Re: [HCP-Users] Downloading movement regressors from HYA release
Thank you very much!
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Hodge, Michael"
Date: Thursday, May 30, 2019 at 7:24 AM
To: "Harms, Michael" , Leonardo Tozzi ,
"hcp-users@humanconnectome.org"
Subject: RE: [HCP-Users] Downloading movement regressors from HYA release
Hi Leonardo,
There was a problem with the resource catalogs for those 5 subjects. I believe
the files should now be accessible via the URL you were using. Let me know if
that’s not the case.
Regards,
Mike
From: Harms, Michael
Sent: Wednesday, May 29, 2019 1:51 PM
To: Leonardo Tozzi ; hcp-users@humanconnectome.org
Cc: Hodge, Michael
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Which specific files (i.e., which runs) is curl not finding for those remaining
subjects?
Mike Hodge will likely need to investigate further, because I’m able to find
the expected files on our local file systems for 101006 at least. It may be
something specific to how REST works, with perhaps a small number of files not
“in sync” between what exists on the file systems vs. what the database thinks
is available (just guessing…).
You could simply download the MPP packages for the small number of remaining
subjects through ConnectomeDB.
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: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Wednesday, May 29, 2019 at 1:44 PM
To: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
I did and actually some subjects worked, but not these ones: 101006 159441
926862 927359 942658
I still get a “cannot find file” error (10.4.5).
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Wednesday, May 29, 2019 at 10:39 AM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Did you try downloading again, just in case there was a transfer glitch?
Because the Movement_RelativeRMS.txt files appear to be present in the database
for all 4 rfMRI runs of 101006 (the one subject I checked).
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: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Wednesday, May 29, 2019 at 11:40 AM
To: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Dear Michael,
I have now downloaded the majority of subjects with:
curl -o …/${sub}_${run}_Movement_RelativeRMS.txt -u USER:PASS
https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_CREST/files/MNINonLinear/Results/${run}/Movement_RelativeRMS.txt<https://db.humanconnectome.org/data/projects/HCP_1200/subjects/$%7bsub%7d/experiments/$%7bsub%7d_CREST/files/MNINonLinear/Results/$%7brun%7d/Movement_RelativeRMS.txt>
However, these subjects still seem to be missing: 101006 127226 148335 159441
188145 204016 285345 316835 368551 926862 927359 942658
Is that normal?
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Wednesday, May 15, 2019 at 9:31 AM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Hi,
The M
[HCP-Users] Item data for NIH Emotion battery
Dear Experts, I would like to access the item-level data for the NIH Emotion battery of the young adult release. How can I do that? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Researcher Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Downloading movement regressors from HYA release
I did and actually some subjects worked, but not these ones: 101006 159441
926862 927359 942658
I still get a “cannot find file” error (10.4.5).
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Harms, Michael"
Date: Wednesday, May 29, 2019 at 10:39 AM
To: Leonardo Tozzi , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Did you try downloading again, just in case there was a transfer glitch?
Because the Movement_RelativeRMS.txt files appear to be present in the database
for all 4 rfMRI runs of 101006 (the one subject I checked).
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: Leonardo Tozzi
Date: Wednesday, May 29, 2019 at 11:40 AM
To: "Harms, Michael" , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Dear Michael,
I have now downloaded the majority of subjects with:
curl -o …/${sub}_${run}_Movement_RelativeRMS.txt -u USER:PASS
https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_CREST/files/MNINonLinear/Results/${run}/Movement_RelativeRMS.txt<https://db.humanconnectome.org/data/projects/HCP_1200/subjects/$%7bsub%7d/experiments/$%7bsub%7d_CREST/files/MNINonLinear/Results/$%7brun%7d/Movement_RelativeRMS.txt>
However, these subjects still seem to be missing: 101006 127226 148335 159441
188145 204016 285345 316835 368551 926862 927359 942658
Is that normal?
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Harms, Michael"
Date: Wednesday, May 15, 2019 at 9:31 AM
To: Leonardo Tozzi , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Hi,
The Movement_RelativeRMS.txt files aren’t part of the specific “${run}_FIX”
resource that you tried to reference.
If you have access to outputs in our standard file/directory organization
(e.g., Amazon S3, Connectome-in-a-Box, or our downloaded “packages”), the
Movement_RelativeRMS.txt files can be found at
${subj}/MNINonLinear/Results/${run}.
If not, the “CREST” resource (search the previous HCP-User emails) is what we
are intending users to use, which is intended to mimic the standard
file/directory organization in terms of where files are located.
See FAQ 15 here
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ
and the archived user list posts referenced therein.
Regarding your item (2), I just confirmed that Movement_Regressors.txt exists
for all 4 REST runs for all 6 of those subjects at MNINonLinear/Results/${run}
in our unpacked packages, and thus should exist in Amazon S3,
Connectome-in-a-Box, and via the CREST resource as well.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: on behalf of Leonardo Tozzi
Date: Tuesday, May 14, 2019 at 3:50 PM
To: "hcp-users@humanconnectome.org"
Subject: [HCP-Users] Downloading movement regressors from HYA release
Dear Experts,
Similarly to what described in this thread:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01342.html
I have downloaded motion regressors for files from the healthy young adult
release with the following command:
curl -o …/${sub}_${run}_Movement_ Regressors.txt -u USER:PASSWORD
https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_3T/resources/${run}_FIX/files/${run}/Movement_Regressors.txt
However, I have 2 follow-up questions.
1. I would like to download the relative motion file,
Movement_RelativeRMS.txt, to do some motion censoring on the resting state
data. But if I try the same command with Movement_RelativeRMS.txt instead of
Movement_Regressors.txt I get an error saying that the file does not exist.
2. For some subjects, I can’t find even the Movement_Regressors.txt. Is
there any reason for this? These are the IDs: '127226' '130114' '169040'
'329844' '908860' '971160'
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (6
Re: [HCP-Users] Downloading movement regressors from HYA release
Dear Michael,
I have now downloaded the majority of subjects with:
curl -o …/${sub}_${run}_Movement_RelativeRMS.txt -u USER:PASS
https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_CREST/files/MNINonLinear/Results/${run}/Movement_RelativeRMS.txt<https://db.humanconnectome.org/data/projects/HCP_1200/subjects/$%7bsub%7d/experiments/$%7bsub%7d_CREST/files/MNINonLinear/Results/$%7brun%7d/Movement_RelativeRMS.txt>
However, these subjects still seem to be missing: 101006 127226 148335 159441
188145 204016 285345 316835 368551 926862 927359 942658
Is that normal?
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Researcher
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Harms, Michael"
Date: Wednesday, May 15, 2019 at 9:31 AM
To: Leonardo Tozzi , "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] Downloading movement regressors from HYA release
Hi,
The Movement_RelativeRMS.txt files aren’t part of the specific “${run}_FIX”
resource that you tried to reference.
If you have access to outputs in our standard file/directory organization
(e.g., Amazon S3, Connectome-in-a-Box, or our downloaded “packages”), the
Movement_RelativeRMS.txt files can be found at
${subj}/MNINonLinear/Results/${run}.
If not, the “CREST” resource (search the previous HCP-User emails) is what we
are intending users to use, which is intended to mimic the standard
file/directory organization in terms of where files are located.
See FAQ 15 here
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ
and the archived user list posts referenced therein.
Regarding your item (2), I just confirmed that Movement_Regressors.txt exists
for all 4 REST runs for all 6 of those subjects at MNINonLinear/Results/${run}
in our unpacked packages, and thus should exist in Amazon S3,
Connectome-in-a-Box, and via the CREST resource as well.
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: on behalf of Leonardo Tozzi
Date: Tuesday, May 14, 2019 at 3:50 PM
To: "hcp-users@humanconnectome.org"
Subject: [HCP-Users] Downloading movement regressors from HYA release
Dear Experts,
Similarly to what described in this thread:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01342.html
I have downloaded motion regressors for files from the healthy young adult
release with the following command:
curl -o …/${sub}_${run}_Movement_ Regressors.txt -u USER:PASSWORD
https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_3T/resources/${run}_FIX/files/${run}/Movement_Regressors.txt
However, I have 2 follow-up questions.
1. I would like to download the relative motion file,
Movement_RelativeRMS.txt, to do some motion censoring on the resting state
data. But if I try the same command with Movement_RelativeRMS.txt instead of
Movement_Regressors.txt I get an error saying that the file does not exist.
