[HCP-Users] A question about scene file

[Aaron C]

Dear HCP experts,

The scene file (a structural processing QC scene) I generated in a Linux 
computer doesn't work in a Windows computer. It seems that the file paths were 
hard-coded in the scene file. Is there a way to make it more portable? Thank 
you.

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[HCP-Users] A question about the usage of Connectome Workbench

[Aaron C]

Dear HCP experts,

I have a question about the usage of Connectome Workbench. In the "Volume" tab, 
when using "Montage", how could I control the range of slices? For example, if 
I view multiple parasagittal slices (by clicking the "P" button), how to vary X 
values? Thank you.

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[HCP-Users] A question about the HCP brain registration

[Aaron C]

Dear HCP experts,

Is there any shared script to generate scenes to check brain registration 
quality of the HCP rfMRI and tfMRI data? Thank you.

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Re: [HCP-Users] Probabilistic tractography for dense connectome

[Aaron C]

Hi Stam and Matt,

I have one more question about this. I got the dense connectome and would like 
to calculate structural connectivity between the parcels in Matt's 360-parcel 
parcellation scheme. For the connectivity between parcel A and B, in the dense 
connectome matrix, I first located the rows belonging to A and the columns 
belonging to B, and then summed up the values in this submatrix. I used this 
summed value as the connectivity between parcel A and B. Would this make sense? 
Thank you.

Aaron

From: Stamatios Sotiropoulos 
Sent: Wednesday, May 1, 2019 7:05 PM
To: Glasser, Matthew
Cc: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

This may be the reason indeed.

The Pretractography script creates both native space and MNI space ROIs. You 
need to make sure you use the MNI ones (I.e. created via the 
MakeTrajectorySpace_MNI.sh script).

Stam

On 1 May 2019, at 23:52, Glasser, Matthew 
mailto:glass...@wustl.edu>> wrote:

Is that because this is a native space grayordinates instead of an MNI space 
grayordinates and thus the masks are subject specific?

Matt.

From: Aaron C mailto:aaroncr...@outlook.com>>
Date: Wednesday, May 1, 2019 at 12:27 PM
To: Stamatios Sotiropoulos 
mailto:stamatios.sotiropou...@nottingham.ac.uk>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Hi Stam,

I tried your PreTractography script to generate these files needed for 
probtrackx2, and then used the following command (the command from the HCP 
course for generating dense connectome):

probtrackx2_gpu --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=Connectomes/stop --wtstop=Connectomes/wtstop \
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \
-x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \
--target3=Connectomes/Grayordinates.txt --dir=Connectomes
The command completed without error. I then used the MATLAB to load the 
connectivity matrix:

x=load(''fdt_matrix3.dot');
M=spconvert(x);

However, the dimension of M is only 86392 x 86392, not 91282 x 91282.

So I tried the same probtrackx2 command, but instead used the files from the 
HCP course virtual machine for the input to probtrackx2 (so this time I know 
the input files should be correct), but the dimension is still 86392 x 86392, 
not 91282 x 91282.

If possible, would you please give me some hints to find out the missing 
grayordinates in this connectivity matrix? Thank you!

Aaron

From: Stamatios Sotiropoulos 
mailto:stamatios.sotiropou...@nottingham.ac.uk>>
Sent: Friday, April 26, 2019 10:58 AM
To: Aaron C
Cc: Glasser, Matthew; 
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Hi Aaron

You need the PreTractography script, available in one of the branches of the 
WU-pipelines.

https://github.com/Washington-University/HCPpipelines/tree/diffusion-tractography/DiffusionTractography

Best wishes
Stam



On 26 Apr 2019, at 15:50, Aaron C 
mailto:aaroncr...@outlook.com>> wrote:

Hi Matt,

Thank you for letting me know. The full command I mentioned is as follows:

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 \
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \
-x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \
--target3=Connectomes/GrayOrdinates.txt --dir=Connectomes

It's in the HCP course practical "Fibre Orientation Models and Tractography 
Analysis" taught by Matteo Bastiani. Thank you.

