Re: [HCP-Users] Visualizing Greyordinate Masks

[Glasser, Matthew]

Steve and I think you have the right file, but are not understanding what is 
confusing about viewing that file in Connectome Workbench, assuming you have 
loaded the appropriate surfaces and volumes.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Cathy Chen 
mailto:c...@alumni.princeton.edu>>
Date: Tuesday, October 9, 2018 at 9:11 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Visualizing Greyordinate Masks

Dear HCP experts,

I'm working with subject-specific parcellations (for instance, 
"HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii"
 ) and would like to visualize the greyordinates corresponding to each of the 
15 (or 25, 50, or 100) spatial maps.

I've been using Connectome Workbench, but have not been able to figure out a 
way to do this based on online tutorials -- is it possible to visualize these 
maps with Connectome Workbench? Would I need to save new versions of the data, 
so that the maps lie in a [num_grayordinates x num_maps] matrix rather than a 
[num_maps x num_grayordinates] matrix?

Best,
Cathy

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


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] MSMAll for MultiRunICAFIX

[Glasser, Matthew]

Watch this space for an update on MSMAll with MultiRunFIX.  The pipelines
in the current master aren¹t all working together and we are working on
fixing that.

Matt.

On 10/9/18, 9:58 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Sang-Young Kim"  wrote:

>Dear Experts:
>
>I have a question for MSMAll alignment for MultiRunICAFIX cleaned data.
>Once I run the MultiRunICAFIX pipeline, I get the output like
>"${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii".
>
>But I want to align the data (e.g.,
>${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii) using MSMAll pipeline.
>Running MSMAllPipeline script with above data seems to be fine without
>any error. However, if I run DeDriftAndResamplePipeline script,
>it requires ${fMRIConcatName}.${Hemisphere}.native.func.gii, which is
>absent in ${fMRIConcatName} folder.
>
>I can generate ${fMRIConcatName}.${Hemisphere}.native.func.gii using
>fMRISurfacePipeline.
>But I¹m just wondering that I should run fMRISurfacePipeline for
>MultiRunICAFIX-cleaned data.
>
>This might be silly question as I don¹t clearly understand MSMAllPipeline
>and DeDriftAndResamplePipeline.
>Is there a method to have MSMAll-aligned MultiRunICAFIX-cleaned data?
>
>Below is the scripts that I ran:
>
>## MultiRunICAFIX
>StudyFolder="/Volumes/easystore/projects/HCP"
>Subject="300"
>ConcatName1="rfMRI_REST_Concat_Day1"
>ConcatName2="rfMRI_REST_Concat_Day2"
>ResultFolder="${StudyFolder}/${Subject}/MNINonlinear/Results"
>ICAFIXscriptFolder="/Users/sang-young/projects/Pipelines_master/ICAFIX"
>
>${ICAFIXscriptFolder}/hcp_fix_multi_run
>${ResultFolder}/rfMRI_REST1_AP/rfMRI_REST1_AP.nii.gz@${ResultFolder}/rfMRI
>_REST1_PA/rfMRI_REST1_PA.nii.gz@${ResultFolder}/rfMRI_REST2_AP/rfMRI_REST2
>_AP.nii.gz@${ResultFolder}/rfMRI_REST2_PA/rfMRI_REST2_PA.nii.gz 2000
>${ResultFolder}/${ConcatName1}/${ConcatName1}.nii.gz
>${FSL_FIXDIR}/training_files/HCP_hp2000.RData
>
>${ICAFIXscriptFolder}/hcp_fix_multi_run
>${ResultFolder}/rfMRI_REST3_AP/rfMRI_REST3_AP.nii.gz@${ResultFolder}/rfMRI
>_REST3_PA/rfMRI_REST3_PA.nii.gz@${ResultFolder}/rfMRI_REST4_AP/rfMRI_REST4
>_AP.nii.gz@${ResultFolder}/rfMRI_REST4_PA/rfMRI_REST4_PA.nii.gz 2000
>${ResultFolder}/${ConcatName2}/${ConcatName2}.nii.gz
>${FSL_FIXDIR}/training_files/HCP_hp2000.RData
>
>##MSMAllPipeline
>fMRINames="rfMRI_REST_Concat_Day1 rfMRI_REST_Concat_Day2"
>OutfMRIName="rfMRI_REST"
>HighPass="2000"
>fMRIProcSTRING="_Atlas_hp2000_clean"
>MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
>RegName="MSMAll_InitalReg"
>HighResMesh="164"
>LowResMesh="32"
>InRegName="MSMSulc"
>MatlabMode="1"
>
>${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh \
>  --path=${StudyFolder} \
>  --subject=${Subject} \
>  --fmri-names-list=${fMRINames} \
>  --output-fmri-name=${OutfMRIName} \
>  --high-pass=${HighPass} \
>  --fmri-proc-string=${fMRIProcSTRING} \
>  --msm-all-templates=${MSMAllTemplates} \
>  --output-registration-name=${RegName} \
>  --high-res-mesh=${HighResMesh} \
>  --low-res-mesh=${LowResMesh} \
>  --input-registration-name=${InRegName} \
>  --matlab-run-mode=${MatlabMode}
>
>Thanks.
>
>Sang-Young
>
>
>
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>http://lists.humanconnectome.org/mailman/listinfo/hcp-users



