Re: [HCP-Users] HCP_FIX
In terms of getting the /reg directory needed to run your own FIX training, Matt’s earlier point is that that is handled in the hcp_fix script as well. See the lines following the portion of the script with “mkdir -p reg” i.e., if you’ve already run hcp_fix, you should then be able to run ‘fix -t’ to create your own training file (assuming you’ve added the necessary ‘hand_labels_noise.txt’ file to each .ica directory). 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: Thursday, December 13, 2018 at 2:02 PM To: Shachar Gal Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" , Ido Tavor , Niv Tik Subject: Re: [HCP-Users] HCP_FIX You can specify your own training for to hcp_fix as an optional last argument. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Thursday, December 13, 2018 at 6:39 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>>, Ido Tavor mailto:idota...@gmail.com>>, Niv Tik mailto:niv...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX if I understand correctly, what happens in these line is that if I don't have a training data file, it uses the hcp training data as default. but this is not our purpose - we wish to create our own training data file, based on the hand classification we did on our data. Shachar On Tue, 11 Dec 2018 at 21:58, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: See lines 177-193 from the hcp_fix script. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Tuesday, December 11, 2018 at 6:33 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>>, Ido Tavor mailto:idota...@gmail.com>>, Niv Tik mailto:niv...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX I'm sorry if I'm pressing the issue too much, but I still can't see how the hcp_fix solves the fact the the main FIX script expects several files that do are not available from the registration process in the hcp pipeline. Thanks for your patience, Shachar On Tue, Dec 11, 2018, 14:07 Glasser, Matthew mailto:glass...@wustl.edu>> wrote: You can still do training after running hcp_fix. As for not using hcp_fix initially and just running the main fix script, I haven’t tried that. You might need to ask on the main FSL list. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Tuesday, December 11, 2018 at 5:21 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "Harms, Michael" mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>>, Ido Tavor mailto:idota...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX hey Matt, I was trying to use the FIX script from the fix directory that came with this - downloadable FIX tar file<http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar file. I did so because I didn't see in the content of the hcp_fix script that it runs the training mode, and I needed to create the training file (as I said before, im at the stage where I have hand labelled the components of the resting state data for 10 of my subjects after running MELODIC, and I wish to train FIX using these labels). if I'm mistaken in my workflow, I would appreciate any further instructions as to the correct workflow for using the FIX pipelines. thank you On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Did you use the hcp_fix script or some other method of running FIX on HCP data. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, December 10, 2018 at 7:47 AM To: "Harms, Michael" mailto:mha...@wustl.edu>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>>, Ido Tavor mailto:idota...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX hey again, thanks for pointing out the relevant lines for the dual regression. I have some further questions about the workflow of running FIX. so I did hand classification for 10 of my subjects, and wished to run FIX with the -t option, in order to create the training data. but then I realized t
Re: [HCP-Users] HCP_FIX
You can specify your own training for to hcp_fix as an optional last argument.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Thursday, December 13, 2018 at 6:39 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>, Niv Tik
mailto:niv...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
if I understand correctly, what happens in these line is that if I don't have a
training data file, it uses the hcp training data as default.
but this is not our purpose - we wish to create our own training data file,
based on the hand classification we did on our data.
Shachar
On Tue, 11 Dec 2018 at 21:58, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
See lines 177-193 from the hcp_fix script.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Tuesday, December 11, 2018 at 6:33 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>, Niv Tik
mailto:niv...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
I'm sorry if I'm pressing the issue too much, but I still can't see how the
hcp_fix solves the fact the the main FIX script expects several files that do
are not available from the registration process in the hcp pipeline.
Thanks for your patience,
Shachar
On Tue, Dec 11, 2018, 14:07 Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
You can still do training after running hcp_fix. As for not using hcp_fix
initially and just running the main fix script, I haven’t tried that. You
might need to ask on the main FSL list.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Tuesday, December 11, 2018 at 5:21 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey Matt,
I was trying to use the FIX script from the fix directory that came with this -
downloadable FIX tar file<http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar
file.
I did so because I didn't see in the content of the hcp_fix script that it runs
the training mode, and I needed to create the training file (as I said before,
im at the stage where I have hand labelled the components of the resting state
data for 10 of my subjects after running MELODIC, and I wish to train FIX using
these labels).
if I'm mistaken in my workflow, I would appreciate any further instructions as
to the correct workflow for using the FIX pipelines.
thank you
On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
Did you use the hcp_fix script or some other method of running FIX on HCP data.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, December 10, 2018 at 7:47 AM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey again,
thanks for pointing out the relevant lines for the dual regression.
I have some further questions about the workflow of running FIX.
so I did hand classification for 10 of my subjects, and wished to run FIX with
the -t option, in order to create the training data.
but then I realized that FIX expects my .ica folder to include a /reg folder
inside, which it does not include, because the input data I gave to melodic was
already registered (using all of the hcp pipelines).
so this brings up two questions:
1) if it still expects this kind of structure, after being tweaked to fit the
hcp daa, does this mean that you run melodic with registration and all?
2) if not, then what file do you give him as the highres2example_func.mat?(the
other files it expects /reg folder to include are more obvious)
thanks,
Shachar
On Mon, 26 Nov 2018 at 19:02, Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Hi,
The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the
FIX distribution, which is called by the fix script itself.
The only relevant aspect of hcp_fix to that process is that hcp_fix creates the
following symbolic link:
if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
$FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
Re: [HCP-Users] HCP_FIX
if I understand correctly, what happens in these line is that if I don't
have a training data file, it uses the hcp training data as default.
but this is not our purpose - we wish to create our own training data file,
based on the hand classification we did on our data.
Shachar
On Tue, 11 Dec 2018 at 21:58, Glasser, Matthew wrote:
> See lines 177-193 from the hcp_fix script.
>
> Matt.
>
> From: Shachar Gal
> Date: Tuesday, December 11, 2018 at 6:33 AM
> To: Matt Glasser
> Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>, Ido Tavor , Niv Tik <
> niv...@gmail.com>
> Subject: Re: [HCP-Users] HCP_FIX
>
> I'm sorry if I'm pressing the issue too much, but I still can't see how
> the hcp_fix solves the fact the the main FIX script expects several files
> that do are not available from the registration process in the hcp
> pipeline.
>
> Thanks for your patience,
> Shachar
>
> On Tue, Dec 11, 2018, 14:07 Glasser, Matthew wrote:
>
>> You can still do training after running hcp_fix. As for not using
>> hcp_fix initially and just running the main fix script, I haven’t tried
>> that. You might need to ask on the main FSL list.
>>
>> Matt.
>>
>> From: Shachar Gal
>> Date: Tuesday, December 11, 2018 at 5:21 AM
>> To: Matt Glasser
>> Cc: "Harms, Michael" , "hcp-users@humanconnectome.org"
>> , Ido Tavor
>> Subject: Re: [HCP-Users] HCP_FIX
>>
>> hey Matt,
>> I was trying to use the FIX script from the fix directory that came with
>> this - downloadable FIX tar file
>> <http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar file.
>> I did so because I didn't see in the content of the hcp_fix script that
>> it runs the training mode, and I needed to create the training file (as I
>> said before, im at the stage where I have hand labelled the components of
>> the resting state data for 10 of my subjects after running MELODIC, and I
>> wish to train FIX using these labels).
>> if I'm mistaken in my workflow, I would appreciate any further
>> instructions as to the correct workflow for using the FIX pipelines.
>>
>> thank you
>>
>>
>>
>> On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew
>> wrote:
>>
>>> Did you use the hcp_fix script or some other method of running FIX on
>>> HCP data.
>>>
>>> Matt.
>>>
>>> From: Shachar Gal
>>> Date: Monday, December 10, 2018 at 7:47 AM
>>> To: "Harms, Michael"
>>> Cc: Matt Glasser , "hcp-users@humanconnectome.org" <
>>> hcp-users@humanconnectome.org>, Ido Tavor
>>> Subject: Re: [HCP-Users] HCP_FIX
>>>
>>> hey again,
>>>
>>> thanks for pointing out the relevant lines for the dual regression.
>>>
>>> I have some further questions about the workflow of running FIX.
>>> so I did hand classification for 10 of my subjects, and wished to run
>>> FIX with the -t option, in order to create the training data.
>>> but then I realized that FIX expects my .ica folder to include a /reg
>>> folder inside, which it does not include, because the input data I gave to
>>> melodic was *already registered* (using all of the hcp pipelines).
>>> so this brings up two questions:
>>> 1) if it still expects this kind of structure, after being tweaked to
>>> fit the hcp daa, does this mean that you run melodic with registration and
>>> all?
>>> 2) if not, then what file do you give him as the
>>> highres2example_func.mat?(the other files it expects /reg folder to
>>> include are more obvious)
>>>
>>> thanks,
>>> Shachar
>>>
>>>
>>>
>>> On Mon, 26 Nov 2018 at 19:02, Harms, Michael wrote:
>>>
>>>>
>>>>
>>>> Hi,
>>>>
>>>> The cleaning of the CIFTI data is done automatically in fix_3_clean.m
>>>> of the FIX distribution, which is called by the fix script itself.
>>>>
>>>>
>>>>
>>>> The only relevant aspect of hcp_fix to that process is that hcp_fix
>>>> creates the following symbolic link:
>>>>
>>>>
>>>>
>>>> if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
>>>>
>>>> $FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
>>>>
>>>> fi
>>>>
>>>>
>>>>
>>>> since fix_3_clean.m is hard-coded to look for a file named
&
Re: [HCP-Users] HCP_FIX
See lines 177-193 from the hcp_fix script.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Tuesday, December 11, 2018 at 6:33 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>, Niv Tik
mailto:niv...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
I'm sorry if I'm pressing the issue too much, but I still can't see how the
hcp_fix solves the fact the the main FIX script expects several files that do
are not available from the registration process in the hcp pipeline.