2. For some subjects, I can’t find even the Movement_Regressors.txt. Is
there any reason for this? These are the IDs: '127226' '130114' '169040'
'329844' '908860' '971160'
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
___
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[HCP-Users] Downloading movement regressors from HYA release
Dear Experts,
Similarly to what described in this thread:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01342.html
I have downloaded motion regressors for files from the healthy young adult
release with the following command:
curl -o …/${sub}_${run}_Movement_ Regressors.txt -u USER:PASSWORD
https://db.humanconnectome.org/data/projects/HCP_1200/subjects/${sub}/experiments/${sub}_3T/resources/${run}_FIX/files/${run}/Movement_Regressors.txt
However, I have 2 follow-up questions.
1. I would like to download the relative motion file,
Movement_RelativeRMS.txt, to do some motion censoring on the resting state
data. But if I try the same command with Movement_RelativeRMS.txt instead of
Movement_Regressors.txt I get an error saying that the file does not exist.
2. For some subjects, I can’t find even the Movement_Regressors.txt. Is
there any reason for this? These are the IDs: '127226' '130114' '169040'
'329844' '908860' '971160'
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] ICA FIX output missing
Dear Tim,
True, it had not been added to the path. Now I added it, but I get the error
(in .fix.log):
{^HError using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file /tmp/tp1378796874179334.gii failed.
Error in gifti (line 71)
this = read_gifti_file_standalone(varargin{1},giftistruct);
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 46)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: Timothy Coalson
Date: Tuesday, February 26, 2019 at 4:38 PM
To: Leonardo Tozzi
Cc: "Harms, Michael" , "Glasser, Matthew"
, "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] ICA FIX output missing
That is saying that you don't have the matlab gifti library installed (or it
isn't on your matlab path).
Tim
On Tue, Feb 26, 2019 at 6:09 PM Leonardo Tozzi
mailto:lto...@stanford.edu>> wrote:
Dear Michael,
Thank you very much for all the consideration on the use of FIX for the task
data.
I have tried the addition you suggest. I think the command is detected, but I
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:
{^HUndefined function or variable 'gifti'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 46)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H
Would you have any thoughts on this?
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Harms, Michael" mailto:mha...@wustl.edu>>
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" mailto:glass...@wustl.edu>>,
Leonardo Tozzi mailto:lto...@stanford.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Cc: "Burgess, Gregory" mailto:gburg...@wustl.edu>>
Subject: Re: [HCP-Users] ICA FIX output missing
Hi Leonardo,
Couple things:
1) In the context of FIX, things get a little convoluted, since the FIX
distribution has its own settings.sh file that needs to be set appropriately.
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t
necessarily relevant. In the settings.sh file for FIX on our cluster, we use
the following construction:
if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already
in your path.
2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX,
gets applied again with TaskfMRILevel1.sh. This script needs to be modified to
be smarter regarding the temporal filtering (i.e., provide an option to NOT
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of
the task regressor prior to the GLM, which means that variance removed during
FIX can be reintroduced during the task GLM fitting (depending on the extent to
which the space spanned by the noise regressors overlaps with the task GLM).
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email:
mha...@wustl.edu<mailto:mha...@wustl.edu>
From: "Glasser, Matthew" mailto:glass...@wustl.edu>>
Date: Monday, February 25, 2019 at 6:53 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "Harms,
Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA FIX output missing
You’ll want to be using wb_command 1.3.2. I am not aware of any modifications
that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have
analyzed hundreds of subjects after MR+FIX.
As for this issue, is wb_command set properly here:
https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh
What about on your ${PATH}?
As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as testing
has concluded successfully.
Matt.
From:
mailto:hcp-users-
Re: [HCP-Users] ICA FIX output missing
Dear Michael,
Thank you very much for all the consideration on the use of FIX for the task
data.
I have tried the addition you suggest. I think the command is detected, but I
get the following error in tfMRI_EMOTION_RL_hp2000.ica/.fix.log:
{^HUndefined function or variable 'gifti'.
Error in ciftiopen (line 31)
cifti = gifti([tmpfile '.gii']);
Error in fix_3_clean (line 46)
BO=ciftiopen('Atlas.dtseries.nii',WBC);
}^H
Would you have any thoughts on this?
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Harms, Michael"
Date: Tuesday, February 26, 2019 at 7:37 AM
To: "Glasser, Matthew" , Leonardo Tozzi
, "hcp-users@humanconnectome.org"
Cc: "Burgess, Gregory"
Subject: Re: [HCP-Users] ICA FIX output missing
Hi Leonardo,
Couple things:
1) In the context of FIX, things get a little convoluted, since the FIX
distribution has its own settings.sh file that needs to be set appropriately.
If you’ve hard-coded the FSL_FIX_WBC variable in that settings.sh file, then
the location to wb_command in the Examples/Scripts/SetUpHCPPipeline.sh isn’t
necessarily relevant. In the settings.sh file for FIX on our cluster, we use
the following construction:
if [ -x "$(command -v wb_command)" ]; then
FSL_FIX_WBC=$(command -v wb_command)
else
echo "ERROR in $0: wb_command (Workbench) must be in your path"
exit 1
fi
so that FIX does actually respect that location of wb_command that is already
in your path.
2) Regarding MR-FIX and the TaskfMRIAnalysis scripts, while they may run after
MR-FIX, there are two issues that need to be addressed yet:
a) The temporal filter, which was presumably already applied during MR-FIX,
gets applied again with TaskfMRILevel1.sh. This script needs to be modified to
be smarter regarding the temporal filtering (i.e., provide an option to NOT
reapply the temporal filter).
b) The space spanned by the noise regressors from FIX is not regressed out of
the task regressor prior to the GLM, which means that variance removed during
FIX can be reintroduced during the task GLM fitting (depending on the extent to
which the space spanned by the noise regressors overlaps with the task GLM).
Cheers,
-MH
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: "Glasser, Matthew"
Date: Monday, February 25, 2019 at 6:53 PM
To: Leonardo Tozzi , "Harms, Michael" ,
"hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] ICA FIX output missing
You’ll want to be using wb_command 1.3.2. I am not aware of any modifications
that are necessary to use the TaskfMRIAnalysis scripts on MR+FIX data and have
analyzed hundreds of subjects after MR+FIX.
As for this issue, is wb_command set properly here:
https://github.com/Washington-University/HCPpipelines/blob/master/Examples/Scripts/SetUpHCPPipeline.sh
What about on your ${PATH}?
As for MR+FIX itself, we are only waiting on an FSL 6.0.1 release as testing
has concluded successfully.
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Monday, February 25, 2019 at 5:09 PM
To: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ICA FIX output missing
Dear Michael,
Thank you for pointing me to the logfiles.
It seems like the script is not finding the directory where wb_command is. In
my case, I am loading it as a module in my HPC cluster. I have also put its
path in ICAFIX/fix1.067/settings.sh as follows:
# Set this to the location of the HCP Workbench command for your platform
FSL_FIX_WBC='/share/software/user/open/workbench/1.3.1/bin/wb_command';
However, the script does not seem to “see” this path and instead uses the
setting I was using on my local machine. In the logfile
tfMRI_EMOTION_RL_hp2000.ica/.fix.log, I get the following error:
/bin/bash: /Applications/workbench/bin_macosx64/wb_command: No such file or
directory
Is there another place in the scripts that is overriding my settings.sh?
Concerning the length or the runs, I will look into the multirun
implementation, but indeed my intention was of using the TaskfMRIAnalysis
scripts to get my “activations”.