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] stable pipeline version

[Glasser, Matthew]

If you can wait a week or two we will have some useful updates out.  Also there 
is the impending switch to FreeSurfer 6.0 that would be good to have.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Sanchez, Juan (NYSPI)" 
mailto:juan.sanc...@nyspi.columbia.edu>>
Date: Tuesday, October 9, 2018 at 9:13 AM
To: "hcp-users@humanconnectome.org" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] stable pipeline version


We have been using the 3.4 version of the pipelines to process data acquired 
locally.   Our lab wants to switch over to the latest versions as we upgrade 
our magnet. Is there a stable release of the pipelines? I was going to clone 
the 3.27 version from github and proceed from there. However,  the last time we 
tried this with 3.22, we had to download and implement a number of fixes that 
were not a part of the 3.22 download.  Could you suggest the best way to 
implement the most current and stable versions?  Thanks

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


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] Restricted access

[Hodge, Michael]

Hi Jodi,

If you look at the "Current Project" selector at the top of the page, there 
should be another selector next to the project that says "Open Access".  If you 
see that and select one of the restricted access views, you should get a 
download link for the restricted data.

Regards,

Mike

From: hcp-users-boun...@humanconnectome.org 
 On Behalf Of Gilman, Jodi
Sent: Tuesday, October 9, 2018 1:05 PM
To: hcp-users@humanconnectome.org
Cc: Potter, Kevin 
Subject: [HCP-Users] Restricted access

Hello,

I applied for (and was granted) access to the restricted HCP database; however, 
when I log onto https://db.humanconnectome.org/data/projects/HCP_1200
I no longer see an option to download the restricted data. Please help!

Best,
Jodi

Jodi Gilman, Ph.D.
Associate Professor, Harvard Medical School
Center for Addiction Medicine
Massachusetts General Hospital
101 Merrimac St.
Boston, MA 02114
Tel.:
   617-643-7293
Fax:617-643-1998


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


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

[Timothy Coalson]

You need to update workbench to the latest release, that option is a recent
addition to the command that is failing.

Tim


On Tue, Oct 9, 2018 at 6:08 PM, ARMAN PRAFUL KULKARNI 
wrote:

> Hi,
>
> I have been running the HCP Pipeline (v 3.27.0) on one subject's
> unprocessed data from the HCP-1200 dataset. Below is what I have in the
> SetUpHCPPipeline.sh file. I have been able to run
> PreFreeSurferPipelineBatch.sh and FreeSurferPipelineBatch.sh with no
> issues. However, when running PostFreeSurferPipelineBatch.sh, I get the
> following error after around 10 minutes of the script running: "ERROR:
> Unexpected parameter: -local-affine-method", and I am not sure how to
> proceed. I appreciate any insight into this problem.
>
> Sincerely,
> Arman
> ---
>
> #!/bin/bash
>
> echo "This script must be SOURCED to correctly setup the environment prior
> to running any of the other HCP scripts contained here"
>
> # Set up FSL (if not already done so in the running environment)
> # Uncomment the following 2 lines (remove the leading #) and correct the
> FSLDIR setting for your setup
> #export FSLDIR=/usr/share/fsl/5.0
> #. ${FSLDIR}/etc/fslconf/fsl.sh
>
> # Let FreeSurfer know what version of FSL to use
> # FreeSurfer uses FSL_DIR instead of FSLDIR to determine the FSL version
> export FSL_DIR="${FSLDIR}"
>
> # Set up FreeSurfer (if not already done so in the running environment)
> # Uncomment the following 2 lines (remove the leading #) and correct the
> FREESURFER_HOME setting for your setup
> #export FREESURFER_HOME=/usr/local/bin/freesurfer
> #source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1
>
> # Set up specific environment variables for the HCP Pipeline
> export HCPPIPEDIR=${HOME}//HCP/Pipelines
> #export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
> export CARET7DIR=/usr/local/workbench/bin_linux64
>
> export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
> export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries
> export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config
>
> export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
> export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
> export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
> export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
> export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
> export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts
> export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
> export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts
> export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
> export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
> export MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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

[HCP-Users] Error Running HCP's PostFreeSurferPipelineBatch.sh

[ARMAN PRAFUL KULKARNI]

Hi,

I have been running the HCP Pipeline (v 3.27.0) on one subject's unprocessed 
data from the HCP-1200 dataset. Below is what I have in the SetUpHCPPipeline.sh 
file. I have been able to run PreFreeSurferPipelineBatch.sh and 
FreeSurferPipelineBatch.sh with no issues. However, when running 
PostFreeSurferPipelineBatch.sh, I get the following error after around 10 
minutes of the script running: "ERROR: Unexpected parameter: 
-local-affine-method", and I am not sure how to proceed. I appreciate any 
insight into this problem.

Sincerely,
Arman
---

#!/bin/bash

echo "This script must be SOURCED to correctly setup the environment prior to 
running any of the other HCP scripts contained here"

# Set up FSL (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the FSLDIR 
setting for your setup
#export FSLDIR=/usr/share/fsl/5.0
#. ${FSLDIR}/etc/fslconf/fsl.sh

# Let FreeSurfer know what version of FSL to use
# FreeSurfer uses FSL_DIR instead of FSLDIR to determine the FSL version
export FSL_DIR="${FSLDIR}"

# Set up FreeSurfer (if not already done so in the running environment)
# Uncomment the following 2 lines (remove the leading #) and correct the 
FREESURFER_HOME setting for your setup
#export FREESURFER_HOME=/usr/local/bin/freesurfer
#source ${FREESURFER_HOME}/SetUpFreeSurfer.sh > /dev/null 2>&1

# Set up specific environment variables for the HCP Pipeline
export HCPPIPEDIR=${HOME}//HCP/Pipelines
#export CARET7DIR=${HOME}/tools/workbench/bin_rh_linux64
export CARET7DIR=/usr/local/workbench/bin_linux64

export HCPPIPEDIR_Templates=${HCPPIPEDIR}/global/templates
export HCPPIPEDIR_Bin=${HCPPIPEDIR}/global/binaries
export HCPPIPEDIR_Config=${HCPPIPEDIR}/global/config

export HCPPIPEDIR_PreFS=${HCPPIPEDIR}/PreFreeSurfer/scripts
export HCPPIPEDIR_FS=${HCPPIPEDIR}/FreeSurfer/scripts
export HCPPIPEDIR_PostFS=${HCPPIPEDIR}/PostFreeSurfer/scripts
export HCPPIPEDIR_fMRISurf=${HCPPIPEDIR}/fMRISurface/scripts
export HCPPIPEDIR_fMRIVol=${HCPPIPEDIR}/fMRIVolume/scripts
export HCPPIPEDIR_tfMRI=${HCPPIPEDIR}/tfMRI/scripts
export HCPPIPEDIR_dMRI=${HCPPIPEDIR}/DiffusionPreprocessing/scripts
export HCPPIPEDIR_dMRITract=${HCPPIPEDIR}/DiffusionTractography/scripts
export HCPPIPEDIR_Global=${HCPPIPEDIR}/global/scripts
export HCPPIPEDIR_tfMRIAnalysis=${HCPPIPEDIR}/TaskfMRIAnalysis/scripts
export MSMBINDIR=${HCPPIPEDIR}/global/templates/MSMAll


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

Re: [HCP-Users] Restricted access

[Elam, Jennifer]

Hi Jodi,

Let me have the database people look into this.