Thanks for your patience,
Shachar
On Tue, Dec 11, 2018, 14:07 Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
You can still do training after running hcp_fix. As for not using hcp_fix
initially and just running the main fix script, I haven’t tried that. You
might need to ask on the main FSL list.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Tuesday, December 11, 2018 at 5:21 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey Matt,
I was trying to use the FIX script from the fix directory that came with this -
downloadable FIX tar file<http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar
file.
I did so because I didn't see in the content of the hcp_fix script that it runs
the training mode, and I needed to create the training file (as I said before,
im at the stage where I have hand labelled the components of the resting state
data for 10 of my subjects after running MELODIC, and I wish to train FIX using
these labels).
if I'm mistaken in my workflow, I would appreciate any further instructions as
to the correct workflow for using the FIX pipelines.
thank you
On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
Did you use the hcp_fix script or some other method of running FIX on HCP data.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, December 10, 2018 at 7:47 AM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey again,
thanks for pointing out the relevant lines for the dual regression.
I have some further questions about the workflow of running FIX.
so I did hand classification for 10 of my subjects, and wished to run FIX with
the -t option, in order to create the training data.
but then I realized that FIX expects my .ica folder to include a /reg folder
inside, which it does not include, because the input data I gave to melodic was
already registered (using all of the hcp pipelines).
so this brings up two questions:
1) if it still expects this kind of structure, after being tweaked to fit the
hcp daa, does this mean that you run melodic with registration and all?
2) if not, then what file do you give him as the highres2example_func.mat?(the
other files it expects /reg folder to include are more obvious)
thanks,
Shachar
On Mon, 26 Nov 2018 at 19:02, Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Hi,
The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the
FIX distribution, which is called by the fix script itself.
The only relevant aspect of hcp_fix to that process is that hcp_fix creates the
following symbolic link:
if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
$FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
fi
since fix_3_clean.m is hard-coded to look for a file named Atlas.dtseries.nii
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 Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Friday, November 23, 2018 at 2:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] HCP_FIX
hey matt,
the thing is, I didn't see anything in the hip_fix script the pr
Re: [HCP-Users] HCP_FIX
hey Matt,
I was trying to use the FIX script from the fix directory that came with
this - downloadable FIX tar file
<http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar file.
I did so because I didn't see in the content of the hcp_fix script that it
runs the training mode, and I needed to create the training file (as I said
before, im at the stage where I have hand labelled the components of the
resting state data for 10 of my subjects after running MELODIC, and I wish
to train FIX using these labels).
if I'm mistaken in my workflow, I would appreciate any further instructions
as to the correct workflow for using the FIX pipelines.
thank you
On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew wrote:
> Did you use the hcp_fix script or some other method of running FIX on HCP
> data.
>
> Matt.
>
> From: Shachar Gal
> Date: Monday, December 10, 2018 at 7:47 AM
> To: "Harms, Michael"
> Cc: Matt Glasser , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>, Ido Tavor
> Subject: Re: [HCP-Users] HCP_FIX
>
> hey again,
>
> thanks for pointing out the relevant lines for the dual regression.
>
> I have some further questions about the workflow of running FIX.
> so I did hand classification for 10 of my subjects, and wished to run FIX
> with the -t option, in order to create the training data.
> but then I realized that FIX expects my .ica folder to include a /reg
> folder inside, which it does not include, because the input data I gave to
> melodic was *already registered* (using all of the hcp pipelines).
> so this brings up two questions:
> 1) if it still expects this kind of structure, after being tweaked to fit
> the hcp daa, does this mean that you run melodic with registration and all?
> 2) if not, then what file do you give him as the highres2example_func.mat?(the
> other files it expects /reg folder to include are more obvious)
>
> thanks,
> Shachar
>
>
>
> On Mon, 26 Nov 2018 at 19:02, Harms, Michael wrote:
>
>>
>>
>> Hi,
>>
>> The cleaning of the CIFTI data is done automatically in fix_3_clean.m of
>> the FIX distribution, which is called by the fix script itself.
>>
>>
>>
>> The only relevant aspect of hcp_fix to that process is that hcp_fix
>> creates the following symbolic link:
>>
>>
>>
>> if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
>>
>> $FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
>>
>> fi
>>
>>
>>
>> since fix_3_clean.m is hard-coded to look for a file named
>> Atlas.dtseries.nii
>>
>>
>>
>> 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 Shachar Gal
>>
>> *Date: *Friday, November 23, 2018 at 2:37 AM
>> *To: *"Glasser, Matthew"
>> *Cc: *"hcp-users@humanconnectome.org"
>> *Subject: *Re: [HCP-Users] HCP_FIX
>>
>>
>>
>> hey matt,
>>
>> the thing is, I didn't see anything in the hip_fix script the projects
>> the "fix cleaned" volume to surface, so when does that happen?
>>
>> considering that you mentioned you're currently editing these scripts, I
>> think we would just use the original FSL FIX, and later project the fix
>> cleaned volume to surface using your 'fMRISurface' pipeline.
>>
>>
>>
>> thanks,
>>
>> Shachar
>>
>>
>>
>>
>>
>> On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew
>> wrote:
>>
>> The hcp_fix script is for enabling a few enhancements specific to
>> HCP-Style processing. These scripts are currently being edited and tested
>> and we will have new versions announced soon. PostFix generates the
>> Workbench scenes for hand classification of components.
>>
>>
>>
>> Matt.
>>
>>
>>
>> *From: * on behalf of Shachar Gal
>>
>> *Date: *Monday, November 19, 2018 at 3:30 AM
>> *To: *"hcp-users@humanconnectome.org"
>> *Subject: *[HCP-Users] HCP_FIX
>>
>>
>>
>> Dear experts,
>>
>> I was was looking for some documentation regarding the differences
>> between the st
Re: [HCP-Users] HCP_FIX
I'm sorry if I'm pressing the issue too much, but I still can't see how the
hcp_fix solves the fact the the main FIX script expects several files that
do are not available from the registration process in the hcp pipeline.
Thanks for your patience,
Shachar
On Tue, Dec 11, 2018, 14:07 Glasser, Matthew wrote:
> You can still do training after running hcp_fix. As for not using hcp_fix
> initially and just running the main fix script, I haven’t tried that. You
> might need to ask on the main FSL list.
>
> Matt.
>
> From: Shachar Gal
> Date: Tuesday, December 11, 2018 at 5:21 AM
> To: Matt Glasser
> Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>, Ido Tavor
> Subject: Re: [HCP-Users] HCP_FIX
>
> hey Matt,
> I was trying to use the FIX script from the fix directory that came with
> this - downloadable FIX tar file
> <http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar file.
> I did so because I didn't see in the content of the hcp_fix script that it
> runs the training mode, and I needed to create the training file (as I said
> before, im at the stage where I have hand labelled the components of the
> resting state data for 10 of my subjects after running MELODIC, and I wish
> to train FIX using these labels).
> if I'm mistaken in my workflow, I would appreciate any further
> instructions as to the correct workflow for using the FIX pipelines.
>
> thank you
>
>
>
> On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew wrote:
>
>> Did you use the hcp_fix script or some other method of running FIX on HCP
>> data.
>>
>> Matt.
>>
>> From: Shachar Gal
>> Date: Monday, December 10, 2018 at 7:47 AM
>> To: "Harms, Michael"
>> Cc: Matt Glasser , "hcp-users@humanconnectome.org" <
>> hcp-users@humanconnectome.org>, Ido Tavor
>> Subject: Re: [HCP-Users] HCP_FIX
>>
>> hey again,
>>
>> thanks for pointing out the relevant lines for the dual regression.
>>
>> I have some further questions about the workflow of running FIX.
>> so I did hand classification for 10 of my subjects, and wished to run FIX
>> with the -t option, in order to create the training data.
>> but then I realized that FIX expects my .ica folder to include a /reg
>> folder inside, which it does not include, because the input data I gave to
>> melodic was *already registered* (using all of the hcp pipelines).
>> so this brings up two questions:
>> 1) if it still expects this kind of structure, after being tweaked to fit
>> the hcp daa, does this mean that you run melodic with registration and all?
>> 2) if not, then what file do you give him as the
>> highres2example_func.mat?(the other files it expects /reg folder to
>> include are more obvious)
>>
>> thanks,
>> Shachar
>>
>>
>>
>> On Mon, 26 Nov 2018 at 19:02, Harms, Michael wrote:
>>
>>>
>>>
>>> Hi,
>>>
>>> The cleaning of the CIFTI data is done automatically in fix_3_clean.m
>>> of the FIX distribution, which is called by the fix script itself.
>>>
>>>
>>>
>>> The only relevant aspect of hcp_fix to that process is that hcp_fix
>>> creates the following symbolic link:
>>>
>>>
>>>
>>> if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
>>>
>>> $FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
>>>
>>> fi
>>>
>>>
>>>
>>> since fix_3_clean.m is hard-coded to look for a file named
>>> Atlas.dtseries.nii
>>>
>>>
>>>
>>> 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 Shachar
>>> Gal
>>> *Date: *Friday, November 23, 2018 at 2:37 AM
>>> *To: *"Glasser, Matthew"
>>> *Cc: *"hcp-users@humanconnectome.org"
>>> *Subject: *Re: [HCP-Users] HCP_FIX
>>>
>>>
>>>
>>> hey matt,
>>>
>>> the thing is, I di
Re: [HCP-Users] HCP_FIX
You can still do training after running hcp_fix. As for not using hcp_fix
initially and just running the main fix script, I haven’t tried that. You
might need to ask on the main FSL list.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Tuesday, December 11, 2018 at 5:21 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey Matt,
I was trying to use the FIX script from the fix directory that came with this -
downloadable FIX tar file<http://www.fmrib.ox.ac.uk/~steve/ftp/fix.tar.gz> tar
file.
