Re: [HCP-Users] ICA+FIX error

[Marta Moreno]

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_fMRI_1/RS_fMRI_1.nii.gz@RS_fMRI_2/RS_fMRI_2.nii.gz RS_fMRI_MR 2000 TRUE
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - HCPPIPEDIR: 
/usr/local/bin/HCP/Pipelines
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - CARET7DIR: 
/Applications/workbench/bin_macosx64/
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSLDIR: /usr/local/fsl
Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSL_FIXDIR: 
/usr/local/bin/HCP/Pipelines/ICAFIX/hcp_fix_multi_run
readlink: illegal option -- f
usage: readlink [-n] [file …]

Thanks!,
Leah.



> On Apr 1, 2019, at 9:29 AM, Harms, Michael  wrote:
> 
>  
> 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 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 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 ${fmrihp}.ica/filtered_func_data_clean 
> ${fmrihp}_clean”, which could not find a supported file with prefix 
> ".ica/filtered_func_data_clean”
>  
> (…)
> Sun Mar 31 19:18:12 EDT 2019 - hcp_fix - Done running FIX
> Sun Mar 31 19:18:13 EDT 2019 - hcp_fix - ABORTING: Something went wrong;  
> RS_fMRI_2_hp2000.ica/Atlas_clean.dtseries.nii wasn't created
>  
> How can I solve this problem?
>  
> Thanks,
>  
> Leah.
>  
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 
>  
> 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.

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Re: [HCP-Users] ICA+FIX error

[Harms, Michael]

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 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 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 ${fmrihp}.ica/filtered_func_data_clean 
${fmrihp}_clean”, which could not find a supported file with prefix 
".ica/filtered_func_data_clean”

(…)
Sun Mar 31 19:18:12 EDT 2019 - hcp_fix - Done running FIX
Sun Mar 31 19:18:13 EDT 2019 - hcp_fix - ABORTING: Something went wrong;  
RS_fMRI_2_hp2000.ica/Atlas_clean.dtseries.nii wasn't created

How can I solve this problem?

Thanks,

Leah.


___
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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.

___
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Re: [HCP-Users] ICA+FIX error

[Glasser, Matthew]

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-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 ${fmrihp}.ica/filtered_func_data_clean 
${fmrihp}_clean”, which could not find a supported file with prefix 
".ica/filtered_func_data_clean”

(…)
Sun Mar 31 19:18:12 EDT 2019 - hcp_fix - Done running FIX
Sun Mar 31 19:18:13 EDT 2019 - hcp_fix - ABORTING: Something went wrong;  
RS_fMRI_2_hp2000.ica/Atlas_clean.dtseries.nii wasn't created

How can I solve this problem?

Thanks,

Leah.



___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users


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.

___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] ICA FIX output missing

[Glasser, Matthew]

Do the ciftiopen and ciftisave functions work in this environment?

Matt.

From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Thursday, February 28, 2019 at 3:04 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, 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 it, but I get the error 
(in .fix.log):


{^HError using read_gifti_file_standalone (line 20)

[GIFTI] Loading of XML file /tmp/tp1378796874179334.gii failed.



Error in gifti (line 71)

this = read_gifti_file_standalone(varargin{1},giftistruct);



Error in ciftiopen (line 31)

cifti = gifti([tmpfile '.gii']);



Error in fix_3_clean (line 46)

  BO=ciftiopen('Atlas.dtseries.nii',WBC);

}^H



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Tuesday, February 26, 2019 at 4:38 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, "Glasser, 
Matthew" 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

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 Leonardo Tozzi 
mailto:lto...@stanford.edu>> wrote:
Dear Michael,

Thank you very much for all the consideration on the use of FIX for the task 
data.

I have tried the addition you suggest. I think the command is detected, but I 
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:


{^HUndefined function or variable 'gifti'.

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H




Would you have any thoughts on this?
Thank you,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, 
Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Cc: "Burgess, Gregory" mailto:gburg...@wustl.edu>>
Subject: Re: [HCP-Users] ICA FIX output missing


Hi Leonardo,
Couple things:

1)  In the context of FIX, things get a little convoluted, since the FIX 
distribution has its own settings.sh file that needs to be set appropriately.  
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then 
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t 
necessarily relevant.  In the settings.sh file for FIX on our cluster, we use 
the following construction:

if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already 
in your path.

2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after 
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX, 
gets applied again with TaskfMRILevel1.sh.  This script needs to be modified to 
be smarter regarding the temporal filtering (i.e., provide an option to NOT 
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of 
the task regressor prior to the GLM, which means that variance removed during 
FIX can be reintroduced during the task GLM fitting (depending on the extent to 
which the space spanned by the noise regressors overlaps with the task GLM).