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: hcp-users-boun...@humanconnectome.org 
 on behalf of Gilman, Jodi 

Sent: Tuesday, October 9, 2018 1:05:11 PM
To: hcp-users@humanconnectome.org
Cc: Potter, Kevin
Subject: [HCP-Users] Restricted access

Hello,

I applied for (and was granted) access to the restricted HCP database; however, 
when I log onto https://db.humanconnectome.org/data/projects/HCP_1200
I no longer see an option to download the restricted data. Please help!

Best,
Jodi

Jodi Gilman, Ph.D.
Associate Professor, Harvard Medical School
Center for Addiction Medicine
Massachusetts General Hospital
101 Merrimac St.
Boston, MA 02114
Tel.:617-643-7293
Fax:617-643-1998


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

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

[HCP-Users] Restricted access

[Gilman, Jodi]

Hello,

I applied for (and was granted) access to the restricted HCP database; however, 
when I log onto https://db.humanconnectome.org/data/projects/HCP_1200
I no longer see an option to download the restricted data. Please help!

Best,
Jodi

Jodi Gilman, Ph.D.
Associate Professor, Harvard Medical School
Center for Addiction Medicine
Massachusetts General Hospital
101 Merrimac St.
Boston, MA 02114
Tel.:617-643-7293
Fax:617-643-1998


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

Re: [HCP-Users] drawing borders

[Gaurav Patel]

here’s a screen shot of the draw borders output vs. a finished border (symbol 
diameter set to 2mm).  I tried to change the ID sphere size property, and that 
did not change.  On a machine with 1.23 still installed, the draw borders 
output is the same size as the 2mm diameter finalized borders.  I am drawing 
this on the tutorial surface



 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net

> On Oct 9, 2018, at 1:07 PM, Harwell, John  wrote:
> 
> How huge is huge?  When drawing a new border, the symbol size should be about 
> 3% of the longest surface axis.  On a human surface, that appears be about 
> 5mm.  There is no way for the user to adjust the symbol size when drawing.
> 
> I am using Workbench version 1.3.2 and the size should be the same in 1.3.1.
> 
> John Harwell
> 
>> On Oct 9, 2018, at 11:37 AM, Gaurav Patel  wrote:
>> 
>> Hi—when I am drawing borders in wb_view 1.31, the diameters of the red 
>> spheres is huge, making is difficult to see what I am drawing.  This was not 
>> the case in 1.23.  Is there a way to change that setting?  Finishing the 
>> border reduces the size of the spheres to the setting in the borders menu, 
>> so that setting doesn’t make a difference.  Thanks
>> 
>> gaurav patel
>> gauravpa...@gmail.com
>> pateldsclab.net
>> 
>> 
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
> 


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

Re: [HCP-Users] drawing borders

[Dierker, Donna]

I had an issue with baby brains where the sphere had too small a diameter.

This caused an issue where ID nodes were displaying with a sphere larger than 
the surface.

This is probably not your issue -- sorry.



From: Gaurav Patel  on behalf of Gaurav Patel 

Sent: Tuesday, October 9, 2018 11:50 AM
To: Dierker, Donna
Cc: Gaurav Patel; hcp-users@humanconnectome.org Users
Subject: Re: [HCP-Users] drawing borders

In the borders menu?  Changing that changes the size of the final border, but 
not the border as I draw it

_
 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net

On Oct 9, 2018, at 12:42 PM, Dierker, Donna 
mailto:do...@wustl.edu>> wrote:


Check the diameter of your sphere, Gaurav.



