questions about those, ICA+FIX questions might be best asked on the FSL list,
as the FSL programmers don’t watch this list. Here we can answer questions
about CIFTI or approaching clean up of resting state data.
Peace
Indeed if you already have a matlab license and the toolboxes, it is probably
easier to use the interpreted matlab code.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Joey Contreras
mailto:joey.contre...@loni.usc.edu>>
Date: Friday, October 27, 2017 at 2:14 P
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
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 locally-acquired HCP-like resting
23 matches
Mail list logo