I did so because I didn't see in the content of the hcp_fix script that it runs
the training mode, and I needed to create the training file (as I said before,
im at the stage where I have hand labelled the components of the resting state
data for 10 of my subjects after running MELODIC, and I wish to train FIX using
these labels).
if I'm mistaken in my workflow, I would appreciate any further instructions as
to the correct workflow for using the FIX pipelines.
thank you
On Mon, 10 Dec 2018 at 23:13, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
Did you use the hcp_fix script or some other method of running FIX on HCP data.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, December 10, 2018 at 7:47 AM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey again,
thanks for pointing out the relevant lines for the dual regression.
I have some further questions about the workflow of running FIX.
so I did hand classification for 10 of my subjects, and wished to run FIX with
the -t option, in order to create the training data.
but then I realized that FIX expects my .ica folder to include a /reg folder
inside, which it does not include, because the input data I gave to melodic was
already registered (using all of the hcp pipelines).
so this brings up two questions:
1) if it still expects this kind of structure, after being tweaked to fit the
hcp daa, does this mean that you run melodic with registration and all?
2) if not, then what file do you give him as the highres2example_func.mat?(the
other files it expects /reg folder to include are more obvious)
thanks,
Shachar
On Mon, 26 Nov 2018 at 19:02, Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Hi,
The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the
FIX distribution, which is called by the fix script itself.
The only relevant aspect of hcp_fix to that process is that hcp_fix creates the
following symbolic link:
if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
$FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
fi
since fix_3_clean.m is hard-coded to look for a file named Atlas.dtseries.nii
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 Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Friday, November 23, 2018 at 2:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] HCP_FIX
hey matt,
the thing is, I didn't see anything in the hip_fix script the projects the "fix
cleaned" volume to surface, so when does that happen?
considering that you mentioned you're currently editing these scripts, I think
we would just use the original FSL FIX, and later project the fix cleaned
volume to surface using your 'fMRISurface' pipeline.
thanks,
Shachar
On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
The hcp_fix script is for enabling a few enhancements specific to HCP-Style
processing. These scripts are currently being edited and tested and we will
have new versions announced soon. PostFix generates the Workbench scenes for
hand classification of components.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, November 19, 2018 at 3:30 AM
To: "hcp-user
Re: [HCP-Users] HCP_FIX
Did you use the hcp_fix script or some other method of running FIX on HCP data.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, December 10, 2018 at 7:47 AM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey again,
thanks for pointing out the relevant lines for the dual regression.
I have some further questions about the workflow of running FIX.
so I did hand classification for 10 of my subjects, and wished to run FIX with
the -t option, in order to create the training data.
but then I realized that FIX expects my .ica folder to include a /reg folder
inside, which it does not include, because the input data I gave to melodic was
already registered (using all of the hcp pipelines).
so this brings up two questions:
1) if it still expects this kind of structure, after being tweaked to fit the
hcp daa, does this mean that you run melodic with registration and all?
2) if not, then what file do you give him as the highres2example_func.mat?(the
other files it expects /reg folder to include are more obvious)
thanks,
Shachar
On Mon, 26 Nov 2018 at 19:02, Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Hi,
The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the
FIX distribution, which is called by the fix script itself.
The only relevant aspect of hcp_fix to that process is that hcp_fix creates the
following symbolic link:
if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
$FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
fi
since fix_3_clean.m is hard-coded to look for a file named Atlas.dtseries.nii
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 Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Friday, November 23, 2018 at 2:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] HCP_FIX
hey matt,
the thing is, I didn't see anything in the hip_fix script the projects the "fix
cleaned" volume to surface, so when does that happen?
considering that you mentioned you're currently editing these scripts, I think
we would just use the original FSL FIX, and later project the fix cleaned
volume to surface using your 'fMRISurface' pipeline.
thanks,
Shachar
On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
The hcp_fix script is for enabling a few enhancements specific to HCP-Style
processing. These scripts are currently being edited and tested and we will
have new versions announced soon. PostFix generates the Workbench scenes for
hand classification of components.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, November 19, 2018 at 3:30 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP_FIX
Dear experts,
I was was looking for some documentation regarding the differences between the
standard FSL FIX script, and the HCP's modified version, but could not find
such.
could you point me to such a documentation, if exists, or perhaps elaborate
briefly on the subject?
on the same subject, is there any similar documentation regarding postfix? I'm
not sure what's its purpose in the cleaning and applying procedure.
thanks.
Shachar Gal
___
HCP-Users mailing list
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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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mail
Re: [HCP-Users] HCP_FIX
hey again,
thanks for pointing out the relevant lines for the dual regression.
I have some further questions about the workflow of running FIX.
so I did hand classification for 10 of my subjects, and wished to run FIX
with the -t option, in order to create the training data.
but then I realized that FIX expects my .ica folder to include a /reg
folder inside, which it does not include, because the input data I gave to
melodic was *already registered* (using all of the hcp pipelines).
so this brings up two questions:
1) if it still expects this kind of structure, after being tweaked to fit
the hcp daa, does this mean that you run melodic with registration and all?
2) if not, then what file do you give him as the highres2example_func.mat?(the
other files it expects /reg folder to include are more obvious)
thanks,
Shachar
On Mon, 26 Nov 2018 at 19:02, Harms, Michael wrote:
>
>
> Hi,
>
> The cleaning of the CIFTI data is done automatically in fix_3_clean.m of
> the FIX distribution, which is called by the fix script itself.
>
>
>
> The only relevant aspect of hcp_fix to that process is that hcp_fix
> creates the following symbolic link:
>
>
>
> if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
>
> $FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
>
> fi
>
>
>
> since fix_3_clean.m is hard-coded to look for a file named
> Atlas.dtseries.nii
>
>
>
> 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 Shachar Gal <
> gal.shac...@gmail.com>
> *Date: *Friday, November 23, 2018 at 2:37 AM
> *To: *"Glasser, Matthew"
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] HCP_FIX
>
>
>
> hey matt,
>
> the thing is, I didn't see anything in the hip_fix script the projects the
> "fix cleaned" volume to surface, so when does that happen?
>
> considering that you mentioned you're currently editing these scripts, I
> think we would just use the original FSL FIX, and later project the fix
> cleaned volume to surface using your 'fMRISurface' pipeline.
>
>
>
> thanks,
>
> Shachar
>
>
>
>
>
> On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew wrote:
>
> The hcp_fix script is for enabling a few enhancements specific to
> HCP-Style processing. These scripts are currently being edited and tested
> and we will have new versions announced soon. PostFix generates the
> Workbench scenes for hand classification of components.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> *Date: *Monday, November 19, 2018 at 3:30 AM
> *To: *"hcp-users@humanconnectome.org"
> *Subject: *[HCP-Users] HCP_FIX
>
>
>
> Dear experts,
>
> I was was looking for some documentation regarding the differences between
> the standard FSL FIX script, and the HCP's modified version, but could not
> find such.
>
> could you point me to such a documentation, if exists, or perhaps
> elaborate briefly on the subject?
>
> on the same subject, is there any similar documentation regarding postfix?
> I'm not sure what's its purpose in the cleaning and applying procedure.
>
>
>
> thanks.
>
> Shachar Gal
>
>
>
> ___
> 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.
>
> ___
> 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.
>
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] HCP_FIX
Hi,
The cleaning of the CIFTI data is done automatically in fix_3_clean.m of the
FIX distribution, which is called by the fix script itself.
The only relevant aspect of hcp_fix to that process is that hcp_fix creates the
following symbolic link:
if [ -f ../${fmri_orig}_Atlas.dtseries.nii ] ; then
$FSLDIR/bin/imln ../${fmri_orig}_Atlas.dtseries.nii Atlas.dtseries.nii
fi
since fix_3_clean.m is hard-coded to look for a file named Atlas.dtseries.nii
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 Shachar Gal
Date: Friday, November 23, 2018 at 2:37 AM
To: "Glasser, Matthew"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] HCP_FIX
hey matt,
the thing is, I didn't see anything in the hip_fix script the projects the "fix
cleaned" volume to surface, so when does that happen?
considering that you mentioned you're currently editing these scripts, I think
we would just use the original FSL FIX, and later project the fix cleaned
volume to surface using your 'fMRISurface' pipeline.
thanks,
Shachar
On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew
mailto:glass...@wustl.edu>> wrote:
The hcp_fix script is for enabling a few enhancements specific to HCP-Style
processing. These scripts are currently being edited and tested and we will
have new versions announced soon. PostFix generates the Workbench scenes for
hand classification of components.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, November 19, 2018 at 3:30 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP_FIX
Dear experts,
I was was looking for some documentation regarding the differences between the
standard FSL FIX script, and the HCP's modified version, but could not find
such.
could you point me to such a documentation, if exists, or perhaps elaborate
briefly on the subject?
on the same subject, is there any similar documentation regarding postfix? I'm
not sure what's its purpose in the cleaning and applying procedure.
thanks.