From: 
hcp-users-boun...@humanconnectome.org
 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Gaurav Patel mailto:gauravpa...@gmail.com>>
Sent: Tuesday, October 9, 2018 11:37 AM
To: hcp-users@humanconnectome.org Users
Subject: [HCP-Users] drawing borders

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net


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





The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] drawing borders

[Gaurav Patel]

In the borders menu?  Changing that changes the size of the final border, but 
not the border as I draw it

_
 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net

> On Oct 9, 2018, at 12:42 PM, Dierker, Donna  wrote:
> 
> Check the diameter of your sphere, Gaurav.
> 
> 
> From: hcp-users-boun...@humanconnectome.org 
>  on behalf of Gaurav Patel 
> 
> Sent: Tuesday, October 9, 2018 11:37 AM
> To: hcp-users@humanconnectome.org Users
> Subject: [HCP-Users] drawing borders
>  
> Hi—when I am drawing borders in wb_view 1.31, the diameters of the red 
> spheres is huge, making is difficult to see what I am drawing.  This was not 
> the case in 1.23.  Is there a way to change that setting?  Finishing the 
> border reduces the size of the spheres to the setting in the borders menu, so 
> that setting doesn’t make a difference.  Thanks
> 
>  gaurav patel
>  gauravpa...@gmail.com
>  pateldsclab.net
> 
> 
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>  
> 
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.

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

Re: [HCP-Users] drawing borders

[Dierker, Donna]

Check the diameter of your sphere, Gaurav.



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Gaurav Patel 

Sent: Tuesday, October 9, 2018 11:37 AM
To: hcp-users@humanconnectome.org Users
Subject: [HCP-Users] drawing borders

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net


___
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] drawing borders

[Gaurav Patel]

Hi—when I am drawing borders in wb_view 1.31, the diameters of the red spheres 
is huge, making is difficult to see what I am drawing.  This was not the case 
in 1.23.  Is there a way to change that setting?  Finishing the border reduces 
the size of the spheres to the setting in the borders menu, so that setting 
doesn’t make a difference.  Thanks

 gaurav patel
 gauravpa...@gmail.com
 pateldsclab.net


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

Re: [HCP-Users] T1w_acpc_dc_restore_brain.nii.gz

[X K]

Thanks so much Michael!
This link is also very helpful
https://github.com/Washington-University/HCPpipelines/blob/master/PreFreeSurfer/PreFreeSurferPipeline.sh

Best,
Xiangzhen

On Tue, Oct 9, 2018 at 4:44 PM Harms, Michael  wrote:

>
>
> Hi,
>
> See http://www.ncbi.nlm.nih.gov/pubmed/23668970
>
> specifically Figure 9.
>
>
>
> “dc” is the readout distortion correction.
>
> “restore” is the bias field correction (for the receive bias field)
>
>
>
> The gradient distortion correction is not included as part of the
> filename, so the file could just as well have been named
> “T1w_gdc_acpc_rdc_restore_brain.nii.gz”
>
>
>
> 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 X K <
> bnu...@gmail.com>
> *Date: *Tuesday, October 9, 2018 at 8:50 AM
> *To: *"hcp-users@humanconnectome.org" 
> *Subject: *[HCP-Users] T1w_acpc_dc_restore_brain.nii.gz
>
>
>
> Hi,
>
>
>
> I am using the HCP data. Here I came across a question about the file
> *T1w_acpc_dc_restore_brain.nii.gz*
>
> I am curious what have been done between T1w.nii.gz and this file. From
> the document, I guess that
>
> *acpc* indicate linear registriation (flirt) with dof=6;
>
> *dc* might indicate distortion correction, but how was this done? using
> flirt with dof=12?
>
> I am not sure whether '*restore*' has particiulat meaning.
>
>
>
> Thanks.
>
>
>
> Best,
>
> Xiangzhen
>
>
>
> --
>
>
> -
>
> Xiangzhen Kong (孔祥祯)
>
> Research Staff
>
> Language and Genetics Department,
>
> Max Planck Institute for Psycholinguistics,
>
> Wundtlaan 1, 6525 XD, The Netherlands.
>
>
> -
>
>
>
> ___
> 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.
>


-- 
-
Xiangzhen Kong (孔祥祯)
Research Staff
Language and Genetics Department,
Max Planck Institute for Psycholinguistics,
Wundtlaan 1, 6525 XD, The Netherlands.
-

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

[HCP-Users] MSMAll for MultiRunICAFIX

[Sang-Young Kim]

Dear Experts:

I have a question for MSMAll alignment for MultiRunICAFIX cleaned data. 
Once I run the MultiRunICAFIX pipeline, I get the output like 
"${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii". 