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: 
mha...@wustl.edu<mailto:mha...@wustl.edu>

From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Monday, February 25, 2019 at 6:53 PM
To: Leonardo Tozzi mailt

Re: [HCP-Users] ICA FIX output missing

[Leonardo Tozzi]

Dear Tim,


True, it had not been added to the path. Now I added it, but I get the error 
(in .fix.log):


{^HError using read_gifti_file_standalone (line 20)

[GIFTI] Loading of XML file /tmp/tp1378796874179334.gii failed.



Error in gifti (line 71)

this = read_gifti_file_standalone(varargin{1},giftistruct);



Error in ciftiopen (line 31)

cifti = gifti([tmpfile '.gii']);



Error in fix_3_clean (line 46)

  BO=ciftiopen('Atlas.dtseries.nii',WBC);

}^H



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
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 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 Leonardo Tozzi 
mailto:lto...@stanford.edu>> wrote:
Dear Michael,

Thank you very much for all the consideration on the use of FIX for the task 
data.

I have tried the addition you suggest. I think the command is detected, but I 
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:


{^HUndefined function or variable 'gifti'.

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H




Would you have any thoughts on this?
Thank you,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, 
Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Cc: "Burgess, Gregory" mailto:gburg...@wustl.edu>>
Subject: Re: [HCP-Users] ICA FIX output missing


Hi Leonardo,
Couple things:

1)  In the context of FIX, things get a little convoluted, since the FIX 
distribution has its own settings.sh file that needs to be set appropriately.  
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then 
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t 
necessarily relevant.  In the settings.sh file for FIX on our cluster, we use 
the following construction:

if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already 
in your path.

2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after 
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX, 
gets applied again with TaskfMRILevel1.sh.  This script needs to be modified to 
be smarter regarding the temporal filtering (i.e., provide an option to NOT 
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of 
the task regressor prior to the GLM, which means that variance removed during 
FIX can be reintroduced during the task GLM fitting (depending on the extent to 
which the space spanned by the noise regressors overlaps with the task GLM).

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: 
mha...@wustl.edu<mailto:mha...@wustl.edu>

From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Monday, February 25, 2019 at 6:53 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "Harms, 
Michael" mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto: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 modifications 
that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have 
analyzed hundreds of subjects after MR+FIX.

As for this issue, is wb_command set properly here: 
https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh

What about on your ${PATH}?

As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as testing 

Re: [HCP-Users] ICA FIX output missing

[Glasser, Matthew]

A) Sure but that isn’t a reason not to clean your task data.
B) This assumes there is noise in the task GLM, where is the noise coming from? 
 We have already demonstrated a clear benefit to cleaning your data with 
sICA+FIX before task analysis.  Therefore this has to be a secondary concern 
that may lead to an underestimate in the magnitude of this benefit.  Again, not 
a reason not to clean your task data.

Matt.

From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 8:42 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, Timothy 
Coalson 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 answer, but if for nothing else than speed of 
execution, TaskfMRILevel1.sh should be smarter and have an option to not apply 
a temporal filter a second time.

b) If it turns out that the space-spanned by the FIX noise components overlaps 
with the task GLM (for whatever reason), then noise will be re-introduced to 
some degree.  That’s simply the math.  You’re arguing that as a practical 
matter that won’t be the case, or that the effect will be tiny, which may 
indeed turn out to be the case, but that should be empirically demonstrated 
first.

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: 
mha...@wustl.edu<mailto:mha...@wustl.edu>

From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 8:19 PM
To: NEUROSCIENCE tim mailto:tsc...@mst.edu>>, Leonardo Tozzi 
mailto:lto...@stanford.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA FIX output missing

Regarding task analysis, I don’t really agree with Mike:

a) The sICA+FIX filter is essentially equivalent to a linear detrend whereas 
the task filter is more aggressive.  Thus, applying both is going to give 
essentially the same answer as applying the more aggressive one.
b) Because the noise component removal is done as a non-aggressive regression 
(where the neural signal is protected by the neural components) and the task 
design is noiseless, I don’t see how the task design will reintroduce noise.  
There could be statistical efficiency benefits to exactly replicating the 
regression on the task design, but these are likely to be small.  Overall, this 
is not an effect that should lead one to avoid cleaning data before running a 
task analysis, as the statistical benefits of cleaning are clear, both from the 
perspective of removing biases and reducing uncorrelated variance.

Matt.

From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Tuesday, February 26, 2019 at 6:37 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, 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

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 Leonardo Tozzi 
mailto:lto...@stanford.edu>> wrote:
Dear Michael,

Thank you very much for all the consideration on the use of FIX for the task 
data.

I have tried the addition you suggest. I think the command is detected, but I 
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:


{^HUndefined function or variable 'gifti'.