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
Re: [HCP-Users] ICA FIX output missing
Dear Michael, Thank you for pointing me to the logfiles. It seems like the script is not finding the directory where wb_command is. In my case, I am loading it as a module in my HPC cluster. I have also put its path in ICAFIX/fix1.067/settings.sh as follows: # Set this to the location of the HCP Workbench command for your platform FSL_FIX_WBC='/share/software/user/open/workbench/1.3.1/bin/wb_command'; However, the script does not seem to “see” this path and instead uses the setting I was using on my local machine. In the logfile tfMRI_EMOTION_RL_hp2000.ica/.fix.log, I get the following error: /bin/bash: /Applications/workbench/bin_macosx64/wb_command: No such file or directory Is there another place in the scripts that is overriding my settings.sh? Concerning the length or the runs, I will look into the multirun implementation, but indeed my intention was of using the TaskfMRIAnalysis scripts to get my “activations”. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" Date: Monday, February 25, 2019 at 9:59 AM To: Leonardo Tozzi , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] ICA FIX output missing Hi, The log files for ICA FIX are a bit scattered. In the .ica directory check: .fix_2b_predict.log (from the prediction – i.e,. R code) and .fix.log (from the cleaning stage). And in the .ica/fix directory, check logMatlab.txt (I believe that is from the feature extraction stage). Note that our recommendation is to use “multi-run” FIX on the task data, due to its shorter run length. We hope to have an announcement on that in the near future. In that regard, you would implement your desired filtering as part of the MR-FIX cleaning (and there is a new “polynomial detrend” option, for faster execution), although I believe that we haven’t quite gotten around to adapting the TaskfMRIAnalysis scripts to work on data from MR-FIX. Cheers, -MH -- Michael Harms, Ph.D. --- Associate Professor of Psychiatry Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu From: on behalf of Leonardo Tozzi Date: Monday, February 25, 2019 at 11:42 AM To: "hcp-users@humanconnectome.org" Subject: [HCP-Users] ICA FIX output missing Dear Experts, I have been trying to use ICA FIX to denoise task data of a large number of subjects from the HYA release. I have managed to make it run with no errors on our local HPC cluster, but I still have one problem. In the vast majority of subjects, even if FIX works and produces a file (“fix4melview_HCP_hp2000_thr10.txt”) which shows which components are noise, I don’t get the final output, for example “tfMRI_EMOTION_RL_Atlas_hp2000_clean.dtseries.nii”. This is especially puzzling since it does seem to work for a minority of subjects. The matlab log also shows no errors. A related question I would have is what filter you would recommend for task data. My intention is to use a GLM on the cleaned data, so is 2000 (linear detrending) ok, since then a lower high-pass will be applied in the GLM step? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ 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
[HCP-Users] ICA FIX output missing
Dear Experts, I have been trying to use ICA FIX to denoise task data of a large number of subjects from the HYA release. I have managed to make it run with no errors on our local HPC cluster, but I still have one problem. In the vast majority of subjects, even if FIX works and produces a file (“fix4melview_HCP_hp2000_thr10.txt”) which shows which components are noise, I don’t get the final output, for example “tfMRI_EMOTION_RL_Atlas_hp2000_clean.dtseries.nii”. This is especially puzzling since it does seem to work for a minority of subjects. The matlab log also shows no errors. A related question I would have is what filter you would recommend for task data. My intention is to use a GLM on the cleaned data, so is 2000 (linear detrending) ok, since then a lower high-pass will be applied in the GLM step? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Regress confounds out of CIFTIs
Dear Matt, Looks like I really need to improve my linear algebra. Thank you very much! Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" Date: Thursday, January 24, 2019 at 3:05 PM To: Leonardo Tozzi , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Regress confounds out of CIFTIs We do this in matlab. It is not necessary to loop, just use proper matrix math. For example: newdtseries = dtseries - (demean(regressor) * (pinv(demean(regressor)) * dtseries'))’; Where demean(regressor) removes the mean of each regressor. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Thursday, January 24, 2019 at 2:04 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Regress confounds out of CIFTIs Dear Experts, I have a text file of confound regressors that I would like to regress out of a resting state .dtseries.nii file and save the residuals of this procedure as a new .dtseries.nii file. I was wondering if there is a computationally efficient way of doing this, possibly using the wb_command. Right now, the only thing I can think about is using matlab but it is obviously impractical to loop over the 90k greyordinates. I have looked into the fsl_glm command, but it doesn’t take in CIFTIs, so I would have to then work on the NIFTI and transform it to CIFTI again, for example by rerunning the surface preprocessing step. Would you have any suggestions? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ 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] Regress confounds out of CIFTIs
Dear Experts, I have a text file of confound regressors that I would like to regress out of a resting state .dtseries.nii file and save the residuals of this procedure as a new .dtseries.nii file. I was wondering if there is a computationally efficient way of doing this, possibly using the wb_command. Right now, the only thing I can think about is using matlab but it is obviously impractical to loop over the 90k greyordinates. I have looked into the fsl_glm command, but it doesn’t take in CIFTIs, so I would have to then work on the NIFTI and transform it to CIFTI again, for example by rerunning the surface preprocessing step. Would you have any suggestions? Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis
Dear Experts, I had a brief follow-up question on what was mentioned in this thread about running a group ICA following FIX. In the case where subjects have 2 sessions, for example resting state or the tasks in the HCP data, is it possible to run a multi-subject multi-session group ICA? From the MELODIC FSL page (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC) it seems that tensor ICA can only handle multiple subjects with one session having the same design (as is the case in the HCP data). Is this where the multi-run pipeline you mentioned would come in? Would you have any alternative suggestions on how to handle multi-session data at the group level? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Leonardo Tozzi Date: Wednesday, January 9, 2019 at 9:02 AM To: "Glasser, Matthew" , "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis It worked! Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" Date: Tuesday, January 8, 2019 at 3:52 PM To: Leonardo Tozzi , "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Point it to the folder where those functions are. Matt. From: Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 5:50 PM To: "Harms, Michael" mailto:mha...@wustl.edu>>, Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear Michael, The hcp_fix in the master works with fix1.067 up to the last step. It does compute and I think classify the components, but it throws an error when it should clean up the data: FIX Applying cleanup using cleanup file: rfMRI_REST1_PA_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 0 Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean" Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean_vn" I found a thread on the mailing list related to this problem here: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg07077.html Timothy Coalson answered saying: .”fix.log says that the specified path for the cifti matlab functions is wrong (nonexistent directory).”. Indeed my .fix.log file says: [Warning: Name is nonexistent or not a directory: /vols/Data/HCP/workbench/CIFTIMatlabReaderWriter] I think this comes from the file: fix1.067/settings.sh. Inside it, it says: # Set this to CIFTI Matlab Reader/Writer for use within HCP pipelines FSL_FIX_CIFTIRW='/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter'; I am unsure what is meant here and where I should point this variable: I am using the ciftiopen and ciftisave functions to open and read cifti files. Would you have any suggestion on what the FSL_FIX_CIFTIRW variable should be so that I can write the cleaned timeseries? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" mailto:mha...@wustl.edu>> Date: Tuesday, January 8, 2019 at 1:58 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis We run a group ICA following FIX (ICA) cleanup all the time. BTW: The whole HCP FIX suite is getting a thorough updating. I’m not sure if the ‘hcp_fix’ currently in the github master even works or not. Hopefully we’ll have GitHub updated within a week. The main issue then with MR-FIX will be the need for a new FSL release (which is pending as well). 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: Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 3:49 PM To: "Harms, Michael" mailto:mha...@wustl.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>>, "hcp-users@h
Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis
It worked! Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" Date: Tuesday, January 8, 2019 at 3:52 PM To: Leonardo Tozzi , "Harms, Michael" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Point it to the folder where those functions are. Matt. From: Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 5:50 PM To: "Harms, Michael" mailto:mha...@wustl.edu>>, Matt Glasser mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear Michael, The hcp_fix in the master works with fix1.067 up to the last step. It does compute and I think classify the components, but it throws an error when it should clean up the data: FIX Applying cleanup using cleanup file: rfMRI_REST1_PA_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 0 Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean" Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean_vn" I found a thread on the mailing list related to this problem here: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg07077.html Timothy Coalson answered saying: .”fix.log says that the specified path for the cifti matlab functions is wrong (nonexistent directory).”. Indeed my .fix.log file says: [Warning: Name is nonexistent or not a directory: /vols/Data/HCP/workbench/CIFTIMatlabReaderWriter] I think this comes from the file: fix1.067/settings.sh. Inside it, it says: # Set this to CIFTI Matlab Reader/Writer for use within HCP pipelines FSL_FIX_CIFTIRW='/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter'; I am unsure what is meant here and where I should point this variable: I am using the ciftiopen and ciftisave functions to open and read cifti files. Would you have any suggestion on what the FSL_FIX_CIFTIRW variable should be so that I can write the cleaned timeseries? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" mailto:mha...@wustl.edu>> Date: Tuesday, January 8, 2019 at 1:58 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis We run a group ICA following FIX (ICA) cleanup all the time. BTW: The whole HCP FIX suite is getting a thorough updating. I’m not sure if the ‘hcp_fix’ currently in the github master even works or not. Hopefully we’ll have GitHub updated within a week. The main issue then with MR-FIX will be the need for a new FSL release (which is pending as well). 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: Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 3:49 PM To: "Harms, Michael" mailto:mha...@wustl.edu>>, "Glasser, Matthew" mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear Matthew and Michael, Thank you very much for your suggestions! I will then wait for your release of the multi-run fix, in the meantime I will try to run it on the individual tasks/resting state sessions. Just a follow-up question: would it make sense to you to first run FIX to remove artifacts, then run MELODIC ICA on the cleaned data at the group level to get some group components and then get the individual components with double regression? Or is there some problem you see in running an ICA after an ICA? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" mailto:mha...@wustl.edu>> Date: Tuesday, January 8, 2019 at 1:40 PM To: "Glasser, Matthew" mailto:glass...@wustl.edu>>, Leonardo Tozzi mailto:lto...@stanford.ed
Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis
Dear Michael, The hcp_fix in the master works with fix1.067 up to the last step. It does compute and I think classify the components, but it throws an error when it should clean up the data: FIX Applying cleanup using cleanup file: rfMRI_REST1_PA_hp2000.ica/fix4melview_HCP_hp2000_thr10.txt and motion cleanup set to 0 Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean" Could not find a supported file with prefix "rfMRI_REST1_PA_hp2000.ica/filtered_func_data_clean_vn" I found a thread on the mailing list related to this problem here: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg07077.html Timothy Coalson answered saying: .”fix.log says that the specified path for the cifti matlab functions is wrong (nonexistent directory).”. Indeed my .fix.log file says: [Warning: Name is nonexistent or not a directory: /vols/Data/HCP/workbench/CIFTIMatlabReaderWriter] I think this comes from the file: fix1.067/settings.sh. Inside it, it says: # Set this to CIFTI Matlab Reader/Writer for use within HCP pipelines FSL_FIX_CIFTIRW='/vols/Data/HCP/workbench/CIFTIMatlabReaderWriter'; I am unsure what is meant here and where I should point this variable: I am using the ciftiopen and ciftisave functions to open and read cifti files. Would you have any suggestion on what the FSL_FIX_CIFTIRW variable should be so that I can write the cleaned timeseries? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" Date: Tuesday, January 8, 2019 at 1:58 PM To: Leonardo Tozzi , "Glasser, Matthew" Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis We run a group ICA following FIX (ICA) cleanup all the time. BTW: The whole HCP FIX suite is getting a thorough updating. I’m not sure if the ‘hcp_fix’ currently in the github master even works or not. Hopefully we’ll have GitHub updated within a week. The main issue then with MR-FIX will be the need for a new FSL release (which is pending as well). 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: Leonardo Tozzi Date: Tuesday, January 8, 2019 at 3:49 PM To: "Harms, Michael" , "Glasser, Matthew" , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear Matthew and Michael, Thank you very much for your suggestions! I will then wait for your release of the multi-run fix, in the meantime I will try to run it on the individual tasks/resting state sessions. Just a follow-up question: would it make sense to you to first run FIX to remove artifacts, then run MELODIC ICA on the cleaned data at the group level to get some group components and then get the individual components with double regression? Or is there some problem you see in running an ICA after an ICA? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" Date: Tuesday, January 8, 2019 at 1:40 PM To: "Glasser, Matthew" , Leonardo Tozzi Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Hi Leonardo, Note that we’re in the middle of a rather large set of modifications related to “multi-run” FIX, and it isn’t quite ready for easy public use. Hopefully soon. 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: Tuesday, January 8, 2019 at 3:20 PM To: Leonardo Tozzi , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis I would recommend running the multi-run FIX pipeline for that on all the fMRI data together. That works on the volume data and then also cleans the CIFTI data at the same time. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 11:35 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HC
Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis
Dear Matthew and Michael, Thank you very much for your suggestions! I will then wait for your release of the multi-run fix, in the meantime I will try to run it on the individual tasks/resting state sessions. Just a follow-up question: would it make sense to you to first run FIX to remove artifacts, then run MELODIC ICA on the cleaned data at the group level to get some group components and then get the individual components with double regression? Or is there some problem you see in running an ICA after an ICA? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Harms, Michael" Date: Tuesday, January 8, 2019 at 1:40 PM To: "Glasser, Matthew" , Leonardo Tozzi Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis Hi Leonardo, Note that we’re in the middle of a rather large set of modifications related to “multi-run” FIX, and it isn’t quite ready for easy public use. Hopefully soon. 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: Tuesday, January 8, 2019 at 3:20 PM To: Leonardo Tozzi , "hcp-users@humanconnectome.org" Subject: Re: [HCP-Users] Identifying noise components in group MELODIC on ciftis I would recommend running the multi-run FIX pipeline for that on all the fMRI data together. That works on the volume data and then also cleans the CIFTI data at the same time. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, January 8, 2019 at 11:35 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Identifying noise components in group MELODIC on ciftis Dear experts, I have preprocessed with the minimal preprocessing pipeline some data which includes resting state and 3 fMRI tasks. I have then ran MELODIC group ICA on the resulting dtseries.nii files (for each task separately). My question is this: I have only greyordinate data in the outputs, so how can I optimally identify the noise components since I have no data for example from the CSF or white matter? I am also wondering if running the ICA on the greyordinate data is already somehow excluding the noise components that are predominantly in the CSF and white matter. I was thinking one way I could proceed is to use the statistics produced from MELODIC of the comparison between the components and the “background noise” (although I am unsure about how this is defined) and/or enter the GLMs of my tasks in MELODIC and see if I find components that correlate with the design (but then I would not know what to do with resting state). Another possibility would be to use the FIX pipeline, but I am not sure if it’s implemented for tasks and if it can be used at the group level. In any case, I wanted to make sure that the processing is the same for resting state and task data. Also, I would probably need to retrain the classifier, since we are conducting our experiment at a different site and on a GE magnet, correct? I would appreciate any pointers on how to best proceed with this matter. Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ 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 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 o
[HCP-Users] Identifying noise components in group MELODIC on ciftis
Dear experts, I have preprocessed with the minimal preprocessing pipeline some data which includes resting state and 3 fMRI tasks. I have then ran MELODIC group ICA on the resulting dtseries.nii files (for each task separately). My question is this: I have only greyordinate data in the outputs, so how can I optimally identify the noise components since I have no data for example from the CSF or white matter? I am also wondering if running the ICA on the greyordinate data is already somehow excluding the noise components that are predominantly in the CSF and white matter. I was thinking one way I could proceed is to use the statistics produced from MELODIC of the comparison between the components and the “background noise” (although I am unsure about how this is defined) and/or enter the GLMs of my tasks in MELODIC and see if I find components that correlate with the design (but then I would not know what to do with resting state). Another possibility would be to use the FIX pipeline, but I am not sure if it’s implemented for tasks and if it can be used at the group level. In any case, I wanted to make sure that the processing is the same for resting state and task data. Also, I would probably need to retrain the classifier, since we are conducting our experiment at a different site and on a GE magnet, correct? I would appreciate any pointers on how to best proceed with this matter. Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Binary label from surface
To Whom It May Concern,
I apologise in advance since this is probably a trivial question, but I tried
browsing the list and couldn’t find a clear answer. I would like to obtain a
binary dlabel for a surface. The overarching goal is to create a network mask
converting it from some volumetric clusters.
So far I have done:
wb_command -volume-to-surface-mapping $maskdir/$mask.nii.gz
$subsdir/$sub/MNINonLinear/fsaverage_LR32k/${sub}.R.midthickness.32k_fs_LR.surf.gii
${sub}_${mask}_R.func.gii -ribbon-constrained
$subsdir/$sub/MNINonLinear/fsaverage_LR32k/${sub}.R.white.32k_fs_LR.surf.gii
$subsdir/$sub/MNINonLinear/fsaverage_LR32k/${sub}.R.pial.32k_fs_LR.surf.gii
To map the network clusters in MNI space to the individual grey matter surface
(for left and right). I get two .func.gii files (one for the left cortex, one
for the right).