But I want to align the data (e.g., 
${fMRIConcatName}_Atlas_hp2000_clean.dtseries.nii) using MSMAll pipeline. 
Running MSMAllPipeline script with above data seems to be fine without any 
error. However, if I run DeDriftAndResamplePipeline script, 
it requires ${fMRIConcatName}.${Hemisphere}.native.func.gii, which is absent in 
${fMRIConcatName} folder.

I can generate ${fMRIConcatName}.${Hemisphere}.native.func.gii using 
fMRISurfacePipeline. 
But I’m just wondering that I should run fMRISurfacePipeline for 
MultiRunICAFIX-cleaned data. 

This might be silly question as I don’t clearly understand MSMAllPipeline and 
DeDriftAndResamplePipeline. 
Is there a method to have MSMAll-aligned MultiRunICAFIX-cleaned data?

Below is the scripts that I ran:

## MultiRunICAFIX 
StudyFolder="/Volumes/easystore/projects/HCP"
Subject="300"
ConcatName1="rfMRI_REST_Concat_Day1"
ConcatName2="rfMRI_REST_Concat_Day2"
ResultFolder="${StudyFolder}/${Subject}/MNINonlinear/Results"
ICAFIXscriptFolder="/Users/sang-young/projects/Pipelines_master/ICAFIX"
 
${ICAFIXscriptFolder}/hcp_fix_multi_run 
${ResultFolder}/rfMRI_REST1_AP/rfMRI_REST1_AP.nii.gz@${ResultFolder}/rfMRI_REST1_PA/rfMRI_REST1_PA.nii.gz@${ResultFolder}/rfMRI_REST2_AP/rfMRI_REST2_AP.nii.gz@${ResultFolder}/rfMRI_REST2_PA/rfMRI_REST2_PA.nii.gz
 2000 ${ResultFolder}/${ConcatName1}/${ConcatName1}.nii.gz 
${FSL_FIXDIR}/training_files/HCP_hp2000.RData

${ICAFIXscriptFolder}/hcp_fix_multi_run 
${ResultFolder}/rfMRI_REST3_AP/rfMRI_REST3_AP.nii.gz@${ResultFolder}/rfMRI_REST3_PA/rfMRI_REST3_PA.nii.gz@${ResultFolder}/rfMRI_REST4_AP/rfMRI_REST4_AP.nii.gz@${ResultFolder}/rfMRI_REST4_PA/rfMRI_REST4_PA.nii.gz
 2000 ${ResultFolder}/${ConcatName2}/${ConcatName2}.nii.gz 
${FSL_FIXDIR}/training_files/HCP_hp2000.RData

##MSMAllPipeline
fMRINames="rfMRI_REST_Concat_Day1 rfMRI_REST_Concat_Day2"
OutfMRIName="rfMRI_REST"
HighPass="2000"
fMRIProcSTRING="_Atlas_hp2000_clean"
MSMAllTemplates="${HCPPIPEDIR}/global/templates/MSMAll"
RegName="MSMAll_InitalReg"
HighResMesh="164"
LowResMesh="32"
InRegName="MSMSulc"
MatlabMode="1"

${HCPPIPEDIR}/MSMAll/MSMAllPipeline.sh \
  --path=${StudyFolder} \
  --subject=${Subject} \
  --fmri-names-list=${fMRINames} \
  --output-fmri-name=${OutfMRIName} \
  --high-pass=${HighPass} \
  --fmri-proc-string=${fMRIProcSTRING} \
  --msm-all-templates=${MSMAllTemplates} \
  --output-registration-name=${RegName} \
  --high-res-mesh=${HighResMesh} \
  --low-res-mesh=${LowResMesh} \
  --input-registration-name=${InRegName} \
  --matlab-run-mode=${MatlabMode}

Thanks. 

Sang-Young



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

Re: [HCP-Users] T1w_acpc_dc_restore_brain.nii.gz

[Harms, Michael]

Hi,

See http://www.ncbi.nlm.nih.gov/pubmed/23668970
specifically Figure 9.