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H




Would you have any thoughts on this?
Thank you,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, 
Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Cc: "Burgess, Gregory" mailto:gburg...@wustl.edu>>
Subject: Re: [HCP-Users] ICA FIX output m

Re: [HCP-Users] ICA FIX output missing

[Harms, Michael]

a) It may give the same answer, but if for nothing else than speed of 
execution, TaskfMRILevel1.sh should be smarter and have an option to not apply 
a temporal filter a second time.

b) If it turns out that the space-spanned by the FIX noise components overlaps 
with the task GLM (for whatever reason), then noise will be re-introduced to 
some degree.  That’s simply the math.  You’re arguing that as a practical 
matter that won’t be the case, or that the effect will be tiny, which may 
indeed turn out to be the case, but that should be empirically demonstrated 
first.

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: 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 don’t really agree with Mike:

a) The sICA+FIX filter is essentially equivalent to a linear detrend whereas 
the task filter is more aggressive.  Thus, applying both is going to give 
essentially the same answer as applying the more aggressive one.
b) Because the noise component removal is done as a non-aggressive regression 
(where the neural signal is protected by the neural components) and the task 
design is noiseless, I don’t see how the task design will reintroduce noise.  
There could be statistical efficiency benefits to exactly replicating the 
regression on the task design, but these are likely to be small.  Overall, this 
is not an effect that should lead one to avoid cleaning data before running a 
task analysis, as the statistical benefits of cleaning are clear, both from the 
perspective of removing biases and reducing uncorrelated variance.

Matt.

From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Tuesday, February 26, 2019 at 6:37 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, 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

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 Leonardo Tozzi 
mailto:lto...@stanford.edu>> wrote:
Dear Michael,

Thank you very much for all the consideration on the use of FIX for the task 
data.

I have tried the addition you suggest. I think the command is detected, but I 
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:


{^HUndefined function or variable 'gifti'.

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H




Would you have any thoughts on this?
Thank you,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, 
Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Cc: "Burgess, Gregory" mailto:gburg...@wustl.edu>>
Subject: Re: [HCP-Users] ICA FIX output missing


Hi Leonardo,
Couple things:

1)  In the context of FIX, things get a little convoluted, since the FIX 
distribution has its own settings.sh file that needs to be set appropriately.  
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then 
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t 
necessarily relevant.  In the settings.sh file for FIX on our cluster, we use 
the following construction:

if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already 
in your path.

2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after 
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX, 
gets applied again with TaskfMRILevel1.sh.  This script needs to be modified to 
be smarter regarding the temporal filtering (i.e., provide an option to NO

Re: [HCP-Users] ICA FIX output missing

[Glasser, Matthew]

Regarding task analysis, I don’t really agree with Mike:

a) The sICA+FIX filter is essentially equivalent to a linear detrend whereas 
the task filter is more aggressive.  Thus, applying both is going to give 
essentially the same answer as applying the more aggressive one.
b) Because the noise component removal is done as a non-aggressive regression 
(where the neural signal is protected by the neural components) and the task 
design is noiseless, I don’t see how the task design will reintroduce noise.  
There could be statistical efficiency benefits to exactly replicating the 
regression on the task design, but these are likely to be small.  Overall, this 
is not an effect that should lead one to avoid cleaning data before running a 
task analysis, as the statistical benefits of cleaning are clear, both from the 
perspective of removing biases and reducing uncorrelated variance.

Matt.

From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Tuesday, February 26, 2019 at 6:37 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, 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

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 Leonardo Tozzi 
mailto:lto...@stanford.edu>> wrote:
Dear Michael,

Thank you very much for all the consideration on the use of FIX for the task 
data.

I have tried the addition you suggest. I think the command is detected, but I 
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:


{^HUndefined function or variable 'gifti'.

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H




Would you have any thoughts on this?
Thank you,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, 
Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Cc: "Burgess, Gregory" mailto:gburg...@wustl.edu>>
Subject: Re: [HCP-Users] ICA FIX output missing


Hi Leonardo,
Couple things:

1)  In the context of FIX, things get a little convoluted, since the FIX 
distribution has its own settings.sh file that needs to be set appropriately.  
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then 
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t 
necessarily relevant.  In the settings.sh file for FIX on our cluster, we use 
the following construction:

if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already 
in your path.

2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after 
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX, 
gets applied again with TaskfMRILevel1.sh.  This script needs to be modified to 
be smarter regarding the temporal filtering (i.e., provide an option to NOT 
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of 
the task regressor prior to the GLM, which means that variance removed during 
FIX can be reintroduced during the task GLM fitting (depending on the extent to 
which the space spanned by the noise regressors overlaps with the task GLM).