But then if I do:
wb_command -cifti-create-label ${sub}_${mask}.dlabel.nii -left-label
$subsdir/$sub/MNINonLinear/fsaverage_LR32k/${sub}.L.aparc.32k_fs_LR.label.gii
-roi-left ${sub}_${mask}_L.func.gii -right-label
$subsdir/$sub/MNINonLinear/fsaverage_LR32k/${sub}.R.aparc.32k_fs_LR.label.gii
-roi-right ${sub}_${mask}_R.func.gii
I get a parcellation whose labels correspond for example to the Freesurfer
atlas. Is there a way to simply have all the greyordinates of my network be 1
and have my own custom label, say “Network1”? I could change the values in
matlab but I was wondering if there is a way to do it “properly” in wb_command.
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
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Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation
Dear Matt,
In my previous call, I did get a matrix called fdt_matrix1.dot, which is large
(1.33 GB). I guess this is a dense matrix, but then I wonder again, there might
be something wrong there as well with the positioning of the subcortical
structures, since I used them as seeds.
So I could make the same call as before, with the –avoid flag for the CSF but I
guess I would still at least need to input the GrayOrdinates.txt which is still
a list of seeds (-x option). How would I obtain the seed list for the
grayordinates?
Thank you,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: "Glasser, Matthew"
Date: Friday, November 9, 2018 at 5:17 PM
To: Leonardo Tozzi , NEUROSCIENCE tim
Cc: Stamatios Sotiropoulos , hcp-users
Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and
subcortical parcellation
I think that --omatrix1 always outputs a dense matrix.
Matt.
From: Leonardo Tozzi mailto:lto...@stanford.edu>>
Date: Friday, November 9, 2018 at 7:15 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, Stamatios
Sotiropoulos
mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>,
hcp-users mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and
subcortical parcellation
Dear Timothy,
Exactly, the goal was to have a structural connectome that has the same parcels
as a functional one and covers the whole brain.
The problem with the surface ROI is that I would be missing the subcortical
structures, which I would like to retain. Maybe there is a simpler way of doing
this that I am missing. I could compute a dense connectome and parcellate it in
a second step maybe? I thought that doing a ROI to ROI approach would be
simpler, but I might have been mistaken.
Looking at the tutorial document, it seems I can obtain a dense connectome with
the following call:
probtrackx2 --samples=../T1w/Diffusion.bedpostX/merged
--mask=../T1w/Diffusion.bedpostX/nodif_brain_mask --xfm=xfms/standard2acpc_dc
--invxfm=xfms/acpc_dc2standard --seedref=T1w_restore.2.nii.gz --loopcheck
--forcedir -c 0.2 --sampvox=2 --randfib=1 --stop=Connectome/stop
--wtstop=Connectome/wtstop –forcefirststep
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 -x Connectomes/GrayOrdinates.txt
--omatrix1 --dir=Connectomes
I am just wondering, what are these inputs and how would I obtain them:
--stop=Connectome/stop, --wtstop=Connectome/wtstop,
waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 and Connectomes/GrayOrdinates.txt ?
Thank you very much,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: Timothy Coalson mailto:tsc...@mst.edu>>
Date: Friday, November 9, 2018 at 5:02 PM
To: Leonardo Tozzi mailto:lto...@stanford.edu>>
Cc: "Glasser, Matthew" mailto:glass...@wustl.edu>>,
Stamatios Sotiropoulos
mailto:stamatios.sotiropou...@ndcn.ox.ac.uk>>,
hcp-users mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and
subcortical parcellation
So, it gets a little complicated, because you have to be careful about what
order the different sections of seeds were put together in. I don't know how
specifying multiple ROIs to probtrackx works, keeping it simple and doing a
single combined surface ROI that covers all the areas you want is more likely
to be usable. The likely reason for the volume loop is because in cifti, the
different subcortical structures are stored as separate sections, but the
entire used part of a surface is stored contiguously in vertex order.
I am still missing the big picture here: why do you want to use labels to
constrain the tractography? Is what you actually want an all parcels by all
parcels matrix?
Tim
On Fri, Nov 9, 2018 at 6:37 PM, Leonardo Tozzi
mailto:lto...@stanford.edu>> wrote:
Dear Timothy,
Thank you very much for your quick response.
To clarify some points: some ROIs were surface based and some voxel based. To
create them, I followed the steps I outlined along this thread, which I am
summarizing below:
# creating cortical labels
wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_LEFT
cortL.label.gii
wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_RIGHT
cortR.label.gii
# creating subcortical labels
wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all subcort.nii.gz
# creating the cortical ROIs
for region in R_V1_ROI R_MST_ROI (etc.)
do
wb_command -gifti-label-to-roi cortR.gii $PWD/ROIs/${region}.func.gii -name
$region
wb_command -gifti-label-to-roi cortL.gii $PWD/ROIs/${region}.func.gii -name
$region
done
# creating the subcortical ROIs
Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation
Dear Timothy,
Exactly, the goal was to have a structural connectome that has the same parcels
as a functional one and covers the whole brain.
The problem with the surface ROI is that I would be missing the subcortical
structures, which I would like to retain. Maybe there is a simpler way of doing
this that I am missing. I could compute a dense connectome and parcellate it in
a second step maybe? I thought that doing a ROI to ROI approach would be
simpler, but I might have been mistaken.
Looking at the tutorial document, it seems I can obtain a dense connectome with
the following call:
probtrackx2 --samples=../T1w/Diffusion.bedpostX/merged
--mask=../T1w/Diffusion.bedpostX/nodif_brain_mask --xfm=xfms/standard2acpc_dc
--invxfm=xfms/acpc_dc2standard --seedref=T1w_restore.2.nii.gz --loopcheck
--forcedir -c 0.2 --sampvox=2 --randfib=1 --stop=Connectome/stop
--wtstop=Connectome/wtstop –forcefirststep
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 -x Connectomes/GrayOrdinates.txt
--omatrix1 --dir=Connectomes
I am just wondering, what are these inputs and how would I obtain them:
--stop=Connectome/stop, --wtstop=Connectome/wtstop,
waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 and Connectomes/GrayOrdinates.txt ?
Thank you very much,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: Timothy Coalson
Date: Friday, November 9, 2018 at 5:02 PM
To: Leonardo Tozzi
Cc: "Glasser, Matthew" , Stamatios Sotiropoulos
, hcp-users
Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and
subcortical parcellation
So, it gets a little complicated, because you have to be careful about what
order the different sections of seeds were put together in. I don't know how
specifying multiple ROIs to probtrackx works, keeping it simple and doing a
single combined surface ROI that covers all the areas you want is more likely
to be usable. The likely reason for the volume loop is because in cifti, the
different subcortical structures are stored as separate sections, but the
entire used part of a surface is stored contiguously in vertex order.
I am still missing the big picture here: why do you want to use labels to
constrain the tractography? Is what you actually want an all parcels by all
parcels matrix?
Tim
On Fri, Nov 9, 2018 at 6:37 PM, Leonardo Tozzi
mailto:lto...@stanford.edu>> wrote:
Dear Timothy,
Thank you very much for your quick response.
To clarify some points: some ROIs were surface based and some voxel based. To
create them, I followed the steps I outlined along this thread, which I am
summarizing below:
# creating cortical labels
wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_LEFT
cortL.label.gii
wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_RIGHT
cortR.label.gii
# creating subcortical labels
wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all subcort.nii.gz
# creating the cortical ROIs
for region in R_V1_ROI R_MST_ROI (etc.)
do
wb_command -gifti-label-to-roi cortR.gii $PWD/ROIs/${region}.func.gii -name
$region
wb_command -gifti-label-to-roi cortL.gii $PWD/ROIs/${region}.func.gii -name
$region
done
# creating the subcortical ROIs
for region in L_Amygdala R_Amygdala (etc.)
do
wb_command -volume-label-to-roi subcort.nii.gz
$PWD/ROIs_subcort/${region}.nii.gz -name $region
done
# converting cortical ROIs to ASCII
for region in R_V1_ROI R_MST_ROI (etc.)
do
surf2surf -i
/Users/leonardotozzi/Desktop/DiffusionConnectivityTest/conn008/MNINonLinear/fsaverage_LR32k/conn008.R.white.32k_fs_LR.surf.gii
-o $PWD/ROIs_cort/$region.asc --values=$PWD/ROIs_cort/$region.func.gii
--outputtype=ASCII
done
Then I added all these resulting ROIs (cortical + subcortical) into the
seeds.txt file, which is an input to probtrack.