Shachar Gal
___
HCP-Users mailing list
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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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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] HCP_FIX
Hi Michael, the context is that we are currently in the last stages of planning our new research, after finishing a pilot experiment, and we want to be sure we understand each processing and analysis step we take along the way. we have some experience in the lab with using FSL's FIX, and after implementing the HCP's surface based analysis and processing on all the other stages of analysing our data, we wanted to understand the differences between the two approaches of Ica-cleaning (volume and surface), and the way your FIX pipeline works. Cheers, Shachar On Thu, 22 Nov 2018 at 16:49, Harms, Michael wrote: > > > Hi, > > What is the overall context of this inquiry? Are you getting errors with > running the version of hcp_fix in ICAFIX/hcp_fix? If so, simply revert to > using the version of hcp_fix supplied with the FIX distribution itself. > That doesn’t include some of the enhancements that Matt mentioned are being > worked on, but it works. > > > > 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 "Glasser, > Matthew" > *Date: *Thursday, November 22, 2018 at 8:29 AM > *To: *Shachar Gal > *Cc: *"hcp-users@humanconnectome.org" > *Subject: *Re: [HCP-Users] HCP_FIX > > > > hcp_fix cleans both the volume and CIFTI data in parallel. If you regress > the spatial ICA timecourses from the volume-based ICA into the CIFTI data, > you produce CIFTI spatial maps. > > > > Matt. > > > > *From: *Shachar Gal > *Date: *Thursday, November 22, 2018 at 6:10 AM > *To: *Matt Glasser > *Cc: *"hcp-users@humanconnectome.org" > *Subject: *Re: [HCP-Users] HCP_FIX > > > > hey matt, > > the thing is, I didn't see anything in the hip_fix script the projects the > "fix cleaned" volume to surface, so when does that happen? > > considering that you mentioned you're currently editing these scripts, I > think we would just use the original FSL FIX, and later project the fix > cleaned volume to surface using your 'fMRISurface' pipeline. > > > > thanks, > > Shachar > > > > > > On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew wrote: > > The hcp_fix script is for enabling a few enhancements specific to > HCP-Style processing. These scripts are currently being edited and tested > and we will have new versions announced soon. PostFix generates the > Workbench scenes for hand classification of components. > > > > Matt. > > > > *From: * on behalf of Shachar Gal < > gal.shac...@gmail.com> > *Date: *Monday, November 19, 2018 at 3:30 AM > *To: *"hcp-users@humanconnectome.org" > *Subject: *[HCP-Users] HCP_FIX > > > > Dear experts, > > I was was looking for some documentation regarding the differences between > the standard FSL FIX script, and the HCP's modified version, but could not > find such. > > could you point me to such a documentation, if exists, or perhaps > elaborate briefly on the subject? > > on the same subject, is there any similar documentation regarding postfix? > I'm not sure what's its purpose in the cleaning and applying procedure. > > > > thanks. > > Shachar Gal > > > > ___ > 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. > > > -- > > 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
Re: [HCP-Users] HCP_FIX
and if I can be more specific on what we don't really understand regarding the procedure- the procedure when using FSL's FIX is as follows: we run melodic -> then we hand-classify the components and create the label files -> the we train the FIX algorithm -> the we use it to clean all of our data. but in the hcp_fix script, i saw it calls melodic by itself, so im a bit confused about the parallel step-by-step procedure, that includes the hcp_fix script and the PostFix script. hope this clears things up. thanks, Shachar On Thu, 22 Nov 2018 at 17:43, Shachar Gal wrote: > Hi Michael, > the context is that we are currently in the last stages of planning our > new research, after finishing a pilot experiment, and we want to be sure we > understand each processing and analysis step we take along the way. > we have some experience in the lab with using FSL's FIX, and after > implementing the HCP's surface based analysis and processing on all the > other stages of analysing our data, we wanted to understand the differences > between the two approaches of Ica-cleaning (volume and surface), and the > way your FIX pipeline works. > > Cheers, > Shachar > > On Thu, 22 Nov 2018 at 16:49, Harms, Michael wrote: > >> >> >> Hi, >> >> What is the overall context of this inquiry? Are you getting errors with >> running the version of hcp_fix in ICAFIX/hcp_fix? If so, simply revert to >> using the version of hcp_fix supplied with the FIX distribution itself. >> That doesn’t include some of the enhancements that Matt mentioned are being >> worked on, but it works. >> >> >> >> 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 "Glasser, >> Matthew" >> *Date: *Thursday, November 22, 2018 at 8:29 AM >> *To: *Shachar Gal >> *Cc: *"hcp-users@humanconnectome.org" >> *Subject: *Re: [HCP-Users] HCP_FIX >> >> >> >> hcp_fix cleans both the volume and CIFTI data in parallel. If you >> regress the spatial ICA timecourses from the volume-based ICA into the >> CIFTI data, you produce CIFTI spatial maps. >> >> >> >> Matt. >> >> >> >> *From: *Shachar Gal >> *Date: *Thursday, November 22, 2018 at 6:10 AM >> *To: *Matt Glasser >> *Cc: *"hcp-users@humanconnectome.org" >> *Subject: *Re: [HCP-Users] HCP_FIX >> >> >> >> hey matt, >> >> the thing is, I didn't see anything in the hip_fix script the projects >> the "fix cleaned" volume to surface, so when does that happen? >> >> considering that you mentioned you're currently editing these scripts, I >> think we would just use the original FSL FIX, and later project the fix >> cleaned volume to surface using your 'fMRISurface' pipeline. >> >> >> >> thanks, >> >> Shachar >> >> >> >> >> >> On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew >> wrote: >> >> The hcp_fix script is for enabling a few enhancements specific to >> HCP-Style processing. These scripts are currently being edited and tested >> and we will have new versions announced soon. PostFix generates the >> Workbench scenes for hand classification of components. >> >> >> >> Matt. >> >> >> >> *From: * on behalf of Shachar Gal >> >> *Date: *Monday, November 19, 2018 at 3:30 AM >> *To: *"hcp-users@humanconnectome.org" >> *Subject: *[HCP-Users] HCP_FIX >> >> >> >> Dear experts, >> >> I was was looking for some documentation regarding the differences >> between the standard FSL FIX script, and the HCP's modified version, but >> could not find such. >> >> could you point me to such a documentation, if exists, or perhaps >> elaborate briefly on the subject? >> >> on the same subject, is there any similar documentation regarding >> postfix? I'm not sure what's its purpose in the cleaning and applying >> procedure. >> >> >> >> thanks. >> >> Shachar Gal >> >> >> >> ___
Re: [HCP-Users] HCP_FIX
hey matt, the thing is, I didn't see anything in the hip_fix script the projects the "fix cleaned" volume to surface, so when does that happen? considering that you mentioned you're currently editing these scripts, I think we would just use the original FSL FIX, and later project the fix cleaned volume to surface using your 'fMRISurface' pipeline. thanks, Shachar On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew wrote: > The hcp_fix script is for enabling a few enhancements specific to > HCP-Style processing. These scripts are currently being edited and tested > and we will have new versions announced soon. PostFix generates the > Workbench scenes for hand classification of components. > > Matt. > > From: on behalf of Shachar Gal < > gal.shac...@gmail.com> > Date: Monday, November 19, 2018 at 3:30 AM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] HCP_FIX > > Dear experts, > I was was looking for some documentation regarding the differences between > the standard FSL FIX script, and the HCP's modified version, but could not > find such. > could you point me to such a documentation, if exists, or perhaps > elaborate briefly on the subject? > on the same subject, is there any similar documentation regarding postfix? > I'm not sure what's its purpose in the cleaning and applying procedure. > > thanks. > Shachar Gal > > ___ > 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. > ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] HCP_FIX
The hcp_fix script assumes melodic was already trained and is an automated pipeline for cleaning both the volume and CIFTI data together. PostFix is a script for making a Connectome Workbench scene file that can be used to check the FIX component classification (analogous to Melview but with surface info as well). Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Thursday, November 22, 2018 at 9:54 AM To: "Harms, Michael" mailto:mha...@wustl.edu>> Cc: Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>>, Ido Tavor mailto:idota...@gmail.com>> Subject: Re: [HCP-Users] HCP_FIX and if I can be more specific on what we don't really understand regarding the procedure- the procedure when using FSL's FIX is as follows: we run melodic -> then we hand-classify the components and create the label files -> the we train the FIX algorithm -> the we use it to clean all of our data. but in the hcp_fix script, i saw it calls melodic by itself, so im a bit confused about the parallel step-by-step procedure, that includes the hcp_fix script and the PostFix script. hope this clears things up. thanks, Shachar On Thu, 22 Nov 2018 at 17:43, Shachar Gal mailto:gal.shac...@gmail.com>> wrote: Hi Michael, the context is that we are currently in the last stages of planning our new research, after finishing a pilot experiment, and we want to be sure we understand each processing and analysis step we take along the way. we have some experience in the lab with using FSL's FIX, and after implementing the HCP's surface based analysis and processing on all the other stages of analysing our data, we wanted to understand the differences between the two approaches of Ica-cleaning (volume and surface), and the way your FIX pipeline works. Cheers, Shachar On Thu, 22 Nov 2018 at 16:49, Harms, Michael mailto:mha...