From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Thursday, April 25, 2019 7:04 PM
To: Aaron C; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Cc: Stamatios Sotiropoulos
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Not as far as I am aware, but Stam might know.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Thursday, April 25, 2019 at 9:15 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Probabilistic tractography for dense connectome

Dear HC

[HCP-Users] A question about the HCP pipeline 4.0.0

[Aaron C]

Dear HCP experts,

I have a question about the HCP pipeline 4.0.0. When using 
FreeSurferPipelineBatch.sh, it cannot find recon-all.v6.hires, conf2hires, and 
longmc. Is there a specific version of FreeSurfer 6.0 for HCP? Thank you.

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Re: [HCP-Users] Probabilistic tractography for dense connectome

[Aaron C]

Hi Stam,

I tried your PreTractography script to generate these files needed for 
probtrackx2, and then used the following command (the command from the HCP 
course for generating dense connectome):

probtrackx2_gpu --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=Connectomes/stop --wtstop=Connectomes/wtstop \
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \
-x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \
--target3=Connectomes/Grayordinates.txt --dir=Connectomes
The command completed without error. I then used the MATLAB to load the 
connectivity matrix:

x=load(''fdt_matrix3.dot');
M=spconvert(x);

However, the dimension of M is only 86392 x 86392, not 91282 x 91282.

So I tried the same probtrackx2 command, but instead used the files from the 
HCP course virtual machine for the input to probtrackx2 (so this time I know 
the input files should be correct), but the dimension is still 86392 x 86392, 
not 91282 x 91282.

If possible, would you please give me some hints to find out the missing 
grayordinates in this connectivity matrix? Thank you!

Aaron

From: Stamatios Sotiropoulos 
Sent: Friday, April 26, 2019 10:58 AM
To: Aaron C
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Hi Aaron

You need the PreTractography script, available in one of the branches of the 
WU-pipelines.

https://github.com/Washington-University/HCPpipelines/tree/diffusion-tractography/DiffusionTractography

Best wishes
Stam



On 26 Apr 2019, at 15:50, Aaron C 
mailto:aaroncr...@outlook.com>> wrote:

Hi Matt,

Thank you for letting me know. The full command I mentioned is as follows:

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 \
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \
-x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \
--target3=Connectomes/GrayOrdinates.txt --dir=Connectomes

It's in the HCP course practical "Fibre Orientation Models and Tractography 
Analysis" taught by Matteo Bastiani. Thank you.

From: Glasser, Matthew mailto:glass...@wustl.edu>>
Sent: Thursday, April 25, 2019 7:04 PM
To: Aaron C; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Cc: Stamatios Sotiropoulos
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Not as far as I am aware, but Stam might know.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Thursday, April 25, 2019 at 9:15 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Probabilistic tractography for dense connectome

Dear HCP experts,

I have a question about the probabilistic tractography command used for 
generating dense connectome 
(https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7). Are there any 
shared scripts for generating "pial.L.asc", "white.L.asc", 
"Whole_Brain_Trajectory_ROI_2.nii.gz", and the files such as 
"CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz" used in the probabilistic tractography 
command?
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Re: [HCP-Users] Probabilistic tractography for dense connectome

[Aaron C]

Hi Matt,

Thank you for letting me know. The full command I mentioned is as follows:

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 \
--waypoints=ROIs/Whole_Brain_Trajectory_ROI_2 \
-x ROIs/Whole_Brain_Trajectory_ROI_2 --omatrix3 \
--target3=Connectomes/GrayOrdinates.txt --dir=Connectomes

It's in the HCP course practical "Fibre Orientation Models and Tractography 
Analysis" taught by Matteo Bastiani. Thank you.

From: Glasser, Matthew 
Sent: Thursday, April 25, 2019 7:04 PM
To: Aaron C; hcp-users@humanconnectome.org
Cc: Stamatios Sotiropoulos
Subject: Re: [HCP-Users] Probabilistic tractography for dense connectome

Not as far as I am aware, but Stam might know.

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Thursday, April 25, 2019 at 9:15 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Probabilistic tractography for dense connectome

Dear HCP experts,

I have a question about the probabilistic tractography command used for 
generating dense connectome 
(https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7). Are there any 
shared scripts for generating "pial.L.asc", "white.L.asc", 
"Whole_Brain_Trajectory_ROI_2.nii.gz", and the files such as 
"CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz" used in the probabilistic tractography 
command?

