[HCP-Users] MEG leadfield computation

[Felix Yuan]

Dear HCP experts,

Sorry to bother you, I am going to computing the leadfield of resting state MEG 
preprocessed data.

But in the fieldtrip pipeline, I need to give the coordsys as a parameter.
Can I use the anatomy data and MEG resting state data in the preprocessed 
folder I downloaded from HCP?
Do I also need to transform the coordinate space of anatomy data to MEG data 
space? Could you tell me Whether they have been co-registrated to the same 
space or not?

In this website, 
http://www.fieldtriptoolbox.org/faq/how_are_the_different_head_and_mri_coordinate_systems_defined
I found that if the anatomy data is in the CTF MRI (ALS) space, and MEG data is 
in the 4D/BTi space (ALS), the units of them are different, with mm and m, 
respectively.


Thank you for your attention.
Best wishes,
Felix

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Re: [HCP-Users] Trouble with CIFTI files using FSL 5.0.10 MELODIC

[Glasser, Matthew]

That would be a question for the FSL list.  CIFTI support is somewhat beta at 
this point.

Peace,

Matt.

From: Sarah Ann Levy >
Date: Tuesday, January 9, 2018 at 2:35 PM
To: Matt Glasser >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Trouble with CIFTI files using FSL 5.0.10 MELODIC

Hi Matt,

We were in the GUI. Should we only use terminal for running CIFTI files?

Thank you,
Sarah

From: "Glasser, Matthew" >
Date: Tuesday, January 9, 2018 at 3:34 PM
To: Sarah Ann Levy >, 
"hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Trouble with CIFTI files using FSL 5.0.10 MELODIC

Did you try the --CIFTI flag?

Matt.

From: 
>
 on behalf of Sarah Ann Levy 
>
Date: Tuesday, January 9, 2018 at 2:31 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Trouble with CIFTI files using FSL 5.0.10 MELODIC

Hello,

I would like to run a group analysis on the HCP 1200 resting state data using 
MELODIC. I am running FSL 5.0.10. I have tried inputting this file for MELODIC 
4D data:  rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii but I receive 
an error and it does not accept the file.

I would like to directly run MELODIC on the CIFTI files rather than converting 
to NIFTI, back to CIFTI, etc.

Thank you,
Sarah

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Re: [HCP-Users] Trouble with CIFTI files using FSL 5.0.10 MELODIC

[Glasser, Matthew]

Did you try the --CIFTI flag?

Matt.

From: 
>
 on behalf of Sarah Ann Levy 
>
Date: Tuesday, January 9, 2018 at 2:31 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Trouble with CIFTI files using FSL 5.0.10 MELODIC

Hello,

I would like to run a group analysis on the HCP 1200 resting state data using 
MELODIC. I am running FSL 5.0.10. I have tried inputting this file for MELODIC 
4D data:  rfMRI_REST1_LR_Atlas_MSMAll_hp2000_clean.dtseries.nii but I receive 
an error and it does not accept the file.

I would like to directly run MELODIC on the CIFTI files rather than converting 
to NIFTI, back to CIFTI, etc.

Thank you,
Sarah

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Re: [HCP-Users] Resting State processing

[Timothy Coalson]

To further explain: "latest master" means you should *not* go to the
"releases" page on github.  Instead, go to the main page,
https://github.com/Washington-University/Pipelines , and click the green
"clone or download" button on the upper right above the file list.

Tim


On Tue, Jan 9, 2018 at 11:25 AM, Glasser, Matthew 
wrote:

> See my response to his question.  It should work if you have the latest
> version of master with MSM v2 and everything is installed.
>
> Peace,
>
> Matt.
>
> From: "Sanchez, Juan (NYSPI)" 
> Date: Tuesday, January 9, 2018 at 11:24 AM
> To: Timothy Hendrickson , Matt Glasser <
> glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" 
>
> Subject: Re: [HCP-Users] Resting State processing
>
> I was having the same problem with the 3_22
> *FreeSurfer2CaretConvertAndRegisterNonlinear.sh*
> *and was able to download the msm binaried and the params file
> from https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v1/
> *
>
> however I am runinng into a problem with the script at
>
> ${MSMBin}/msm --levels=4 --conf=${MSMBin}/allparameterssulcDRconf
> --inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${
> Hemisphere}.sphere.rot.native.surf.gii --trans="$AtlasSpaceFolder"/"$
> NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
> --refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".
> sphere."$HighResMesh"k_fs_LR.surf.gii --indata="$AtlasSpaceFolder"/"
> $NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii
> --refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.
> refsulc."$HighResMesh"k_fs_LR.shape.gii --out="$AtlasSpaceFolder"/"$
> NativeFolder"/MSMSulc/${Hemisphere}. --verbose
>
> cd $DIR
>
>cp 
> "$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii
> "$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${
> Hemisphere}.sphere.MSMSulc.native.surf.gii
>
> The HIGHRES file does not exist.
> --
> *From:* hcp-users-boun...@humanconnectome.org  humanconnectome.org> on behalf of Timothy Hendrickson 
> *Sent:* Tuesday, January 9, 2018 12:11:20 PM
> *To:* Glasser, Matthew
> *Cc:* hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] Resting State processing
>
>
> *ATTENTION: This email came from an external source. Do not open
> attachments or click on links from unknown senders or unexpected emails.*
> Hi Matthew,
>
> The file does not exist. I see now that the PostFreeSurfer pipeline I have
> locally is different than the latest version found on github (specifically 
> *FreeSurfer2CaretConvertAndRegisterNonlinear.sh).
> *I see that the line referencing *allparameterssulcDRconf *has been
> commented out in favor of *MSMSulcStrainFinalconf*, however, this file
> does not appear to exist either. Which version of MSM HOCR is the most
> recent that should be used? I am using version 2)
>
> On a completely other note why aren't these configuration files already
> included in the HCP pipelines? It seems very burdensome to require each
> user to mimic the exact version of the MSM binaries that 
> *FreeSurfer2CaretConvertAndRegisterNonlinear.sh
> *expects.
>
> -Tim
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Bioinformatics and Computational Biology M.S. Candidate
> Office: 612-624-6441 <(612)%20624-6441>
> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay)
>
> On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew 
> wrote:
>
> Does the file exist?  That might be the old config file it is looking for
> suggesting that you don’t have the latest master.
>
> Peace,
>
> Matt.
>
> From: Timothy Hendrickson 
> Date: Monday, January 8, 2018 at 9:15 AM
> To: "hcp-users@humanconnectome.org" 
> Cc: Matt Glasser 
> Subject: Re: [HCP-Users] Resting State processing
>
> Hello all,
>
> Despite having the most recent version of the hcp pipeline (3.22) and
> downloading the MSM configuration binaries, however, I am still receiving
> an error when I attempt to run the PreFreeSurfer pipeline with
> RegName="MSMSulc". This is the error message I receive:
> */opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
> Couldn't open the file! *
> -Tim
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Bioinformatics and Computational Biology M.S. Candidate
> Office: 612-624-6441 <(612)%20624-6441>
> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay)
>
>
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> HCP-Users mailing list
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
> ___
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> HCP-Users@humanconnectome.org
> 

Re: [HCP-Users] Confusion about physiological data

[Elam, Jennifer]

Hi Anders,

Yes, the line will be corrected in next version of the Reference Manual to read:

“In the aggregate file the first column is used for the trigger pulse 
information, the second for respiratory information, and the third column for 
pulse oximeter (i.e., cardiac) information."


Best,

Jenn


Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: Glasser, Matthew
Sent: Tuesday, January 9, 2018 11:29:57 AM
To: Anders Eklund; hcp-users@humanconnectome.org
Cc: Elam, Jennifer
Subject: Re: [HCP-Users] Confusion about physiological data

Here is what I have in my physio preprocessing code:

Columns="1,2,3" #Trigger,Respiratory,Cardiac

Peace,

Matt.

From: 
>
 on behalf of Anders Eklund >
Date: Tuesday, January 9, 2018 at 3:57 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Confusion about physiological data

Hello,

I'm trying to use the physiological data for fMRI analysis.

In the reference manual (page 39) it states that

"In the aggregate file the first column is used for the trigger pulse 
information, the second for pulse oximeter (i.e., cardiac) information, and the 
third column for respiratory information."

https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Reference_Manual.pdf

However, according to this conversation on the mailing list the second column 
is respiration, is the manual or the mailing list correct?

https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01484.html

- Anders

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Re: [HCP-Users] Confusion about physiological data

[Glasser, Matthew]

Here is what I have in my physio preprocessing code:

Columns="1,2,3" #Trigger,Respiratory,Cardiac

Peace,

Matt.

From: 
>
 on behalf of Anders Eklund >
Date: Tuesday, January 9, 2018 at 3:57 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Confusion about physiological data

Hello,

I'm trying to use the physiological data for fMRI analysis.