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: 
mha...@wustl.edu<mailto:mha...@wustl.edu>

From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Monday, February 25, 2019 at 6:53 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "Harms, 
Michael" mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA FIX output missing

You’ll want to be using wb_c

Re: [HCP-Users] ICA FIX output missing

[Timothy Coalson]

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 Leonardo Tozzi  wrote:

> Dear Michael,
>
>
>
> Thank you very much for all the consideration on the use of FIX for the
> task data.
>
> I have tried the addition you suggest. I think the command is detected,
> but I get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:
>
>
>
> {^HUndefined function or variable 'gifti'.
>
>
>
> Error in ciftiopen (line 31)
>
> cifti = gifti([tmpfile '.gii']);
>
>
>
> Error in fix_3_clean (line 46)
>
>   BO=ciftiopen('Atlas.dtseries.nii',WBC);
>
> }^H
>
>
>
>
>
> Would you have any thoughts on this?
>
> Thank you,
>
>
>
>
>
> Leonardo 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, Matthew" , Leonardo Tozzi <
> lto...@stanford.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> *Cc: *"Burgess, Gregory" 
> *Subject: *Re: [HCP-Users] ICA FIX output missing
>
>
>
>
>
> Hi Leonardo,
>
> Couple things:
>
>
>
> 1)  In the context of FIX, things get a little convoluted, since the FIX
> distribution has its own settings.sh file that needs to be set
> appropriately.  If you’ve hard-coded the FSL_FIX_WBC variable in that
> settings.sh file, then the location to wb_command in the
> Examples/Scripts/SetUpHCPPipeline.sh isn’t necessarily relevant.  In the
> settings.sh file for FIX on our cluster, we use the following construction:
>
>
>
> if [ -x "$(command -v wb_command)" ]; then
>
> FSL_FIX_WBC=$(command -v wb_command)
>
> else
>
> echo "ERROR in $0: wb_command (Workbench) must be in your path"
>
> exit 1
>
> fi
>
> so that FIX *does* actually respect that location of wb_command that is
> already in your path.
>
>
>
> 2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run
> after MR-FIX, there are two issues that need to be addressed yet:
>
> a) The temporal filter, which was presumably already applied during
> MR-FIX, gets applied again with TaskfMRILevel1.sh.  This script needs to be
> modified to be smarter regarding the temporal filtering (i.e., provide an
> option to NOT reapply the temporal filter).
>
> b) The space spanned by the noise regressors from FIX is not regressed out
> of the task regressor prior to the GLM, which means that variance removed
> during FIX can be reintroduced during the task GLM fitting (depending on
> the extent to which the space spanned by the noise regressors overlaps with
> the task GLM).
>
>
>
> 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: mha...@wustl.edu
>
>
>
> *From: *"Glasser, Matthew" 
> *Date: *Monday, February 25, 2019 at 6:53 PM
> *To: *Leonardo Tozzi , "Harms, Michael" <
> mha...@wustl.edu>, "hcp-users@humanconnectome.org" <
> 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
> modifications that are necessary to use the TaskfMRIAnalysis scripts on
> MR+FIX data and have analyzed hundreds of subjects after MR+FIX.
>
>
>
> As for this issue, is wb_command set properly here:
> https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh
>
>
>
> What about on your ${PATH}?
>
>
>
> As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as
> testing has concluded successfully.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Leonardo
> Tozzi 
> *Date: *Monday, February 25, 2019 at 5:09 PM
> *To: *"Harms, Michael" , "hcp-users@humanconnectome.org"
> 
> *Subject: *Re: [HCP-Users] ICA FIX output missing
>
>
>
> Dear Michael,
>
>
>
> Thank you for pointing me to the logfiles.
>
> It seems like the script is not finding the directory where wb_command is.
> In my c

Re: [HCP-Users] ICA FIX output missing

[Leonardo Tozzi]

Dear Michael,

Thank you very much for all the consideration on the use of FIX for the task 
data.

I have tried the addition you suggest. I think the command is detected, but I 
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:


{^HUndefined function or variable 'gifti'.

Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);

Error in fix_3_clean (line 46)
  BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H




Would you have any thoughts on this?
Thank you,


Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford 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" 
Subject: Re: [HCP-Users] ICA FIX output missing


Hi Leonardo,
Couple things:

1)  In the context of FIX, things get a little convoluted, since the FIX 
distribution has its own settings.sh file that needs to be set appropriately.  
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then 
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t 
necessarily relevant.  In the settings.sh file for FIX on our cluster, we use 
the following construction:

if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already 
in your path.

2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after 
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX, 
gets applied again with TaskfMRILevel1.sh.  This script needs to be modified to 
be smarter regarding the temporal filtering (i.e., provide an option to NOT 
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of 
the task regressor prior to the GLM, which means that variance removed during 
FIX can be reintroduced during the task GLM fitting (depending on the extent to 
which the space spanned by the noise regressors overlaps with the task GLM).