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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
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[HCP-Users] Probabilistic tractography for dense connectome

[Aaron C]

Dear HCP experts,

I have a question about the probabilistic tractography command used for 
generating dense connectome 
(https://wustl.app.box.com/s/wna2cu94pqgt8zskg687mj8zlmfj1pq7). Are there any 
shared scripts for generating "pial.L.asc", "white.L.asc", 
"Whole_Brain_Trajectory_ROI_2.nii.gz", and the files such as 
"CIFTI_STRUCTURE_ACCUMBENS_LEFT.nii.gz" used in the probabilistic tractography 
command?

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Re: [HCP-Users] Some questions about the HCP structural processing pipeline

[Aaron C]

Hi Matt,

I called the FreeSurfer pipeline using the script "FreeSurferPipelineBatch.sh" 
in the "Examples" folder. Do you mean that these brain extracted T1w and T2w 
images "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz" were actually not used in the FreeSurfer 
pipeline? Thank you.

Aaron


From: Glasser, Matthew 
Sent: Monday, April 8, 2019 10:50 PM
To: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Some questions about the HCP structural processing 
pipeline

The brain masked file should not be used for surface estimation.  How are you 
calling the FreeSurfer pipeline?

Matt.

From: 
mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C mailto:aaroncr...@outlook.com>>
Date: Monday, April 8, 2019 at 9:41 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] Some questions about the HCP structural processing pipeline

Dear HCP experts,

I have some questions about the HCP structural processing pipeline.

  1.  The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the T1w 
folder has excessive voxels removed in the cortical surface, which resulted in 
erroneous pial surface estimation. Is there a way that I could adjust any 
parameters of brain extraction in the PreFreeSurfer.sh file to have a larger 
brain mask?
  2.  There is another file "brainmask_fs.nii.gz". Is this the same mask 
derived from "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz"?
  3.  In the structural processing QC scene, is there a way that I could also 
display the boundary of the extracted brain alongside with pial and white 
surfaces in the coronal brain?

Thank you.

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[HCP-Users] Some questions about the HCP structural processing pipeline

[Aaron C]

Dear HCP experts,

I have some questions about the HCP structural processing pipeline.

  1.  The brain extracted file "T1w_acpc_dc_restore_brain.nii.gz" in the T1w 
folder has excessive voxels removed in the cortical surface, which resulted in 
erroneous pial surface estimation. Is there a way that I could adjust any 
parameters of brain extraction in the PreFreeSurfer.sh file to have a larger 
brain mask?
  2.  There is another file "brainmask_fs.nii.gz". Is this the same mask 
derived from "T1w_acpc_dc_restore_brain.nii.gz" and 
"T2w_acpc_dc_restore_brain.nii.gz"?
  3.  In the structural processing QC scene, is there a way that I could also 
display the boundary of the extracted brain alongside with pial and white 
surfaces in the coronal brain?

Thank you.

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[HCP-Users] A question about generating quality control scene file for the resting-state data

[Aaron C]

Dear HCP experts,

I have a question about the quality control of rfMRI data processed by the HCP 
pipeline. Is there any shared script to create the quality control scene file 
("rfMRI_1.scene") described in the HCP course practical material 5 
(https://wustl.app.box.com/s/xfs2506iz6pa6t7bfhhkno3baphnppvy)?

Also, for the attached figure (native space), is this indicating a problem in 
using the HCP structural preprocessing pipeline? Thank you.

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[HCP-Users] Some questions about an HCP course material for DTI

[Aaron C]

Dear HCP experts,

I have a question about an HCP course material ("Diffusion MRI, Distortion 
Correction and DTI Practical": 
https://wustl.box.com/s/6aox0ugssgnsn4lquizfgb5w06eyz8s2 ). If I understand 
correctly, in this document, were all the processing steps before the section 
"Fitting Diffusion Tensors" already completed in the HCP diffusion pipeline?

Also, in the section "Fitting Diffusion Tensors", there is a command of 
registering diffusion image to T1w image in the same subject. For the 
processing using TBSS, do I still need to do this diffusion to T1w registration 
prior to TBSS analysis? Thank you.

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[HCP-Users] Some questions about using HCP structural preprocessing pipeline

[Aaron C]

Dear HCP experts,


I have some questions about using the HCP structural preprocessing pipeline.