@wustl.edu>> wrote: Hi, What is the overall context of this inquiry? Are you getting errors with running the version of hcp_fix in ICAFIX/hcp_fix? If so, simply revert to using the version of hcp_fix supplied with the FIX distribution itself. That doesn’t include some of the enhancements that Matt mentioned are being worked on, but it works. 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 "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Thursday, November 22, 2018 at 8:29 AM To: Shachar Gal mailto:gal.shac...@gmail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] HCP_FIX hcp_fix cleans both the volume and CIFTI data in parallel. If you regress the spatial ICA timecourses from the volume-based ICA into the CIFTI data, you produce CIFTI spatial maps. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Thursday, November 22, 2018 at 6:10 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] HCP_FIX hey matt, the thing is, I didn't see anything in the hip_fix script the projects the "fix cleaned" volume to surface, so when does that happen? considering that you mentioned you're currently editing these scripts, I think we would just use the original FSL FIX, and later project the fix cleaned volume to surface using your 'fMRISurface' pipeline. thanks, Shachar On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: The hcp_fix script is for enabling a few enhancements specific to HCP-Style processing. These scripts are currently being edited and tested and we will have new versions announced soon. PostFix generates the Workbench scenes for hand classification of components. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, November 19, 2018 at 3:30 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Dear experts, I was was looking for some documentation regarding the differences between the standard FSL FIX script, and the HCP's modified version, but could not find such. could you point me to such a documentation, if exist
Re: [HCP-Users] HCP_FIX
Hi, What is the overall context of this inquiry? Are you getting errors with running the version of hcp_fix in ICAFIX/hcp_fix? If so, simply revert to using the version of hcp_fix supplied with the FIX distribution itself. That doesn’t include some of the enhancements that Matt mentioned are being worked on, but it works. 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 "Glasser, Matthew" Date: Thursday, November 22, 2018 at 8:29 AM To: Shachar Gal Cc: "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] HCP_FIX hcp_fix cleans both the volume and CIFTI data in parallel. If you regress the spatial ICA timecourses from the volume-based ICA into the CIFTI data, you produce CIFTI spatial maps. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Thursday, November 22, 2018 at 6:10 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] HCP_FIX hey matt, the thing is, I didn't see anything in the hip_fix script the projects the "fix cleaned" volume to surface, so when does that happen? considering that you mentioned you're currently editing these scripts, I think we would just use the original FSL FIX, and later project the fix cleaned volume to surface using your 'fMRISurface' pipeline. thanks, Shachar On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: The hcp_fix script is for enabling a few enhancements specific to HCP-Style processing. These scripts are currently being edited and tested and we will have new versions announced soon. PostFix generates the Workbench scenes for hand classification of components. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, November 19, 2018 at 3:30 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Dear experts, I was was looking for some documentation regarding the differences between the standard FSL FIX script, and the HCP's modified version, but could not find such. could you point me to such a documentation, if exists, or perhaps elaborate briefly on the subject? on the same subject, is there any similar documentation regarding postfix? I'm not sure what's its purpose in the cleaning and applying procedure. thanks. Shachar Gal ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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. ___ 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] HCP_FIX
hcp_fix cleans both the volume and CIFTI data in parallel. If you regress the spatial ICA timecourses from the volume-based ICA into the CIFTI data, you produce CIFTI spatial maps. Matt. From: Shachar Gal mailto:gal.shac...@gmail.com>> Date: Thursday, November 22, 2018 at 6:10 AM To: Matt Glasser mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] HCP_FIX hey matt, the thing is, I didn't see anything in the hip_fix script the projects the "fix cleaned" volume to surface, so when does that happen? considering that you mentioned you're currently editing these scripts, I think we would just use the original FSL FIX, and later project the fix cleaned volume to surface using your 'fMRISurface' pipeline. thanks, Shachar On Tue, 20 Nov 2018 at 04:10, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: The hcp_fix script is for enabling a few enhancements specific to HCP-Style processing. These scripts are currently being edited and tested and we will have new versions announced soon. PostFix generates the Workbench scenes for hand classification of components. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, November 19, 2018 at 3:30 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Dear experts, I was was looking for some documentation regarding the differences between the standard FSL FIX script, and the HCP's modified version, but could not find such. could you point me to such a documentation, if exists, or perhaps elaborate briefly on the subject? on the same subject, is there any similar documentation regarding postfix? I'm not sure what's its purpose in the cleaning and applying procedure. thanks. Shachar Gal ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] HCP_FIX
The hcp_fix script is for enabling a few enhancements specific to HCP-Style processing. These scripts are currently being edited and tested and we will have new versions announced soon. PostFix generates the Workbench scenes for hand classification of components. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Shachar Gal mailto:gal.shac...@gmail.com>> Date: Monday, November 19, 2018 at 3:30 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Dear experts, I was was looking for some documentation regarding the differences between the standard FSL FIX script, and the HCP's modified version, but could not find such. could you point me to such a documentation, if exists, or perhaps elaborate briefly on the subject? on the same subject, is there any similar documentation regarding postfix? I'm not sure what's its purpose in the cleaning and applying procedure. thanks. Shachar Gal ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] HCP_FIX
Dear experts, I was was looking for some documentation regarding the differences between the standard FSL FIX script, and the HCP's modified version, but could not find such. could you point me to such a documentation, if exists, or perhaps elaborate briefly on the subject? on the same subject, is there any similar documentation regarding postfix? I'm not sure what's its purpose in the cleaning and applying procedure. thanks. Shachar Gal ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp_fix question
Dear Experts,
I have installed all required versions from packages kernlab, party, etc. in R
successfully, but after running hcp_fix I found the following error in
.fix.log. Please advice (see below):
/bin/bash: /Applications/workbench/bin_macosx64: is a directory
Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file
/private/var/folders/j2/__433pcd02l1cw9qkydkqs5hgn/T/tp8475904261983465.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);
Thanks,
-L
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Re: [HCP-Users] hcp_fix script and settings
He Leah,
It should not be necessary for you to change any of the lines you show
below from the FIX settings.sh file.
Of course, there are certainly lines after those lines in sections
labeled "Part I MATLAB settings", "Part II Octave settings", and "Part
III General Settings" that you will need to review and update to reflect
your environment. But I believe that the lines you have copied into your
email should be fine "as is".
Tim
On 11/02/2017 04:28 PM, Marta Moreno wrote:
Dear experts,
I want to use the “hcp_fix" script for clean up of resting state data
after HCP pipelines. I am editing “settings.sh" and wanted to know if
I have to edit these lines copied below:
# Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.065
# (actually this version is 1.065 - see wiki page for details)
# Get the OS and CPU type
FSL_FIX_OS=`uname -s`
FSL_FIX_ARCH=`uname -m`
if [ -z "${FSL_FIXDIR}" ]; then
FSL_FIXDIR=$( cd $(dirname $0) ; pwd)
export FSL_FIXDIR
fi
Thank you very much,
Leah
On Oct 30, 2017, at 10:29 AM, Marta Moreno > wrote:
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 >
Date: Sunday, October 29, 2017 at 12:03 PM
To: Matt Glasser >
Cc: HCP Users >
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 > 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 >
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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--
/Timothy B. Brown
Business & Technology Application Analyst III
Pipeline Developer (Connectome Coordination Facility)
tbbrown(at)wustl.edu
/
The material in this message is private and may contain Protected
Healthcare Information (PHI). 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] hcp_fix script and settings
Dear experts,
I want to use the “hcp_fix" script for clean up of resting state data after HCP
pipelines. I am editing “settings.sh" and wanted to know if I have to edit
these lines copied below:
# Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.065
# (actually this version is 1.065 - see wiki page for details)
# Get the OS and CPU type
FSL_FIX_OS=`uname -s`
FSL_FIX_ARCH=`uname -m`
if [ -z "${FSL_FIXDIR}" ]; then
FSL_FIXDIR=$( cd $(dirname $0) ; pwd)
export FSL_FIXDIR
fi
Thank you very much,
Leah
> On Oct 30, 2017, at 10:29 AM, Marta Moreno wrote:
>
> 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 > >
>> Date: Sunday, October 29, 2017 at 12:03 PM
>> To: Matt Glasser >
>> Cc: HCP Users > >
>> 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 >> > 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
>>> >
>>> 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.