I am wondering if there is not something wrong with my surf2surf call. The
command seems to take caret as convention by default, but are the ROIs at this
point in Freesurfer space? The FDT help gives some info about additional steps
to use Freesurfer ROIs here
(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide) but I am unsure about
whether these apply to output of the HCP pipeline. I am having difficulties
navigating between all these different spaces (MNI, Freesurfer, diffusion
etc.). Also, the subcortical ROIs seem to be in MNI space, which makes me
wonder in what space the cortical ROIs are.
About Matrix1, it’s not symmetric, I built a connectivity matrix by taking the
upper triangle. I think it should track from all my ROIs to all my ROIs.
Concerning wb_command -probtrackx-dot-convert, it requires a few inputs but I
am not sure what files to use.
I hope this adds more information, thank you very much,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry
Rd<https://maps.google.com/?q=401+Quarry+Rd=gma
Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation
Dear Timothy,
Thank you very much for your quick response.
To clarify some points: some ROIs were surface based and some voxel based. To
create them, I followed the steps I outlined along this thread, which I am
summarizing below:
# creating cortical labels
wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_LEFT
cortL.label.gii
wb_command -cifti-separate merged.dlabel.nii COLUMN -label CORTEX_RIGHT
cortR.label.gii
# creating subcortical labels
wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all subcort.nii.gz
# creating the cortical ROIs
for region in R_V1_ROI R_MST_ROI (etc.)
do
wb_command -gifti-label-to-roi cortR.gii $PWD/ROIs/${region}.func.gii -name
$region
wb_command -gifti-label-to-roi cortL.gii $PWD/ROIs/${region}.func.gii -name
$region
done
# creating the subcortical ROIs
for region in L_Amygdala R_Amygdala (etc.)
do
wb_command -volume-label-to-roi subcort.nii.gz
$PWD/ROIs_subcort/${region}.nii.gz -name $region
done
# converting cortical ROIs to ASCII
for region in R_V1_ROI R_MST_ROI (etc.)
do
surf2surf -i
/Users/leonardotozzi/Desktop/DiffusionConnectivityTest/conn008/MNINonLinear/fsaverage_LR32k/conn008.R.white.32k_fs_LR.surf.gii
-o $PWD/ROIs_cort/$region.asc --values=$PWD/ROIs_cort/$region.func.gii
--outputtype=ASCII
done
Then I added all these resulting ROIs (cortical + subcortical) into the
seeds.txt file, which is an input to probtrack.
I am wondering if there is not something wrong with my surf2surf call. The
command seems to take caret as convention by default, but are the ROIs at this
point in Freesurfer space? The FDT help gives some info about additional steps
to use Freesurfer ROIs here
(https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide) but I am unsure about
whether these apply to output of the HCP pipeline. I am having difficulties
navigating between all these different spaces (MNI, Freesurfer, diffusion
etc.). Also, the subcortical ROIs seem to be in MNI space, which makes me
wonder in what space the cortical ROIs are.
About Matrix1, it’s not symmetric, I built a connectivity matrix by taking the
upper triangle. I think it should track from all my ROIs to all my ROIs.
Concerning wb_command -probtrackx-dot-convert, it requires a few inputs but I
am not sure what files to use.
I hope this adds more information, thank you very much,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
From: Timothy Coalson
Date: Friday, November 9, 2018 at 4:11 PM
To: Leonardo Tozzi
Cc: "Glasser, Matthew" , Stamatios Sotiropoulos
, hcp-users
Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and
subcortical parcellation
There is wb_command -probtrackx-dot-convert which should be able to convert the
fdt_matrix1.dot file, which should allow a better visualization of the results.
I'm not entirely clear on the arguments to your probtrackx command, or what
the actual ROIs you used are, but it looks like they were purely voxel-based.
You may need to take something the nodif_brain_mask and turn it into a label
volume with the label name set to "OTHER" (just as a placeholder that should
work), and then we can figure out whether each voxel list needs to be on a row
or a column option (you may need to do something manually to get one of the
voxel lists, depending on the details of what matrix1 does).
I don't know the specifics of matrix1, Stam or Matt can you give me the details
(is it symmetric, and if so is it stored as lower-triangle, what it actually
tracks from and to)?
Tim
On Fri, Nov 9, 2018 at 4:58 PM, Leonardo Tozzi
mailto:lto...@stanford.edu>> wrote:
Dear Matthew,
Thank you, I am rerunning the tractography with that flag (it will take a
while).
In the meantime, I have taken the coordinate file from the output
(“coords_for_fdt_matrix1”, which I think for each seed reports its coordinates
and in which ROI it is), averaged all coordinates with the same label and used
Matlab graph plotting functions to see if the centers of the seeds resembled a
cortical surface.
I am attaching a few images of this. Image 1 shows the nodes from a view that
does resemble a coronal section, with no nodes between the hemispheres. Image2
shows the nodes from another perspective. Image3 shows a graph with the nodes +
edges from the connectivity matrix (thresholded at >1000 fibers).
All in all, I think I do get something that looks like a brain, but I am
concerned with a cluster of points that seem outliers with respect to their
coordinates. You can see them in all three images and they are especially
apparent in the 3rd, since they seem to be connected to many of the cortical
regions. My fear is that these could be the subcortical regions, that for some
reason have completely different coordinates.
Does this make sense to you? Is there some transformation I shoul
[HCP-Users] White matter and CSF masks after minimal HCP processing
To Whom it may concern, In this thread: https://www.mail-archive.com/hcp-users@humanconnectome.org/msg06276.html I found a reference to eroded white matter masks for HCP subjects that should be stored in MNINonLinear/ROIs/CSFReg.2.nii MNINonLinear/ROIs/WMReg.2.nii but after running the HCP pipeline on my own data, these outputs don’t seem to be there. Were these files created ad hoc for this release and would you have a recommended way of obtaining comparable masks? To give you a context, I would like to extract white matter and CSF signals to use aCompCor and add confound regressors to my task GLMs. I was also wondering, in the absence of these masks would it make sense to use atlas-based masks in MNI space and extract the signals from the MNI warped images, like for example /Volumes/LT_storage/Trevor_study/EMOTION_PREPROC/100307/MNINonLinear/Results/tfMRI_EMOTION_LR . Would this be acceptable, for example in the case in which I were to download only the task data from your release (so I wouldn’t have the original T1s)? If not, is there another approach you would recommend? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation
Dear all, Following the very useful guide, I have managed to run the complete ROI to ROI tractography. However, I am not sure how to visualize my tracts from the output of probtrackx2. In particular, I would like to make sure that my seeds have been imported in the correct space as well as my CSF mask for the avoid flag. As in the manual, after running bedpostx, my call of probtrackx2 was as follows: probtrackx2 --samples=DiffusionConnectivityTest/conn008/Diffusion/data.bedpostX/merged --mask=DiffusionConnectivityTest/conn008/Diffusion/data.bedpostX/nodif_brain_mask --seed=DiffusionConnectivityTest/ROIcreation/allseeds.txt --xfm=DiffusionConnectivityTest/conn008/MNINonLinear/xfms/standard2acpc_dc --invxfm=DiffusionConnectivityTest/conn008/MNINonLinear/xfms/acpc_dc2standard --seedref=DiffusionConnectivityTest/conn008/MNINonLinear/T1w_restore.2.nii.gz --loopcheck --forcedir --network --omatrix1 --avoid=DiffusionConnectivityTest/ROIcreation/T1w_restore_brain_seg_0.nii.gz -V 1 --dir=Network allseeds.txt is the list of the ASCII converted surfaces and volumes. In particular, I would like to be sure that I picked the right inputs for –xfm and –invxfm. The outputs of bedpost and the masks I created are not in the same space. As per manual, the segmented CSF is in standard MNI space. Am I correct in assuming that the output of bedpost (after the minimal diffusion preprocessing) is aligned with respect to the ACPC and what the command is doing “under the hood” is taking the transformation from MNI to this space and applying it to the masks I specified? Also, how are the ROIs affected by all this, considering I created them with the surf2surf command giving as input the conn008.R.white.32k_fs_LR.surf.gii and the gifti files from the atlas? I am a bit confused about how all these images in different space come together. Also, would anyone know of a way to visualize my masks and/or the tracts to make sure the tractography ran as intended? After running probtrackx2 I get the following outputs: coords_for_fdt_matrix1 fdt_matrix1.dot fdt_network_matrix probtrackx.log tmpnetmaskfile waytotal fdt_network_matrix is my connectivity matrix of interest, with what I assume is the number of streamlines. I think the file I would need is “coords_for_fdt_matrix1” would anyone have any tips on how to visualize these coordinates on the diffusion data or any other suggestion to check the positioning of the seeds and the tractography results? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Stamatios Sotiropoulos Date: Wednesday, October 31, 2018 at 1:38 AM To: "hcp-users@humanconnectome.org" Cc: Leonardo Tozzi Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation Hi The HCP course tractography practical would be a good way to start (see page 386 onwards): https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7 Briefly, if you have a number of surfaces (need to convert them to ASCII using surf2surf) and subcortical volumes you can merge them into text files and use those as seeds. This will get you a dense connectome which you can then parcellate using any parcellation scheme you would like. Best wishes Stam On 30 Oct 2018, at 23:35, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Also use the label ones to make GIFTI label files. Matt. From: Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, October 30, 2018 at 6:34 PM To: Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation Dear Matthew, Thank you for the very quick response. So for clarification, you would use the following command: wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all subcort.nii.gz To obtain the subcortical volumes. What about the cortical ones? Is the file Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii already usable as input to FSL? I thought I would need a .gii file. Or do I need to use the option in wb_command -cifti-separate: [-label] - repeatable - separate a surface model into a surface label file. In this case, what would be the argument for “ - the structure to output” ? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Tuesday, October 30, 2018 at 4:22 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Diffusion connectivity
Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation
Dear Stam, Thank you very much, I would then try to use the command -gifti-label-to-roi on the cortical label gifti files to obtain my parcels, as I think that computing a dense connectome and then reparcellate it might be a bit excessive for my purposes. I hope this makes sense to you. I will try going through the steps and see if I manage to make it work. Thank you, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: Stamatios Sotiropoulos Date: Wednesday, October 31, 2018 at 1:38 AM To: "hcp-users@humanconnectome.org" Cc: Leonardo Tozzi Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation Hi The HCP course tractography practical would be a good way to start (see page 386 onwards): https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7 Briefly, if you have a number of surfaces (need to convert them to ASCII using surf2surf) and subcortical volumes you can merge them into text files and use those as seeds. This will get you a dense connectome which you can then parcellate using any parcellation scheme you would like. Best wishes Stam On 30 Oct 2018, at 23:35, Glasser, Matthew mailto:glass...@wustl.edu>> wrote: Also use the label ones to make GIFTI label files. Matt. From: Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, October 30, 2018 at 6:34 PM To: Matt Glasser mailto:glass...@wustl.edu>> Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation Dear Matthew, Thank you for the very quick response. So for clarification, you would use the following command: wb_command -cifti-separate merged.dlabel.nii COLUMN -volume-all subcort.nii.gz To obtain the subcortical volumes. What about the cortical ones? Is the file Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii already usable as input to FSL? I thought I would need a .gii file. Or do I need to use the option in wb_command -cifti-separate: [-label] - repeatable - separate a surface model into a surface label file. In this case, what would be the argument for “ - the structure to output” ? Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 From: "Glasser, Matthew" mailto:glass...@wustl.edu>> Date: Tuesday, October 30, 2018 at 4:22 PM To: Leonardo Tozzi mailto:lto...@stanford.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation I would separate the CIFTI file into GIFTI and NIFTI components with wb_command -cifti-separate and follow the instructions for surface tracking on FSL’s website. Matt. From: mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Leonardo Tozzi mailto:lto...@stanford.edu>> Date: Tuesday, October 30, 2018 at 6:19 PM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation To Whom it may concern, I have created a dlabel file by adding to the Glasser Parcellation from BALSA the subcortical regions of the Freesurfer atlas. Now my goal would be to run a tractography analysis and obtain structural connectivity matrices using this cortical+subcortical parcellation. Could you suggest the simplest way to go from my dlabel file to something that is compatible with diffusion software? I know that probtrackx accepts GIFTIs as input, but I was wondering about how to extend this to subcortical areas. Or rather would the simplest solution be to convert each subject’s parcellation into a series of NIFTI files in native/standard space and input these as ROIs into probtrackx? In this case, could you recommend the correct series of workbench commands? I am also open to other software recommendations besides the FSL suite. Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ 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,
[HCP-Users] Diffusion connectivity matrix with cortical and subcortical parcellation
To Whom it may concern, I have created a dlabel file by adding to the Glasser Parcellation from BALSA the subcortical regions of the Freesurfer atlas. Now my goal would be to run a tractography analysis and obtain structural connectivity matrices using this cortical+subcortical parcellation. Could you suggest the simplest way to go from my dlabel file to something that is compatible with diffusion software? I know that probtrackx accepts GIFTIs as input, but I was wondering about how to extend this to subcortical areas. Or rather would the simplest solution be to convert each subject’s parcellation into a series of NIFTI files in native/standard space and input these as ROIs into probtrackx? In this case, could you recommend the correct series of workbench commands? I am also open to other software recommendations besides the FSL suite. Thank you very much, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Visualizing pconn.nii as graph
To Whom it may concern, I have created a pconn.nii file based on connectivity measures obtained based on a parcellation that I put together (dlabel.nii), which contains cortical and subcortical areas (Glasser + Gordon subcortical). This question might be trivial, but I would like to know if it is possible to visualize this matrix as a graph in workbench, i.e. if I can visualize lines “connecting” my parcels based on the values of the pconn file. If this is not possible, I would ask for any tips on how I could get the coordinates of my parcels in a space that at least resembles the brain, so that I can then connect them in another software. From the information I found in the mailing list, there seem to be ways to extract the greyordinate coordinates based on the dlabel.nii file and a corresponding .gii file. However, I was wondering if someone could outline the procedure for me or have any tips on achieving what I am trying to do in an optimal way. Thank you very much. Yours sincerely, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Cortical labels persisting when merging cortical and subcortical regions to create parcellation
To Whom it may concern,
I followed the indications in this thread:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03976.html
To merge the subcortical labels of
Gordon333_FreesurferSubcortical.32k_fs_LR.dlabel.nii with the cortical ones
from
Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii.
In particular I used -cifti-separate with the -volume-all option, followed by
-cifti-create-dense-from-template. With the same commands reported in:
https://www.mail-archive.com/hcp-users@humanconnectome.org/msg03979.html
When I look at my atlas in connectome workbench, everything “looks” fine: the
subcortical volumes are displayed in the volume tab, the surface colors
correspond with the Glasser parcellation. Clicking in the view window also
displays the correct labels in the information window. However, if I click in
“Edit map labels” in the workbench interface, I noticed that the keys of the
Gordon atlas are still present and the “new” labels seem to start at key 334
(since the Gordon has 333 regions). Opening the dlabel file with ciftiopen in
Matlab also returns data that goes from 0 to 712:
atlas=ciftiopen('mergedatlas.dlabel.nii',
'/Applications/workbench/bin_macosx64/wb_command')
atlas =
struct with fields:
cdata: [91282×1 single]
max(atlas.cdata)
ans =
single
712
Interestingly, doing a task analysis using the HCP pipeline and entering the
merged dlabel file as atlas only returns a cifti with the number of regions I
would expect:
img=ciftiopen(‘tfMRI_EMOTION_LR_Atlas_s2_mergedatlas.ptseries.nii’,
'/Applications/workbench/bin_macosx64/wb_command')
img =
struct with fields:
cdata: [379×176 single]
My question is: why are the labels of the Gordon atlas being displayed in the
workbench? Are they being “carried over” as labels that do not actually
correspond to any greyordinates? Should I be worried that these “Phantom
labels” might affect my analyses?
Thank you very much.
Yours faithfully,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
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[HCP-Users] Error writing .ptseries file in Matlab
To Whom it may concern,
I have created a .dlabel.nii file that is a parcellation covering both cortical
and subcortical areas. Then, I have extracted mean values for each of the
parcels from a contrast map using wb_command -cifti-parcellate.
After loading the resulting ptseries.nii files in matlab (using ft_readcifti),
I would like to perform some operations on the values stored in the ptseries
field, create a new .ptseries.nii file with the new values and visualize it in
workbench.