In the reference manual (page 39) it states that

"In the aggregate file the first column is used for the trigger pulse 
information, the second for pulse oximeter (i.e., cardiac) information, and the 
third column for respiratory information."

https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Reference_Manual.pdf

However, according to this conversation on the mailing list the second column 
is respiration, is the manual or the mailing list correct?

https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01484.html

- Anders

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Re: [HCP-Users] MSMAllPipeline

[Glasser, Matthew]

I would look in your data for any grayordinates with std(tcs)=0.  These would 
need to be removed and time varying data added (e.g. by dilation).

Peace,

Matt.

From: 
>
 on behalf of Sang-Young Kim >
Date: Tuesday, January 9, 2018 at 10:03 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] MSMAllPipeline

Dear Experts:

I’m running MSMAllPipeline on our data acquired with protocol similar to HCP.
After finishing ICA+FIX pipeline, I’ve run MSMAllPipeline on those data. 
Although most of subjects are successfully finished for MSMAllPipeline, some 
subjects showed error message as below:

Error using svd
Input to SVD must not contain NaN or Inf.

Error in pinv (line 18)
[U,S,V] = svd(A,'econ');

Error in MSMregression (line 124)
NODEts=demean((pinv(demean(GM.*DesignWeights)) *
(demean(BO.cdata).*DenseWeights))');



While running:
/Applications/workbench/bin_macosx64/../macosx64_apps/wb_command.app/Contents/MacOS/wb_command
 -cifti-resample 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii
 COLUMN 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii
 COLUMN ADAP_BARY_AREA ENCLOSING_VOXEL 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii
 -surface-postdilate 40 -left-spheres 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.L.sphere.MSMSulc.32k_fs_LR.surf.gii
 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.L.sphere.32k_fs_LR.surf.gii
 -left-area-surfs 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.L.midthickness.32k_fs_LR.surf.gii
 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.L.midthickness.32k_fs_LR.surf.gii
 -right-spheres 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.R.sphere.MSMSulc.32k_fs_LR.surf.gii
 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.R.sphere.32k_fs_LR.surf.gii
 -right-area-surfs 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.R.midthickness.32k_fs_LR.surf.gii
 
/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.R.midthickness.32k_fs_LR.surf.gii

ERROR: failed to open file 
'/Volumes/easystore/projects/HIV/33038/MNINonLinear/fsaverage_LR32k/33038.individual_RSNs_d40_MSMSulc.32k_fs_LR.dscalar.nii',
 file does not exist, or folder permissions prevent seeing it

Given the error message showed, I think I need to fix the data containing NaN 
or Inf.
Could you please help me fix this problem?

Thanks.

Sang-Young




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Re: [HCP-Users] Resting State processing

[Glasser, Matthew]

See my response to his question.  It should work if you have the latest version 
of master with MSM v2 and everything is installed.

Peace,

Matt.

From: "Sanchez, Juan (NYSPI)" 
>
Date: Tuesday, January 9, 2018 at 11:24 AM
To: Timothy Hendrickson >, Matt 
Glasser >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Resting State processing

I was having the same problem with the 3_22  
FreeSurfer2CaretConvertAndRegisterNonlinear.sh
and was able to download the msm binaried and the params file from 
https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v1/

however I am runinng into a problem with the script at

${MSMBin}/msm --levels=4 --conf=${MSMBin}/allparameterssulcDRconf 
--inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
 
--trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
 
--refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
 
--indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii
 
--refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
 --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose

cd $DIR

   cp 
"$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii
 
"$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii

The HIGHRES file does not exist.

From: 
hcp-users-boun...@humanconnectome.org
 
>
 on behalf of Timothy Hendrickson >
Sent: Tuesday, January 9, 2018 12:11:20 PM
To: Glasser, Matthew
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Resting State processing


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


Hi Matthew,

The file does not exist. I see now that the PostFreeSurfer pipeline I have 
locally is different than the latest version found on github (specifically 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh). I see that the line 
referencing allparameterssulcDRconf has been commented out in favor of 
MSMSulcStrainFinalconf, however, this file does not appear to exist either. 
Which version of MSM HOCR is the most recent that should be used? I am using 
version 2)

On a completely other note why aren't these configuration files already 
included in the HCP pipelines? It seems very burdensome to require each user to 
mimic the exact version of the MSM binaries that 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh expects.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew 
> wrote:
Does the file exist?  That might be the old config file it is looking for 
suggesting that you don’t have the latest master.

Peace,

Matt.