>>>
>>>
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>
>>
>
___
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Re: [HCP-Users] hcp_fix and correlation maps
You just go to file menu open file and change to different file types. Peace, Matt. From: Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Thursday, April 6, 2017 at 8:34 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] hcp_fix and correlation maps Exactly Matt, in principal what you explained below is what we need. The wb_view only accepts spec or scene files (unless I am misunderstanding) and not sure how to build or properly add dyconn layer, dtseries, projecting onto cortical and subcritical ROI layers or grayordinates. We are still novice with the wb_view functionality so excuse us. Best. Osama Sent from my mobile phone On Apr 6, 2017, at 5:58 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: If you want to explore the functional connectivity, you can do that by loading the dtseries into Connectome Workbench and selecting the dyconn layer and clicking on the surface or in the subcortical grey matter in the volume. Is this what you are after or something else? Peace, Matt. From: Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 5:54 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] hcp_fix and correlation maps Thanks Matt. Yes, fix.log showed the error location and after correcting it we now can get the "cleaned" series (dense and atlas). What do you recommend the best way for us to display the connectivity map (after running wb_command correlation) for single patient and using different seeding locations. It's preferred to have dynamic seed placement that yields specific connectivity pattern to that specific seed. All the best. Osama From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Wednesday, April 05, 2017 1:52 PM To: Osama Abdullah; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] hcp_fix and correlation maps Unfortunately not all of the errors of ICA+FIX are reported to the main stderr. You’ll need to look in the log files inside the directory created by ICA+FIX to see what the error was (in matlab or R). There isn’t usually any need to add additional files to the spec file (this simply causes them to be opened when you open the spec file). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 2:43 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix and correlation maps Dear HCP Experts, We are applying the hcp_fix pipeline on Prisma-acquired data (according to the Life Span protocol) and it completed without errors (although it took significant effort on installing the proper R packages). Nonetheless, we cannot find the resulting files that are labelled "clean" anywhere despite the lack of errors. The closest time series we see are the rfMRI_REST1_PA_hp2000.nii and rfMRI_REST1_PA_Atlas.dtseries.nii. Are those overwritten to reflect the results after completing the whole hcp_fix procedure? Second question, say we get the cleaned time series, and we use the wb_command to generate the Correlation (connectivity) maps, how can we add the time series and connectivity maps to the existing "spec" files (for example subjectIDr.32k_fs_LR.wb) so that we can evaluate myelin maps along the connectivity maps? We used the wb_command -add-to-spec-file option but the correlation maps didn't show any intensities on wb_view. Thanks. Osama Osama Abdullah, PhD Department of Neurology School of Medicine University of Utah 36 S. Wasatch Drive Salt Lake City, UT 84112 ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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
Re: [HCP-Users] hcp_fix and correlation maps
Exactly Matt, in principal what you explained below is what we need. The wb_view only accepts spec or scene files (unless I am misunderstanding) and not sure how to build or properly add dyconn layer, dtseries, projecting onto cortical and subcritical ROI layers or grayordinates. We are still novice with the wb_view functionality so excuse us. Best. Osama Sent from my mobile phone On Apr 6, 2017, at 5:58 PM, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: If you want to explore the functional connectivity, you can do that by loading the dtseries into Connectome Workbench and selecting the dyconn layer and clicking on the surface or in the subcortical grey matter in the volume. Is this what you are after or something else? Peace, Matt. From: Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 5:54 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] hcp_fix and correlation maps Thanks Matt. Yes, fix.log showed the error location and after correcting it we now can get the "cleaned" series (dense and atlas). What do you recommend the best way for us to display the connectivity map (after running wb_command correlation) for single patient and using different seeding locations. It's preferred to have dynamic seed placement that yields specific connectivity pattern to that specific seed. All the best. Osama From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Wednesday, April 05, 2017 1:52 PM To: Osama Abdullah; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] hcp_fix and correlation maps Unfortunately not all of the errors of ICA+FIX are reported to the main stderr. You’ll need to look in the log files inside the directory created by ICA+FIX to see what the error was (in matlab or R). There isn’t usually any need to add additional files to the spec file (this simply causes them to be opened when you open the spec file). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 2:43 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix and correlation maps Dear HCP Experts, We are applying the hcp_fix pipeline on Prisma-acquired data (according to the Life Span protocol) and it completed without errors (although it took significant effort on installing the proper R packages). Nonetheless, we cannot find the resulting files that are labelled "clean" anywhere despite the lack of errors. The closest time series we see are the rfMRI_REST1_PA_hp2000.nii and rfMRI_REST1_PA_Atlas.dtseries.nii. Are those overwritten to reflect the results after completing the whole hcp_fix procedure? Second question, say we get the cleaned time series, and we use the wb_command to generate the Correlation (connectivity) maps, how can we add the time series and connectivity maps to the existing "spec" files (for example subjectIDr.32k_fs_LR.wb) so that we can evaluate myelin maps along the connectivity maps? We used the wb_command -add-to-spec-file option but the correlation maps didn't show any intensities on wb_view. Thanks. Osama Osama Abdullah, PhD Department of Neurology School of Medicine University of Utah 36 S. Wasatch Drive Salt Lake City, UT 84112 ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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 th
Re: [HCP-Users] hcp_fix and correlation maps
If you want to explore the functional connectivity, you can do that by loading the dtseries into Connectome Workbench and selecting the dyconn layer and clicking on the surface or in the subcortical grey matter in the volume. Is this what you are after or something else? Peace, Matt. From: Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 5:54 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] hcp_fix and correlation maps Thanks Matt. Yes, fix.log showed the error location and after correcting it we now can get the "cleaned" series (dense and atlas). What do you recommend the best way for us to display the connectivity map (after running wb_command correlation) for single patient and using different seeding locations. It's preferred to have dynamic seed placement that yields specific connectivity pattern to that specific seed. All the best. Osama From: Glasser, Matthew [glass...@wustl.edu<mailto:glass...@wustl.edu>] Sent: Wednesday, April 05, 2017 1:52 PM To: Osama Abdullah; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] hcp_fix and correlation maps Unfortunately not all of the errors of ICA+FIX are reported to the main stderr. You’ll need to look in the log files inside the directory created by ICA+FIX to see what the error was (in matlab or R). There isn’t usually any need to add additional files to the spec file (this simply causes them to be opened when you open the spec file). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 2:43 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix and correlation maps Dear HCP Experts, We are applying the hcp_fix pipeline on Prisma-acquired data (according to the Life Span protocol) and it completed without errors (although it took significant effort on installing the proper R packages). Nonetheless, we cannot find the resulting files that are labelled "clean" anywhere despite the lack of errors. The closest time series we see are the rfMRI_REST1_PA_hp2000.nii and rfMRI_REST1_PA_Atlas.dtseries.nii. Are those overwritten to reflect the results after completing the whole hcp_fix procedure? Second question, say we get the cleaned time series, and we use the wb_command to generate the Correlation (connectivity) maps, how can we add the time series and connectivity maps to the existing "spec" files (for example subjectIDr.32k_fs_LR.wb) so that we can evaluate myelin maps along the connectivity maps? We used the wb_command -add-to-spec-file option but the correlation maps didn't show any intensities on wb_view. Thanks. Osama Osama Abdullah, PhD Department of Neurology School of Medicine University of Utah 36 S. Wasatch Drive Salt Lake City, UT 84112 ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp_fix and correlation maps
Thanks Matt. Yes, fix.log showed the error location and after correcting it we now can get the "cleaned" series (dense and atlas). What do you recommend the best way for us to display the connectivity map (after running wb_command correlation) for single patient and using different seeding locations. It's preferred to have dynamic seed placement that yields specific connectivity pattern to that specific seed. All the best. Osama From: Glasser, Matthew [glass...@wustl.edu] Sent: Wednesday, April 05, 2017 1:52 PM To: Osama Abdullah; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] hcp_fix and correlation maps Unfortunately not all of the errors of ICA+FIX are reported to the main stderr. You’ll need to look in the log files inside the directory created by ICA+FIX to see what the error was (in matlab or R). There isn’t usually any need to add additional files to the spec file (this simply causes them to be opened when you open the spec file). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 2:43 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix and correlation maps Dear HCP Experts, We are applying the hcp_fix pipeline on Prisma-acquired data (according to the Life Span protocol) and it completed without errors (although it took significant effort on installing the proper R packages). Nonetheless, we cannot find the resulting files that are labelled "clean" anywhere despite the lack of errors. The closest time series we see are the rfMRI_REST1_PA_hp2000.nii and rfMRI_REST1_PA_Atlas.dtseries.nii. Are those overwritten to reflect the results after completing the whole hcp_fix procedure? Second question, say we get the cleaned time series, and we use the wb_command to generate the Correlation (connectivity) maps, how can we add the time series and connectivity maps to the existing "spec" files (for example subjectIDr.32k_fs_LR.wb) so that we can evaluate myelin maps along the connectivity maps? We used the wb_command -add-to-spec-file option but the correlation maps didn't show any intensities on wb_view. Thanks. Osama Osama Abdullah, PhD Department of Neurology School of Medicine University of Utah 36 S. Wasatch Drive Salt Lake City, UT 84112 ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp_fix and correlation maps
Unfortunately not all of the errors of ICA+FIX are reported to the main stderr. You’ll need to look in the log files inside the directory created by ICA+FIX to see what the error was (in matlab or R). There isn’t usually any need to add additional files to the spec file (this simply causes them to be opened when you open the spec file). Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Osama Abdullah <osama.abdul...@utah.edu<mailto:osama.abdul...@utah.edu>> Date: Wednesday, April 5, 2017 at 2:43 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix and correlation maps Dear HCP Experts, We are applying the hcp_fix pipeline on Prisma-acquired data (according to the Life Span protocol) and it completed without errors (although it took significant effort on installing the proper R packages). Nonetheless, we cannot find the resulting files that are labelled "clean" anywhere despite the lack of errors. The closest time series we see are the rfMRI_REST1_PA_hp2000.nii and rfMRI_REST1_PA_Atlas.dtseries.nii. Are those overwritten to reflect the results after completing the whole hcp_fix procedure? Second question, say we get the cleaned time series, and we use the wb_command to generate the Correlation (connectivity) maps, how can we add the time series and connectivity maps to the existing "spec" files (for example subjectIDr.32k_fs_LR.wb) so that we can evaluate myelin maps along the connectivity maps? We used the wb_command -add-to-spec-file option but the correlation maps didn't show any intensities on wb_view. Thanks. Osama Osama Abdullah, PhD Department of Neurology School of Medicine University of Utah 36 S. Wasatch Drive Salt Lake City, UT 84112 ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp_fix and correlation maps
Dear HCP Experts, We are applying the hcp_fix pipeline on Prisma-acquired data (according to the Life Span protocol) and it completed without errors (although it took significant effort on installing the proper R packages). Nonetheless, we cannot find the resulting files that are labelled "clean" anywhere despite the lack of errors. The closest time series we see are the rfMRI_REST1_PA_hp2000.nii and rfMRI_REST1_PA_Atlas.dtseries.nii. Are those overwritten to reflect the results after completing the whole hcp_fix procedure? Second question, say we get the cleaned time series, and we use the wb_command to generate the Correlation (connectivity) maps, how can we add the time series and connectivity maps to the existing "spec" files (for example subjectIDr.32k_fs_LR.wb) so that we can evaluate myelin maps along the connectivity maps? We used the wb_command -add-to-spec-file option but the correlation maps didn't show any intensities on wb_view. Thanks. Osama Osama Abdullah, PhD Department of Neurology School of Medicine University of Utah 36 S. Wasatch Drive Salt Lake City, UT 84112 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp_fix bug
Please include the error message, I don’t know what you are referring to else. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Timothy Hendrickson <hendr...@umn.edu<mailto:hendr...@umn.edu>> Date: Wednesday, March 22, 2017 at 5:17 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] hcp_fix bug I am getting very similar errors to Nallin. Has this been resolved? Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp_fix bug
I am getting very similar errors to Nallin. Has this been resolved? Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] HCP_FIX Environment Setup