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: mha...@wustl.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 modifications 
that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have 
analyzed hundreds of subjects after MR+FIX.

As for this issue, is wb_command set properly here: 
https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh

What about on your ${PATH}?

As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as testing 
has concluded successfully.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto: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] ICA FIX output missing

Dear Michael,

Thank you for pointing me to the logfiles.

It seems like the script is not finding the directory where wb_command is. In 
my case, I am loading it as a module in my HPC cluster. I have also put its 
path in ICAFIX/fix1.067/settings.sh as follows:


# Set this to the location of the HCP Workbench command for your platform
FSL_FIX_WBC='/share/software/user/open/workbench/1.3.1/bin/wb_command';



However, the script does not seem to “see” this path and instead uses the 
setting I was using on my local machine. In the logfile 
tfMRI_EMOTION_RL_hp2000.ica/.fix.log, I get the following error:


/bin/bash: /Applications/workbench/bin_macosx64/wb_command: No such file or 
directory


Is there another place in the scripts that is overriding my settings.sh?
Concerning the length or the runs, I will look into the multirun 
implementation, but indeed my intention was of using the TaskfMRIAnalysis 
scripts to get my “activations”.
Thank you,

Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lt

Re: [HCP-Users] ICA FIX output missing

[Harms, Michael]

Hi Leonardo,
Couple things:

1)  In the context of FIX, things get a little convoluted, since the FIX 
distribution has its own settings.sh file that needs to be set appropriately.  
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then 
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t 
necessarily relevant.  In the settings.sh file for FIX on our cluster, we use 
the following construction:

if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already 
in your path.

2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after 
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX, 
gets applied again with TaskfMRILevel1.sh.  This script needs to be modified to 
be smarter regarding the temporal filtering (i.e., provide an option to NOT 
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of 
the task regressor prior to the GLM, which means that variance removed during 
FIX can be reintroduced during the task GLM fitting (depending on the extent to 
which the space spanned by the noise regressors overlaps with the task GLM).

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: mha...@wustl.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 modifications 
that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have 
analyzed hundreds of subjects after MR+FIX.

As for this issue, is wb_command set properly here: 
https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh

What about on your ${PATH}?

As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as testing 
has concluded successfully.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto: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] ICA FIX output missing

Dear Michael,

Thank you for pointing me to the logfiles.

It seems like the script is not finding the directory where wb_command is. In 
my case, I am loading it as a module in my HPC cluster. I have also put its 
path in ICAFIX/fix1.067/settings.sh as follows:


# Set this to the location of the HCP Workbench command for your platform
FSL_FIX_WBC='/share/software/user/open/workbench/1.3.1/bin/wb_command';



However, the script does not seem to “see” this path and instead uses the 
setting I was using on my local machine. In the logfile 
tfMRI_EMOTION_RL_hp2000.ica/.fix.log, I get the following error:


/bin/bash: /Applications/workbench/bin_macosx64/wb_command: No such file or 
directory


Is there another place in the scripts that is overriding my settings.sh?
Concerning the length or the runs, I will look into the multirun 
implementation, but indeed my intention was of using the TaskfMRIAnalysis 
scripts to get my “activations”.
Thank you,

Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Monday, February 25, 2019 at 9:59 AM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto: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 stage).
And in the .ica/fix directory, check logMatlab.txt (I believe that is from the 
feature extraction stage).

Note that our recommendation is to use “multi-run” FIX on the task data, due to 
its shorter run length.  We hope to have an announcement on that in the near 
future.  In that regard, you would implement your desired filtering as part of 
the MR-FIX cleaning (and there is a new “polynomia

Re: [HCP-Users] ICA FIX output missing

[Glasser, Matthew]

You’ll want to be using wb_command 1.3.2.  I am not aware of any modifications 
that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have 
analyzed hundreds of subjects after MR+FIX.

As for this issue, is wb_command set properly here: 
https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh

What about on your ${PATH}?

As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as testing 
has concluded successfully.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto: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] ICA FIX output missing

Dear Michael,

Thank you for pointing me to the logfiles.

It seems like the script is not finding the directory where wb_command is. In 
my case, I am loading it as a module in my HPC cluster. I have also put its 
path in ICAFIX/fix1.067/settings.sh as follows:


# Set this to the location of the HCP Workbench command for your platform
FSL_FIX_WBC='/share/software/user/open/workbench/1.3.1/bin/wb_command';



However, the script does not seem to “see” this path and instead uses the 
setting I was using on my local machine. In the logfile 
tfMRI_EMOTION_RL_hp2000.ica/.fix.log, I get the following error:


/bin/bash: /Applications/workbench/bin_macosx64/wb_command: No such file or 
directory


Is there another place in the scripts that is overriding my settings.sh?
Concerning the length or the runs, I will look into the multirun 
implementation, but indeed my intention was of using the TaskfMRIAnalysis 
scripts to get my “activations”.
Thank you,

Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Monday, February 25, 2019 at 9:59 AM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto: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 stage).
And in the .ica/fix directory, check logMatlab.txt (I believe that is from the 
feature extraction stage).