Unfortunately, I can’t succeed in saving a CIFTI file that is read by workbench
correctly.
Given that “cif” is my matlab structure, the output from ft_readcifti, with the
values in cif.ptseries changed with the results of my calculations, I have
attempted to use ft_write_cifti in several ways:
ft_write_cifti('test', cif, 'parameter', 'ptseries', 'brainstructure',
'brainordinate.brainstructure', 'parcellation', 'brainordinate.parcellation')
Returns no errors, but then if I try:
ft_read_cifti('test.ptseries.nii')
Undefined function or variable 'pos'.
Error in ft_read_cifti (line 601)
brainordinate.brainstructure = zeros(size(pos,1),1);
If instead I try:
ft_write_cifti('test', cif, 'parameter', 'ptseries')
I get a long list of regions:
parcelL_Amygdala contains 315 vertices in CIFTI_STRUCTURE_INVALID
parcelR_Amygdala contains 332 vertices in CIFTI_STRUCTURE_INVALID
parcel L_Hippocampus contains 764 vertices in CIFTI_STRUCTURE_INVALID
parcel R_Hippocampus contains 795 vertices in CIFTI_STRUCTURE_INVALID
parcel L_Accumbens contains 135 vertices in CIFTI_STRUCTURE_INVALID
parcel R_Accumbens contains 140 vertices in CIFTI_STRUCTURE_INVALID
parcel L_Caudate contains 728 vertices in CIFTI_STRUCTURE_INVALID
parcel R_Caudate contains 755 vertices in CIFTI_STRUCTURE_INVALID
parcelL_Pallidum contains 297 vertices in CIFTI_STRUCTURE_INVALID
parcelR_Pallidum contains 260 vertices in CIFTI_STRUCTURE_INVALID
parcel L_Putamen contains 1060 vertices in CIFTI_STRUCTURE_INVALID
parcel R_Putamen contains 1010 vertices in CIFTI_STRUCTURE_INVALID
parcelL_Thalamus contains 1288 vertices in CIFTI_STRUCTURE_INVALID
parcelR_Thalamus contains 1248 vertices in CIFTI_STRUCTURE_INVALID
parcel BrainStem contains 3472 vertices in CIFTI_STRUCTURE_INVALID
parcel L_VentralDiencephalon contains 706 vertices in CIFTI_STRUCTURE_INVALID
parcel R_VentralDiencephalon contains 712 vertices in CIFTI_STRUCTURE_INVALID
parcel L_Cerebellum contains 8709 vertices in CIFTI_STRUCTURE_INVALID
parcel R_Cerebellum contains 9144 vertices in CIFTI_STRUCTURE_INVALID
parcel R_V1_ROI contains 787 vertices in
CIFTI_STRUCTURE_CORTEX_RIGHT
parcel R_MST_ROI contains76 vertices in
CIFTI_STRUCTURE_CORTEX_RIGHT
(…)
The file gets written, but if I try to open it I get:
ft_read_cifti('test.ptseries.nii')
Dot indexing is not supported for variables of this type.
Error in ft_read_cifti (line 439)
sel = strcmp({Surface(:).BrainStructure},
Parcel(j).BrainStructure{k});
Workbench also will not open the files generated this way, with two kinds of
errors: for the first file: “xml and nifti header disagree on matrix
dimensions” and for the second one: “Cifti XML error: you must set surfaces
before adding parcels that use them”.
I suspect I am either missing something basic in the syntax of ft_write_cifti
or my original .ptseries.nii files have something strange about them.
Thank you very much.
Yours faithfully,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
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[HCP-Users] Using Glasser parcellation for task activations
To Whom it may concern, I am interested in extracting activations based on an atlas in grayordinate space from the HCP datasets. In particular, I would be interested in using the Glasser parcellation from the BALSA database. In a previous thread on this mailing list I found that this is the file most people have been using: HCP_PhaseTwo/Q1-Q6_RelatedValidation210/MNINonLinear/fsaverage_LR32k/Q1-Q6_RelatedValidation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii I would have a few questions about using this parcellation. My first question (which is probably trivial and I apologize for this) is: does the parcellation also cover subcortical areas or is it just a cortical parcellation? If it’s just cortical, would you have any recommendations on a complementary parcellation to add subcortical areas? I have downloaded some subjects from the 1200 release and I was wondering, do you think it’s reasonable to use this parcellation and apply it to the task contrast maps (zscores) with the wb_command -cifti-parcellate? I know the code to do the individualized parcellation still has to be released, so I was wondering if in the interim this would be an acceptable solution. Thank you very much. Yours faithfully, Leonardo Tozzi, MD, PhD Williams PanLab | Postdoctoral Fellow Stanford University | 401 Quarry Rd lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738 ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
[HCP-Users] Index error in diffusion preprocessing
To Whom it may concern,
I am trying to run the diffusion processing portion of the pipeline on my data,
but it is failing in the eddy step with the following error message:
Wed Aug 1 11:13:12 PDT 2018 - run_eddy.sh:
/share/software/user/open/fsl/5.0.10/bin/eddy_openmp
--imain=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/Pos_Neg
--mask=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/nodif_brain_mask
--index=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/index.txt
--acqp=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/acqparams.txt
--bvecs=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/Pos_Neg.bvecs
--bvals=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/Pos_Neg.bvals
--fwhm=0
--topup=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/topup/topup_Pos_Neg_b0
--out=/scratch/users/ltozzi/HCP_HCPformat/conn009/Diffusion/eddy/eddy_unwarped_images
--flm=quadratic
terminate called after throwing an instance of 'TOPUP::TopupFileIOException'
what(): TopupFileIO:: msg=TopupDatafileReader::ReadOutTime: Invalid index
/home/groups/leanew1/ltozzi/HCPPipeline_3.27.0_sherlock/DiffusionPreprocessing/scripts/run_eddy.sh:
line 380: 33608 Aborted ${eddy_command}
I suspect this is due to the fact that in my data the first volume is not a b0
(the last one is), since in DiffusionPreprocessingBatch.sh I found the
following comment:
# NOTE that PosData defines the reference space in 'topup' and 'eddy' AND it
is assumed that
# each scan series begins with a b=0 acquisition, so that the reference space
in both
# 'topup' and 'eddy' will be defined by the same (initial b=0) volume.
My question is, do you think this is the reason (i.e. the scripts don’t
automatically “reorder” the scans based on the bvals) and if so, what would be
the easiest way to modify them to pick a specific volume instead of the first
one to find the initial b0? I suspect this would involve editing
DiffusionPreprocessing/scripts/basic_preproc.sh, but I was wondering if you
could provide some pointers so make this edit as small as possible (I would
like to avoid “shuffling” my scans, bvals and bvecs before launching the
preprocessing).
Thank you very much.
Yours faithfully,
Leonardo Tozzi, MD, PhD
Williams PanLab | Postdoctoral Fellow
Stanford University | 401 Quarry Rd
lto...@stanford.edu<mailto:lto...@stanford.edu> | (650) 5615738
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[HCP-Users] index.txt file truncated before run_eddy
To Whom it may concern, I am attempting to run the diffusion processing pipeline, by using the scripts from the Washington University github. In particular, I am using the DiffusionPreprocessingBatch.sh script, from the Examples folder. We successfully managed to run the structural preprocessing steps that come before that (Pre and Post freesurfer). The problem I am experiencing with the diffusion scripts is that after running run_topup.sh, the script crashes during run_eddy.sh. With the error message: "eddy: msg=--index must be an 1xN or Nx1 matrix where N is the number of volumes in --imain eddy: msg=Error when attempting to read --index file" The reason for this is that the index.txt file, which is generated by basic_preproc.sh, is only 324 rows long, whereas Pos_Neg.nii.gz, the output of topup, is 328 volumes. Our raw data is encoded in two directions: AP and PA and for each we have a file with 81 and one with 83 directions. So, the number of volumes in Pos_Neg.nii.gz seems to be correct (81+83+81+83=328), but the index file is somehow truncated. Would anyone have some insight in why that could be the case? Thank you very much. Yours faithfully, Leonardo Tozzi, MD., Ph.D. Post-doctoral Fellow Williams PanLab 401 Quarry Road Stanford, CA 94304 United States of America ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