Hi Matt, Thanks again! I didn’t have CIFTI and GIFTI installed, but now that they are installed, the script is fully working. I appreciate your help! Best regards, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Monday, October 24, 2016 10:04 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup You’ll have to look into the logs to see if there has been some other error. They are in several places… Also, do you have CIFTI and GIFTI installed and set up? Peace, Matt. From: "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Monday, October 24, 2016 at 8:59 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] HCP_FIX Environment Setup Hi Matt, Thanks again for the fast reply. It turns out I needed to include the T1_restore_brain.nii.gz in the path specified by the line: $FSLDIR/bin/imln../../../../T1w_restore_brain highres The script is now working without error messages, it is producing text files classifying signal and noise, however there is no ‘_clean’ file outputted. I was wondering if you perhaps know what else I need to configure in order to get the final output - it seems like the fix_3_clean.m script is not outputting the desired file. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Sunday, October 23, 2016 8:27 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you need to delete the prior partial run of FIX and try again? Peace, Matt. From: "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Sunday, October 23, 2016 at 7:23 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] HCP_FIX Environment Setup Hi Matt, Thanks for the fast response! I have now set up the configuration file properly, but am now encountering the same issue seen in the thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02965.html, namely there was an image exception thrown when the fix script was called at the end of hcp_fix: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC running FIX FIX Feature extraction for Melodic output directory: tfMRI_MOTOR_LR_hp2000.ica create edge masks run FAST Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' I was wondering if you perhaps know what could be the issue here. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Thursday, October 20, 2016 7:58 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you didn’t set it to use compiled matlab somewhere in the config? That error suggests it is trying to find a matlab binary in a default FMRIB location. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Thursday, October 20, 2016 at 11:05 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Environment Setup Hello, I am trying to apply the hcp_fix script to task data from the Human Connectome Project, but am encountering difficulties when setting up the environment. I have read through the README file; I setup the compiled Matlab version, and pointed FSL_FIX_MCRROOT to the compiled Matlab version in the settings.sh file. This was the only change I made to the settings.sh file. When I tried running the hcp_fix script, I got a cascade of error messages, beginning with: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC /opt/fmrib/m
Re: [HCP-Users] HCP_FIX Environment Setup
You'll have to look into the logs to see if there has been some other error. They are in several places... Also, do you have CIFTI and GIFTI installed and set up? Peace, Matt. From: "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Monday, October 24, 2016 at 8:59 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] HCP_FIX Environment Setup Hi Matt, Thanks again for the fast reply. It turns out I needed to include the T1_restore_brain.nii.gz in the path specified by the line: $FSLDIR/bin/imln../../../../T1w_restore_brain highres The script is now working without error messages, it is producing text files classifying signal and noise, however there is no '_clean' file outputted. I was wondering if you perhaps know what else I need to configure in order to get the final output - it seems like the fix_3_clean.m script is not outputting the desired file. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Sunday, October 23, 2016 8:27 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you need to delete the prior partial run of FIX and try again? Peace, Matt. From: "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Sunday, October 23, 2016 at 7:23 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] HCP_FIX Environment Setup Hi Matt, Thanks for the fast response! I have now set up the configuration file properly, but am now encountering the same issue seen in the thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02965.html, namely there was an image exception thrown when the fix script was called at the end of hcp_fix: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC running FIX FIX Feature extraction for Melodic output directory: tfMRI_MOTOR_LR_hp2000.ica create edge masks run FAST Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' I was wondering if you perhaps know what could be the issue here. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Thursday, October 20, 2016 7:58 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you didn't set it to use compiled matlab somewhere in the config? That error suggests it is trying to find a matlab binary in a default FMRIB location. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Thursday, October 20, 2016 at 11:05 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Environment Setup Hello, I am trying to apply the hcp_fix script to task data from the Human Connectome Project, but am encountering difficulties when setting up the environment. I have read through the README file; I setup the compiled Matlab version, and pointed FSL_FIX_MCRROOT to the compiled Matlab version in the settings.sh file. This was the only change I made to the settings.sh file. When I tried running the hcp_fix script, I got a cascade of error messages, beginning with: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC /opt/fmrib/matlab/bin/matlab not found! Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' Aborted (core dumped) Does anybody know what could be the issue? Also, once the environment is properly set up, how long does hcp_fix typically take to run? Thanks, Michael ___ HCP-Users mailing list HCP-Users@humancon
Re: [HCP-Users] HCP_FIX Environment Setup
Hi Matt, Thanks again for the fast reply. It turns out I needed to include the T1_restore_brain.nii.gz in the path specified by the line: $FSLDIR/bin/imln../../../../T1w_restore_brain highres The script is now working without error messages, it is producing text files classifying signal and noise, however there is no ‘_clean’ file outputted. I was wondering if you perhaps know what else I need to configure in order to get the final output - it seems like the fix_3_clean.m script is not outputting the desired file. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Sunday, October 23, 2016 8:27 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you need to delete the prior partial run of FIX and try again? Peace, Matt. From: "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Sunday, October 23, 2016 at 7:23 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] HCP_FIX Environment Setup Hi Matt, Thanks for the fast response! I have now set up the configuration file properly, but am now encountering the same issue seen in the thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02965.html, namely there was an image exception thrown when the fix script was called at the end of hcp_fix: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC running FIX FIX Feature extraction for Melodic output directory: tfMRI_MOTOR_LR_hp2000.ica create edge masks run FAST Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' I was wondering if you perhaps know what could be the issue here. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Thursday, October 20, 2016 7:58 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you didn’t set it to use compiled matlab somewhere in the config? That error suggests it is trying to find a matlab binary in a default FMRIB location. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Thursday, October 20, 2016 at 11:05 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Environment Setup Hello, I am trying to apply the hcp_fix script to task data from the Human Connectome Project, but am encountering difficulties when setting up the environment. I have read through the README file; I setup the compiled Matlab version, and pointed FSL_FIX_MCRROOT to the compiled Matlab version in the settings.sh file. This was the only change I made to the settings.sh file. When I tried running the hcp_fix script, I got a cascade of error messages, beginning with: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC /opt/fmrib/matlab/bin/matlab not found! Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' Aborted (core dumped) Does anybody know what could be the issue? Also, once the environment is properly set up, how long does hcp_fix typically take to run? Thanks, Michael ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. The materials in this message
Re: [HCP-Users] HCP_FIX Environment Setup
Perhaps you need to delete the prior partial run of FIX and try again? Peace, Matt. From: "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Sunday, October 23, 2016 at 7:23 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: RE: [HCP-Users] HCP_FIX Environment Setup Hi Matt, Thanks for the fast response! I have now set up the configuration file properly, but am now encountering the same issue seen in the thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02965.html, namely there was an image exception thrown when the fix script was called at the end of hcp_fix: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC running FIX FIX Feature extraction for Melodic output directory: tfMRI_MOTOR_LR_hp2000.ica create edge masks run FAST Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' I was wondering if you perhaps know what could be the issue here. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Thursday, October 20, 2016 7:58 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you didn't set it to use compiled matlab somewhere in the config? That error suggests it is trying to find a matlab binary in a default FMRIB location. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Thursday, October 20, 2016 at 11:05 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Environment Setup Hello, I am trying to apply the hcp_fix script to task data from the Human Connectome Project, but am encountering difficulties when setting up the environment. I have read through the README file; I setup the compiled Matlab version, and pointed FSL_FIX_MCRROOT to the compiled Matlab version in the settings.sh file. This was the only change I made to the settings.sh file. When I tried running the hcp_fix script, I got a cascade of error messages, beginning with: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC /opt/fmrib/matlab/bin/matlab not found! Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' Aborted (core dumped) Does anybody know what could be the issue? Also, once the environment is properly set up, how long does hcp_fix typically take to run? Thanks, Michael ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. 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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] HCP_FIX Environment Setup
Hi Matt, Thanks for the fast response! I have now set up the configuration file properly, but am now encountering the same issue seen in the thread https://www.mail-archive.com/hcp-users@humanconnectome.org/msg02965.html, namely there was an image exception thrown when the fix script was called at the end of hcp_fix: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC running FIX FIX Feature extraction for Melodic output directory: tfMRI_MOTOR_LR_hp2000.ica create edge masks run FAST Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' I was wondering if you perhaps know what could be the issue here. Thanks, Michael From: Glasser, Matthew<mailto:glass...@wustl.edu> Sent: Thursday, October 20, 2016 7:58 PM To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>; hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org> Subject: Re: [HCP-Users] HCP_FIX Environment Setup Perhaps you didn't set it to use compiled matlab somewhere in the config? That error suggests it is trying to find a matlab binary in a default FMRIB location. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Thursday, October 20, 2016 at 11:05 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Environment Setup Hello, I am trying to apply the hcp_fix script to task data from the Human Connectome Project, but am encountering difficulties when setting up the environment. I have read through the README file; I setup the compiled Matlab version, and pointed FSL_FIX_MCRROOT to the compiled Matlab version in the settings.sh file. This was the only change I made to the settings.sh file. When I tried running the hcp_fix script, I got a cascade of error messages, beginning with: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC /opt/fmrib/matlab/bin/matlab not found! Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' Aborted (core dumped) Does anybody know what could be the issue? Also, once the environment is properly set up, how long does hcp_fix typically take to run? Thanks, Michael ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] HCP_FIX Environment Setup
Perhaps you didn't set it to use compiled matlab somewhere in the config? That error suggests it is trying to find a matlab binary in a default FMRIB location. Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of "Michael Kleinman, Mr" <michael.klein...@mail.mcgill.ca<mailto:michael.klein...@mail.mcgill.ca>> Date: Thursday, October 20, 2016 at 11:05 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] HCP_FIX Environment Setup Hello, I am trying to apply the hcp_fix script to task data from the Human Connectome Project, but am encountering difficulties when setting up the environment. I have read through the README file; I setup the compiled Matlab version, and pointed FSL_FIX_MCRROOT to the compiled Matlab version in the settings.sh file. This was the only change I made to the settings.sh file. When I tried running the hcp_fix script, I got a cascade of error messages, beginning with: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC /opt/fmrib/matlab/bin/matlab not found! Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' Aborted (core dumped) Does anybody know what could be the issue? Also, once the environment is properly set up, how long does hcp_fix typically take to run? Thanks, Michael ___ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto: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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] HCP_FIX Environment Setup
Hello, I am trying to apply the hcp_fix script to task data from the Human Connectome Project, but am encountering difficulties when setting up the environment. I have read through the README file; I setup the compiled Matlab version, and pointed FSL_FIX_MCRROOT to the compiled Matlab version in the settings.sh file. This was the only change I made to the settings.sh file. When I tried running the hcp_fix script, I got a cascade of error messages, beginning with: ./fix1.06/hcp_fix tfMRI_MOTOR_LR/tfMRI_MOTOR_LR.nii.gz 2000 processing FMRI file tfMRI_MOTOR_LR with highpass 2000 running highpass running MELODIC /opt/fmrib/matlab/bin/matlab not found! Image Exception : #22 :: ERROR: Could not open image tfMRI_MOTOR_LR_hp2000.ica/reg/highres terminate called after throwing an instance of 'RBD_COMMON::BaseException' Aborted (core dumped) Does anybody know what could be the issue? Also, once the environment is properly set up, how long does hcp_fix typically take to run? Thanks, Michael ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp_fix bug
You also need the GIFTI toolbox installed for Matlab:
http://www.artefact.tk/software/matlab/gifti/
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 6:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
"... " in last Email refer to
/home/fas/glahn/ny87/software/workbench/bin_linux64/
So before running fix_3_clean, I've set
WBC='/home/fas/glahn/ny87/software/workbench/bin_linux64/wb_command' and
CIFTI='/home/fas/glahn/ny87/software/workbench' , which have ciftiopen.m
stored. However, I still met the problem as mentioned before. Do you know what
could be wrong? Thank you!