Note that our recommendation is to use “multi-run” FIX on the task data, due to 
its shorter run length.  We hope to have an announcement on that in the near 
future.  In that regard, you would implement your desired filtering as part of 
the MR-FIX cleaning (and there is a new “polynomial detrend” option, for faster 
execution), although I believe that we haven’t quite gotten around to adapting 
the TaskfMRIAnalysis scripts to work on data from MR-FIX.

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: 
mha...@wustl.edu<mailto:mha...@wustl.edu>

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Monday, February 25, 2019 at 11:42 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-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 vast majority of subjects, even if FIX works and 
produces a file (“fix4melview_HCP_hp2000_thr10.txt”) which shows which 
components are noise, I don’t get the final output, for example 
“tfMRI_EMOTION_RL_Atlas_hp2000_clean.dtseries.nii”. This is especially puzzling 
since it does seem to work for a minority of subjects. The matlab log also 
shows no errors.

A related question I would have is what filter you would recommend for task 
data. My intention is to use a GLM on the cleaned data, so is 2000 (linear 
detrending) ok, since then a lower high-pass will be applied in the GLM step?

Thank you very much,



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
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Re: [HCP-Users] ICA FIX output missing

[Leonardo Tozzi]

Dear Michael,

Thank you for pointing me to the logfiles.

It seems like the script is not finding the directory where wb_command is. In 
my case, I am loading it as a module in my HPC cluster. I have also put its 
path in ICAFIX/fix1.067/settings.sh as follows:


# Set this to the location of the HCP Workbench command for your platform
FSL_FIX_WBC='/share/software/user/open/workbench/1.3.1/bin/wb_command';



However, the script does not seem to “see” this path and instead uses the 
setting I was using on my local machine. In the logfile 
tfMRI_EMOTION_RL_hp2000.ica/.fix.log, I get the following error:


/bin/bash: /Applications/workbench/bin_macosx64/wb_command: No such file or 
directory


Is there another place in the scripts that is overriding my settings.sh?
Concerning the length or the runs, I will look into the multirun 
implementation, but indeed my intention was of using the TaskfMRIAnalysis 
scripts to get my “activations”.
Thank you,

Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


From: "Harms, Michael" 
Date: Monday, February 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 cleaning stage).
And in the .ica/fix directory, check logMatlab.txt (I believe that is from the 
feature extraction stage).

Note that our recommendation is to use “multi-run” FIX on the task data, due to 
its shorter run length.  We hope to have an announcement on that in the near 
future.  In that regard, you would implement your desired filtering as part of 
the MR-FIX cleaning (and there is a new “polynomial detrend” option, for faster 
execution), although I believe that we haven’t quite gotten around to adapting 
the TaskfMRIAnalysis scripts to work on data from MR-FIX.

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: mha...@wustl.edu

From:  on behalf of Leonardo Tozzi 

Date: Monday, February 25, 2019 at 11:42 AM
To: "hcp-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 vast majority of subjects, even if FIX works and 
produces a file (“fix4melview_HCP_hp2000_thr10.txt”) which shows which 
components are noise, I don’t get the final output, for example 
“tfMRI_EMOTION_RL_Atlas_hp2000_clean.dtseries.nii”. This is especially puzzling 
since it does seem to work for a minority of subjects. The matlab log also 
shows no errors.

A related question I would have is what filter you would recommend for task 
data. My intention is to use a GLM on the cleaned data, so is 2000 (linear 
detrending) ok, since then a lower high-pass will be applied in the GLM step?

Thank you very much,



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738


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Re: [HCP-Users] ICA FIX output missing

[Harms, Michael]

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 our recommendation is to use “multi-run” FIX on the task data, due to 
its shorter run length.  We hope to have an announcement on that in the near 
future.  In that regard, you would implement your desired filtering as part of 
the MR-FIX cleaning (and there is a new “polynomial detrend” option, for faster 
execution), although I believe that we haven’t quite gotten around to adapting 
the TaskfMRIAnalysis scripts to work on data from MR-FIX.