From: Timothy Hendrickson >
Date: Monday, January 8, 2018 at 9:15 AM
To: "hcp-users@humanconnectome.org" 
>
Cc: Matt Glasser >
Subject: Re: [HCP-Users] Resting State processing

Hello all,

Despite having the most recent version of the hcp pipeline (3.22) and 
downloading the MSM configuration binaries, however, I am still receiving an 
error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc". 
This is the error message I receive: 
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
 Couldn't open the file!

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)


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Re: [HCP-Users] physical adjacency of MMP1.0 ROIs

[Glasser, Matthew]

Yes you can do this with wb_command -cifti-label-adjacency.  This produces a 
“parcellated connectivity” matrix which has the number of shared links for the 
“connectivity” values, meaning that the longer the border, the more connected 
two areas will appear.  You could of course threshold or binarize this if you 
desired.

Peace,

Matt.

From: 
>
 on behalf of "Shadi, Kamal" 
>
Date: Tuesday, January 9, 2018 at 11:19 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] physical adjacency of MMP1.0 ROIs

Hi all,

How can I test if two MMP1.0 ROIs are physically adjacent? Is there a way to do 
this by web_command?

Thanks,
Kamal

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Re: [HCP-Users] Resting State processing

[Sanchez, Juan (NYSPI)]

I was having the same problem with the 3_22  
FreeSurfer2CaretConvertAndRegisterNonlinear.sh
and was able to download the msm binaried and the params file from 
https://www.doc.ic.ac.uk/~ecr05/MSM_HOCR_v1/

however I am runinng into a problem with the script at

${MSMBin}/msm --levels=4 --conf=${MSMBin}/allparameterssulcDRconf 
--inmesh="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
 
--trans="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii
 
--refmesh="$AtlasSpaceFolder"/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_LR.surf.gii
 
--indata="$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sulc.native.shape.gii
 
--refdata="$AtlasSpaceFolder"/${Subject}.${Hemisphere}.refsulc."$HighResMesh"k_fs_LR.shape.gii
 --out="$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}. --verbose

cd $DIR

cp 
"$AtlasSpaceFolder"/"$NativeFolder"/MSMSulc/${Hemisphere}.HIGHRES_transformed.surf.gii
 
"$AtlasSpaceFolder"/"$NativeFolder"/${Subject}.${Hemisphere}.sphere.MSMSulc.native.surf.gii

The HIGHRES file does not exist.

From: hcp-users-boun...@humanconnectome.org 
 on behalf of Timothy Hendrickson 

Sent: Tuesday, January 9, 2018 12:11:20 PM
To: Glasser, Matthew
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Resting State processing


ATTENTION: This email came from an external source. Do not open attachments or 
click on links from unknown senders or unexpected emails.


Hi Matthew,

The file does not exist. I see now that the PostFreeSurfer pipeline I have 
locally is different than the latest version found on github (specifically 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh). I see that the line 
referencing allparameterssulcDRconf has been commented out in favor of 
MSMSulcStrainFinalconf, however, this file does not appear to exist either. 
Which version of MSM HOCR is the most recent that should be used? I am using 
version 2)

On a completely other note why aren't these configuration files already 
included in the HCP pipelines? It seems very burdensome to require each user to 
mimic the exact version of the MSM binaries that 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh expects.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew 
> wrote:
Does the file exist?  That might be the old config file it is looking for 
suggesting that you don’t have the latest master.

Peace,

Matt.

From: Timothy Hendrickson >
Date: Monday, January 8, 2018 at 9:15 AM
To: "hcp-users@humanconnectome.org" 
>
Cc: Matt Glasser >
Subject: Re: [HCP-Users] Resting State processing

Hello all,

Despite having the most recent version of the hcp pipeline (3.22) and 
downloading the MSM configuration binaries, however, I am still receiving an 
error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc". 
This is the error message I receive: 
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
 Couldn't open the file!

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)


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Re: [HCP-Users] Resting State processing

[Glasser, Matthew]

Those files are in the pipelines: 
https://github.com/Washington-University/Pipelines/tree/master/MSMConfig

Version 2 of MSM is the correct one to use.

It is indeed correct that you use the latest version of the HCP Pipelines with 
the latest version of MSM and make sure that you have installed everything 
correctly.  MSM was not previously publicly available before this version.

Matt.