Best,
Nailin
2016-10-19 19:29 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
I don’t think three dots is valid.
Peace,
Matt.
From: "ynai...@gmail.com<mailto:ynai...@gmail.com>"
<ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 5:04 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPhone
On Oct 19, 2016, at 5:46 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
You could also need to run the add path parts of the command.
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 4:02 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is it a reproducible error? What happens if you try running the fix_3_clean
function with the parameters mentioned below?
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 2:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
It's not compiled matlab.
Best,
Nailin
2016-10-17 13:53 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >&g
Re: [HCP-Users] hcp_fix bug
I don’t think three dots is valid.
Peace,
Matt.
From: "ynai...@gmail.com<mailto:ynai...@gmail.com>"
<ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 5:04 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPhone
On Oct 19, 2016, at 5:46 PM, Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
You could also need to run the add path parts of the command.
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 4:02 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is it a reproducible error? What happens if you try running the fix_3_clean
function with the parameters mentioned below?
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 2:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
It's not compiled matlab.
Best,
Nailin
2016-10-17 13:53 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
The materials in this message are private and may contain
Re: [HCP-Users] hcp_fix bug
Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPhone
> On Oct 19, 2016, at 5:46 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> You could also need to run the add path parts of the command.
>
> Peace,
>
> Matt.
>
> From: nailin yao <ynai...@gmail.com>
> Date: Wednesday, October 19, 2016 at 4:02 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] hcp_fix bug
>
> Hi Matt,
>
>
> I tried to run fix_3_clean on matlab directly, and met the error message
> below:
>
>
> fix_3_clean('.fix',0,1,2000)
>
> TR =
>
> 0.7200
>
> /bin/bash: -cifti-convert: command not found
>
> Undefined function 'gifti' for input arguments of type 'char'.
>
> Error in ciftiopen (line 31)
>
> cifti = gifti([tmpfile '.gii']);
>
> Error in fix_3_clean (line 40)
>
> BO=ciftiopen('Atlas.dtseries.nii',WBC);
>
>
> Do you know why? Thank you very much!
>
> Best,
> Nailin
>
> 2016-10-17 20:12 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>> Is it a reproducible error? What happens if you try running the fix_3_clean
>> function with the parameters mentioned below?
>>
>> Peace,
>>
>> Matt.
>>
>> From: nailin yao <ynai...@gmail.com>
>> Date: Monday, October 17, 2016 at 2:58 PM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] hcp_fix bug
>>
>> Hi Matt,
>>
>> It's not compiled matlab.
>>
>> Best,
>> Nailin
>>
>> 2016-10-17 13:53 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>>> Is this compiled matlab or not compiled?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of nailin yao
>>> <ynai...@gmail.com>
>>> Date: Monday, October 17, 2016 at 11:13 AM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] hcp_fix bug
>>>
>>> Hi ,
>>>
>>> I received the bug report when running hcp_fix for the last step:
>>>
>>> running FIX
>>>
>>> FIX Feature extraction for Melodic output directory:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica
>>>
>>> create edge masks
>>>
>>> run FAST
>>>
>>> registration of standard space masks
>>>
>>> extract features
>>>
>>> FIX Classifying components in Melodic directory:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
>>> /home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
>>> threshold 10
>>>
>>> FIX Applying cleanup using cleanup file:
>>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
>>> motion cleanup set to 1
>>>
>>> sh: line 1: 24221 Bus error (core dumped)
>>> /gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
>>> -nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
>>> addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
>>> fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
>>>
>>>
>>> Does anyone know what's the problem? Thank you very much!
>>>
>>> Best,
>>> Nailin
>>>
>>> --
>>> Nailin Yao, PhD
>>>
>>> Postdoctoral Associate
>>> Department of Psychiatry, Yale University
>>>
>>> ___
>>> 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.
>>>
>>
>&
Re: [HCP-Users] hcp_fix bug
You could also need to run the add path parts of the command.
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Wednesday, October 19, 2016 at 4:02 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is it a reproducible error? What happens if you try running the fix_3_clean
function with the parameters mentioned below?
Peace,
Matt.
From: nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 2:58 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
It's not compiled matlab.
Best,
Nailin
2016-10-17 13:53 GMT-04:00 Glasser, Matthew
<glass...@wustl.edu<mailto:glass...@wustl.edu>>:
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
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.
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
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
Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message
below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Undefined function 'gifti' for input arguments of type 'char'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 40)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
Do you know why? Thank you very much!
Best,
Nailin
2016-10-17 20:12 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
> Is it a reproducible error? What happens if you try running the
> fix_3_clean function with the parameters mentioned below?
>
> Peace,
>
> Matt.
>
> From: nailin yao <ynai...@gmail.com>
> Date: Monday, October 17, 2016 at 2:58 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] hcp_fix bug
>
> Hi Matt,
>
> It's not compiled matlab.
>
> Best,
> Nailin
>
> 2016-10-17 13:53 GMT-04:00 Glasser, Matthew <glass...@wustl.edu>:
>
>> Is this compiled matlab or not compiled?
>>
>> Peace,
>>
>> Matt.
>>
>> From: <hcp-users-boun...@humanconnectome.org> on behalf of nailin yao <
>> ynai...@gmail.com>
>> Date: Monday, October 17, 2016 at 11:13 AM
>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: [HCP-Users] hcp_fix bug
>>
>> Hi ,
>>
>> I received the bug report when running hcp_fix for the last step:
>>
>> running FIX
>>
>> FIX Feature extraction for Melodic output directory:
>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica
>>
>> create edge masks
>>
>> run FAST
>>
>> registration of standard space masks
>>
>> extract features
>>
>> FIX Classifying components in Melodic directory:
>> rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
>> /home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData
>> and threshold 10
>>
>> FIX Applying cleanup using cleanup file: rfMRI_REST1_LR_nonlin_norm_hp2
>> 000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 1
>>
>> sh: line 1: 24221 Bus error (core dumped)
>> /gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay
>> -nodesktop -nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
>> addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
>> fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
>>
>> Does anyone know what's the problem? Thank you very much!
>>
>> Best,
>> Nailin
>>
>> --
>> Nailin Yao, PhD
>>
>> Postdoctoral Associate
>> Department of Psychiatry, Yale University
>>
>> ___
>> 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.
>>
>
>
>
> --
> Nailin Yao, PhD
>
> Postdoctoral Associate
> Department of Psychiatry, Yale University
>
>
> --
>
> 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.
>
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] hcp_fix bug
Is this compiled matlab or not compiled?
Peace,
Matt.
From:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of nailin yao <ynai...@gmail.com<mailto:ynai...@gmail.com>>
Date: Monday, October 17, 2016 at 11:13 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto: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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Melodic directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica using training file:
/home/fas/glahn/ny87/Pipelines/fix1.06/training_files/HCP_hp2000.RData and
threshold 10
FIX Applying cleanup using cleanup file:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and
motion cleanup set to 1
sh: line 1: 24221 Bus error (core dumped)
/gpfs/apps/hpc/Apps/Matlab/R2015b/bin/matlab -nojvm -nodisplay -nodesktop
-nosplash -r "addpath('/home/fas/glahn/ny87/Pipelines/fix1.06');
addpath('/gpfs/apps/hpc/Apps/FSL/5.0.6/fsl/etc/matlab');
fix_3_clean('.fix',0,1,2000)" >> .fix.log 2>&1
Does anyone know what's the problem? Thank you very much!
Best,
Nailin
--
Nailin Yao, PhD
Postdoctoral Associate
Department of Psychiatry, Yale University
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