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: mha...@wustl.edu

From:  on behalf of Leonardo Tozzi 

Date: Monday, February 25, 2019 at 11:42 AM
To: "hcp-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 vast majority of subjects, even if FIX works and 
produces a file (“fix4melview_HCP_hp2000_thr10.txt”) which shows which 
components are noise, I don’t get the final output, for example 
“tfMRI_EMOTION_RL_Atlas_hp2000_clean.dtseries.nii”. This is especially puzzling 
since it does seem to work for a minority of subjects. The matlab log also 
shows no errors.

A related question I would have is what filter you would recommend for task 
data. My intention is to use a GLM on the cleaned data, so is 2000 (linear 
detrending) ok, since then a lower high-pass will be applied in the GLM step?

Thank you very much,



Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu | (650) 5615738


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Re: [HCP-Users] ICA-FIX

[Glasser, Matthew]

Also why do you need to do this to begin with?

Peace,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Stephen Smith mailto:st...@fmrib.ox.ac.uk>>
Date: Friday, April 6, 2018 at 4:45 AM
To: Megan Ní Bhroin mailto:nibhr...@tcd.ie>>
Cc: "hcp-users@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 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 FIX 
cleaning.
Cheers.


On 6 Apr 2018, at 10:41, Megan Ní Bhroin 
mailto:nibhr...@tcd.ie>> wrote:

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 suggestions on how to alter the script, the code already in 
place has a cut off of 2000s but I wish to apply a high pass temporal filter of 
69.444 and low pass temporal filter of 0.7716.

echo "processing FMRI file $fmri with highpass $hp"

if [ $hp -gt 0 ] ; then
  echo "running highpass"
  hptr=`echo "10 k $hp 2 / $tr / p" | dc -`
  ${FSLDIR}/bin/fslmaths $fmri -bptf $hptr -1 ${fmri}_hp$hp
  fmri=${fmri}_hp$hp
fi


I believe the correct data to run this script on is Resting State fMRI 1 & 2 
Preprocessed, can you point me towards the exact files to run this on?

For this script to run successfully I believe that I first have to modify the 
settings.sh file to my own environment for the ICA FIX bash script to run, is 
this correct?

Thank you for your time in advance.
Best,
Megan









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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>
http://www.fmrib.ox.ac.uk/~steve
---

Stop the cultural destruction of Tibet<http://smithinks.net>






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Re: [HCP-Users] ICA-FIX

[Stephen Smith]

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 FIX 
cleaning.
Cheers.


> On 6 Apr 2018, at 10:41, Megan Ní Bhroin  wrote:
> 
> 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 suggestions on how to alter the script, the code already in 
> place has a cut off of 2000s but I wish to apply a high pass temporal filter 
> of 69.444 and low pass temporal filter of 0.7716.
> 
> echo "processing FMRI file $fmri with highpass $hp"
> 
> if [ $hp -gt 0 ] ; then
>   echo "running highpass"
>   hptr=`echo "10 k $hp 2 / $tr / p" | dc -`
>   ${FSLDIR}/bin/fslmaths $fmri -bptf $hptr -1 ${fmri}_hp$hp
>   fmri=${fmri}_hp$hp
> fi
> 
> 
> I believe the correct data to run this script on is Resting State fMRI 1 & 2 
> Preprocessed, can you point me towards the exact files to run this on?
> 
> For this script to run successfully I believe that I first have to modify the 
> settings.sh file to my own environment for the ICA FIX bash script to run, is 
> this correct?
> 
> Thank you for your time in advance.
> Best, 
> Megan
> 
> 
> 
> 
> 
> 
> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve 

---

Stop the cultural destruction of Tibet 






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

[Marta Moreno]

Great. Thank you very much.

> On Oct 29, 2017, at 4:44 PM, Glasser, Matthew  wrote:
> 
> 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 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 already preprocessed with HCP pipelines, after 
> which I get my clean dtseries.nii ready for FC analyses.
> 
> Much appreciation.
> 
> 
> 
> 
>> On Oct 29, 2017, at 11:41 AM, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>> 
>> 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,
>> 
>> Matt.
>> 
>> From: > <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno 
>> mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, October 29, 2017 at 9:11 AM
>> To: HCP Users > <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 working fine and installed locally. I have 
>> downloaded now the tar file with ICA+FIX cleanup scripts. Could you please 
>> give me some guidelines on what are the steps to follow to have them 
>> running? I am using a MacPro.
>> 
>> Much appreciation for your help.
>> 
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org>
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
>> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users>
> 
> 


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

[Glasser, Matthew]

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 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 already preprocessed with HCP pipelines, after which 
I get my clean dtseries.nii ready for FC analyses.

Much appreciation.