From: Timothy Hendrickson >
Date: Tuesday, January 9, 2018 at 11:11 AM
To: Matt Glasser >
Cc: "hcp-users@humanconnectome.org" 
>
Subject: Re: [HCP-Users] Resting State processing

Hi Matthew,

The file does not exist. I see now that the PostFreeSurfer pipeline I have 
locally is different than the latest version found on github (specifically 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh). I see that the line 
referencing allparameterssulcDRconf has been commented out in favor of 
MSMSulcStrainFinalconf, however, this file does not appear to exist either. 
Which version of MSM HOCR is the most recent that should be used? I am using 
version 2)

On a completely other note why aren't these configuration files already 
included in the HCP pipelines? It seems very burdensome to require each user to 
mimic the exact version of the MSM binaries that 
FreeSurfer2CaretConvertAndRegisterNonlinear.sh expects.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew 
> wrote:
Does the file exist?  That might be the old config file it is looking for 
suggesting that you don’t have the latest master.

Peace,

Matt.

From: Timothy Hendrickson >
Date: Monday, January 8, 2018 at 9:15 AM
To: "hcp-users@humanconnectome.org" 
>
Cc: Matt Glasser >
Subject: Re: [HCP-Users] Resting State processing

Hello all,

Despite having the most recent version of the hcp pipeline (3.22) and 
downloading the MSM configuration binaries, however, I am still receiving an 
error when I attempt to run the PreFreeSurfer pipeline with RegName="MSMSulc". 
This is the error message I receive: 
/opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
 Couldn't open the file!

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)


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[HCP-Users] physical adjacency of MMP1.0 ROIs

[Shadi, Kamal]

Hi all,

How can I test if two MMP1.0 ROIs are physically adjacent? Is there a way to do 
this by web_command?

Thanks,
Kamal

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Re: [HCP-Users] Resting State processing

[Timothy Hendrickson]

Hi Matthew,

The file does not exist. I see now that the PostFreeSurfer pipeline I have
locally is different than the latest version found on github
(specifically *FreeSurfer2CaretConvertAndRegisterNonlinear.sh).
*I see that the line referencing *allparameterssulcDRconf *has been
commented out in favor of *MSMSulcStrainFinalconf*, however, this file does
not appear to exist either. Which version of MSM HOCR is the most recent
that should be used? I am using version 2)

On a completely other note why aren't these configuration files already
included in the HCP pipelines? It seems very burdensome to require each
user to mimic the exact version of the MSM binaries that
*FreeSurfer2CaretConvertAndRegisterNonlinear.sh
*expects.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)

On Mon, Jan 8, 2018 at 7:16 PM, Glasser, Matthew  wrote:

> Does the file exist?  That might be the old config file it is looking for
> suggesting that you don’t have the latest master.
>
> Peace,
>
> Matt.
>
> From: Timothy Hendrickson 
> Date: Monday, January 8, 2018 at 9:15 AM
> To: "hcp-users@humanconnectome.org" 
> Cc: Matt Glasser 
> Subject: Re: [HCP-Users] Resting State processing
>
> Hello all,
>
> Despite having the most recent version of the hcp pipeline (3.22) and
> downloading the MSM configuration binaries, however, I am still receiving
> an error when I attempt to run the PreFreeSurfer pipeline with
> RegName="MSMSulc". This is the error message I receive:
> */opt/local/hcp-pipelines-3.22.0/Pipelines-3.22.0/MSMBinaries/allparameterssulcDRconf:
> Couldn't open the file! *
> -Tim
>
> Timothy Hendrickson
> Department of Psychiatry
> University of Minnesota
> Bioinformatics and Computational Biology M.S. Candidate
> Office: 612-624-6441 <(612)%20624-6441>
> Mobile: 507-259-3434 <(507)%20259-3434> (texts okay)
>

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[HCP-Users] MEG coordinate system and coregistration space

[Felix Yuan]

Dear HCP experts,
These days, I am working with the resting state MEG data from the Human 
Connectome Project (Preprocessed data).

And there are some problems with the visualization. So I want to know which 
coordinate system is anatomical data aligned to? Bti or Spm?

And which coregistration space is MEG data aligned to?

Because In the pipeline code, I found spm coordinate system, bti system, ctf 
system. And also I found RAS space, subject headspace, MNI space, BTI space.
I am kind of confused about them.

Thanks for your kindly help,
All the best,
Felix

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[HCP-Users] Confusion about physiological data

[Anders Eklund]

Hello,

I'm trying to use the physiological data for fMRI analysis.

In the reference manual (page 39) it states that

"In the aggregate file the first column is used for the trigger pulse 
information, the second for pulse oximeter (i.e., cardiac) information, and the 
third column for respiratory information."

https://www.humanconnectome.org/storage/app/media/documentation/s1200/HCP_S1200_Release_Reference_Manual.pdf

However, according to this conversation on the mailing list the second column 
is respiration, is the manual or the mailing list correct?

https://www.mail-archive.com/hcp-users@humanconnectome.org/msg01484.html

- Anders

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