“dc” is the readout distortion correction.
“restore” is the bias field correction (for the receive bias field)

The gradient distortion correction is not included as part of the filename, so 
the file could just as well have been named 
“T1w_gdc_acpc_rdc_restore_brain.nii.gz”

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 X K 

Date: Tuesday, October 9, 2018 at 8:50 AM
To: "hcp-users@humanconnectome.org" 
Subject: [HCP-Users] T1w_acpc_dc_restore_brain.nii.gz

Hi,

I am using the HCP data. Here I came across a question about the file 
T1w_acpc_dc_restore_brain.nii.gz
I am curious what have been done between T1w.nii.gz and this file. From the 
document, I guess that
acpc indicate linear registriation (flirt) with dof=6;
dc might indicate distortion correction, but how was this done? using flirt 
with dof=12?
I am not sure whether 'restore' has particiulat meaning.

Thanks.

Best,
Xiangzhen

--
-
Xiangzhen Kong (孔祥祯)
Research Staff
Language and Genetics Department,
Max Planck Institute for Psycholinguistics,
Wundtlaan 1, 6525 XD, The Netherlands.
-


___
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] stable pipeline version

[Sanchez, Juan (NYSPI)]

We have been using the 3.4 version of the pipelines to process data acquired 
locally.   Our lab wants to switch over to the latest versions as we upgrade 
our magnet. Is there a stable release of the pipelines? I was going to clone 
the 3.27 version from github and proceed from there. However,  the last time we 
tried this with 3.22, we had to download and implement a number of fixes that 
were not a part of the 3.22 download.  Could you suggest the best way to 
implement the most current and stable versions?  Thanks

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

[HCP-Users] Visualizing Greyordinate Masks

[Cathy Chen]

Dear HCP experts,

I'm working with subject-specific parcellations (for instance, "
HCP_S1200_PTNmaps_d15_25_50_100\3T_HCP1200_MSMAll_d15_ts2_Z\100206.dtseries.nii"
) and would like to visualize the greyordinates corresponding to each of
the 15 (or 25, 50, or 100) spatial maps.

I've been using Connectome Workbench, but have not been able to figure out
a way to do this based on online tutorials -- is it possible to visualize
these maps with Connectome Workbench? Would I need to save new versions of
the data, so that the maps lie in a [num_grayordinates x num_maps] matrix
rather than a [num_maps x num_grayordinates] matrix?

Best,
Cathy

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

[HCP-Users] T1w_acpc_dc_restore_brain.nii.gz

[X K]

Hi,

I am using the HCP data. Here I came across a question about the file
*T1w_acpc_dc_restore_brain.nii.gz*
I am curious what have been done between T1w.nii.gz and this file. From the
document, I guess that
*acpc* indicate linear registriation (flirt) with dof=6;
*dc* might indicate distortion correction, but how was this done? using
flirt with dof=12?
I am not sure whether '*restore*' has particiulat meaning.

Thanks.

Best,
Xiangzhen

-- 
-
Xiangzhen Kong (孔祥祯)
Research Staff
Language and Genetics Department,
Max Planck Institute for Psycholinguistics,
Wundtlaan 1, 6525 XD, The Netherlands.
-

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

Re: [HCP-Users] archiving the results from HCP pipellines

[Darko Komnenić]

Thanks!

On Mon, Oct 8, 2018 at 9:46 PM Glasser, Matthew  wrote:

> I would save the list of files we release with the HCP Pipelines.  If you
> search the list, you will see some other specific posts about saving
> space.  I would be sure you don’t delete anything in an .spec file either.
>
> Matt.
>
> From:  on behalf of Darko Komnenić
> 
> Date: Monday, October 8, 2018 at 8:33 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] archiving the results from HCP pipellines
>
> Dear HCP experts,
> in my lab, we are trying to free up disk space, and are looking into
> archiving some of the previous analyses we did with HCP pipelines. Since
> the complete data is quite large, we were considering just saving the
> initial T1 and T2 nifti images and the myelin maps that get produced at the
> end of PostFreeSurfer pipeline.
> My question is: would you recommend saving something else as well,
> something  that might be important if another researcher were to test the
> reproducibility of the analysis later etc.?
> Thanks in advance,
> Darko
>
> ___
> 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