[cid:BB89CCAF-C510-43DF-90C6-411C485D4A7A@home]

On Oct 29, 2017, at 11:41 AM, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

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,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Marta Moreno 
mailto:mmorenoort...@icloud.com>>
Date: Sunday, October 29, 2017 at 9:11 AM
To: HCP Users 
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 working fine and installed locally. I have downloaded now the 
tar file with ICA+FIX cleanup scripts. Could you please give me some guidelines 
on what are the steps to follow to have them running? I am using a MacPro.

Much appreciation for your help.



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

[Marta Moreno]

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 appreciation.




> On Oct 29, 2017, at 11:41 AM, Glasser, Matthew  wrote:
> 
> 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,
> 
> Matt.
> 
> From:  > on behalf of Marta Moreno 
> mailto:mmorenoort...@icloud.com>>
> Date: Sunday, October 29, 2017 at 9:11 AM
> To: HCP Users  >
> 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 working fine and installed locally. I have 
> downloaded now the tar file with ICA+FIX cleanup scripts. Could you please 
> give me some guidelines on what are the steps to follow to have them running? 
> I am using a MacPro.
> 
> Much appreciation for your help.
> 
> 
> 
> ___
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> HCP-Users@humanconnectome.org 
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> 


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

[Glasser, Matthew]

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,

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Marta Moreno 
mailto:mmorenoort...@icloud.com>>
Date: Sunday, October 29, 2017 at 9:11 AM
To: HCP Users 
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 working fine and installed locally. I have downloaded now the 
tar file with ICA+FIX cleanup scripts. Could you please give me some guidelines 
on what are the steps to follow to have them running? I am using a MacPro.

Much appreciation for your help.

[cid:BB89CCAF-C510-43DF-90C6-411C485D4A7A@home]


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

[Glasser, Matthew]

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 PM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [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 in the README file 
in the Fix folder)

I skipped to configuration to follow setup instructions and edit paths within 
the settings.sh (Part I Matlab settings). Is this all that would be required? 
From there just running the hip_fix command within the fix folder



Joey Annette Contreras, PhD
Postdoctoral Scholar - Research Associate
Laboratory of Neuro Imaging (LONI)
USC Stevens Neuroimaging and Informatics Institute
Keck School of Medicine, USC
Email: jcontre...@ini.usc.edu

2025 Zonal Ave
Los Angeles, California 90033
Joey Annette Contreras, PhD
Postdoctoral Scholar - Research Associate
Laboratory of Neuro Imaging (LONI)
USC Stevens Neuroimaging and Informatics Institute
Keck School of Medicine, USC
Email: jcontre...@ini.usc.edu

2025 Zonal Ave
Los Angeles, California 90033


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

[Ely, Benjamin]

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/HCP20_hp200.RData<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fmrib.ox.ac.uk_-7Esteve_ftp_HCP20-5Fhp200.RData&d=AwMFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=FUX5Pj9fH7xReJdwrOJyWkCrOYPCCM3Du1A3bMpl278&m=p0mVvpOBOPn-okRB0AkbVhBSTj060ubSoxnRl3xVVg8&s=KNPBpRFfQ1iqPg4MbdFPuJ6SEQ5gz93AIt5T6XeWWj8&e=>
Cheers


On 7 Nov 2016, at 17:45, Ely, Benjamin 
mailto:benjamin@mssm.edu>> 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-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, but this doesn't appear to 
be included in the FIX release. Is this available somewhere else?

Many thanks,
-Ely

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---
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Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.uk<mailto:st...@fmrib.ox.ac.uk>
http://www.fmrib.ox.ac.uk/~steve<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.fmrib.ox.ac.uk_-7Esteve&d=AwMFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=FUX5Pj9fH7xReJdwrOJyWkCrOYPCCM3Du1A3bMpl278&m=p0mVvpOBOPn-okRB0AkbVhBSTj060ubSoxnRl3xVVg8&s=TO3TP87BCT0oi4TeVPrSL8gfLVUrmHns1mU_ib-4Urc&e=>
---

Stop the cultural destruction of 
Tibet<https://urldefense.proofpoint.com/v2/url?u=http-3A__smithinks.net&d=AwMFAw&c=4R1YgkJNMyVWjMjneTwN5tJRn8m8VqTSNCjYLg1wNX4&r=FUX5Pj9fH7xReJdwrOJyWkCrOYPCCM3Du1A3bMpl278&m=p0mVvpOBOPn-okRB0AkbVhBSTj060ubSoxnRl3xVVg8&s=9Lra4FonV8hJLO-NJWigbmptc8twNufgUqXQ0uzywU4&e=>






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

[Stephen Smith]

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-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, but this doesn't appear 
> to be included in the FIX release. Is this available somewhere else?
> 
> Many thanks,
> -Ely
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users 
> 

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Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
st...@fmrib.ox.ac.ukhttp://www.fmrib.ox.ac.uk/~steve 

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Stop the cultural destruction of Tibet 






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