  1.  For the parameters “T1wSampleSpacing” and “T2wSampleSpacing”, are they 
the same across different Skyra scanners? Will this significantly affect 
preprocessing quality if setting them to “NONE”?
  2.  I noticed some cortical regions were excessively removed in the file 
“T2w_acpc_brain.nii.gz” in “T2w” folder. Would this indicate any problem of 
brain extraction? If so, would you please suggest how to fix this problem?
  3.  I received the error “Unexpected parameter: -local-affine-method” when 
using “PostFreeSurferPipelineBatch.sh”. It occurred when the script tried to 
call wb_command to do some operations with the flag “-local-affine-method”. 
Would you please suggest how to fix this error?
  4.  I received a lot of “name collision in input name” warnings. I guess 
these warnings does not matter?
  5.  Will the updated pipeline using FreeSurfer 6.0.0 possibly be available in 
the near future (sometime this month)?

Thank you.


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[HCP-Users] A question about the MSMSulc

[Aaron C]

Dear HCP experts,

I have a question about using the MSMSulc in the HCP structural preprocessing 
pipeline. I set the MSM path to the MSM binaries in the bin folder of the FSL 
6.0.0. But I encountered the error "--regoption. Option doesn't exist". I am 
wondering if the MSM in the FSL 6.0.0 package has been tested with the HCP 
pipeline. Thank you.


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[HCP-Users] Some questions about using the HCP structural preprocessing pipeline

[Aaron C]

Dear HCP experts,

I have some questions about using the HCP structural preprocessing pipeline.

1. To apply this pipeline on non-HCP data, do I have to rename the filenames of 
my data similar to the HCP unprocessed data as follows?

T1w _MPR1/
{Subject_ID}_3T_AFI.nii.gz
{Subject_ID}_3T_BIAS_32CH.nii.gz
{Subject_ID}_3T_BIAS_BC.nii.gz
{Subject_ID}_3T_FieldMap_Magnitude.nii.gz
{Subject_ID}_3T_FieldMap_Phase.nii.gz
{Subject_ID}_3T_T1w _MPR1.nii.gz

T2w _SPC1/
{Subject_ID}_3T_AFI.nii.gz
{Subject_ID}_3T_BIAS_32CH.nii.gz
{Subject_ID}_3T_BIAS_BC.nii.gz
{Subject_ID}_3T_FieldMap_Magnitude.nii.gz
{Subject_ID}_3T_FieldMap_Phase.nii.gz
{Subject_ID}_3T_T2w _SPC1.nii.gz

2. What are the minimum required MRI data to run the HCP structural 
preprocessing pipeline? Are only "{Subject_ID}_3T_T1w _MPR1.nii.gz" and 
"{Subject_ID}_3T_T2w _SPC1.nii.gz" sufficient for the structural analysis?

3. It seems that the two versions of the example data (with or without GDC) for 
the HCP pipeline have the same files in "T1w _MPR1" and "T2w _SPC1" folders?

Thank you.

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[HCP-Users] A question about dtifit for the HCP data

[Aaron C]

Dear HCP experts,

I saw some previous questions in the mailing list regarding dtifit, and some 
experts suggested that the simple tensor model is not appropriate at high 
b-values.  So I tried the two different options of either using "-kurt" flag or 
limiting the fitting to b=1000 shell, but the results from these two options 
were not nearly the same. Would you please suggest if there is any good way to 
evaluate the difference and choose one from these two options? Thank you.

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[HCP-Users] A question about Connectome Workbench

[Aaron C]

Dear HCP experts,

I have a question about Connectome Workbench. For the most recent version of 
Connectome Workbench, given a scene file, is there any command to batch export 
figures as *.bmp files under the command line, instead of doing this manually 
by clicking on “File>Capture Image”? Thank you.

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[HCP-Users] A question about HCP structural data

[Aaron C]

Dear HCP experts,

I have a question about HCP structural data. Are there any intermediate 
preprocessed T1w or T2w images (gradient distortion, readout distortion, and 
bias field all corrected) in MNI space with only linear registration applied 
(without FNIRT being used)? Thank you.

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[HCP-Users] Temporal signal to noise ratio of HCP subjects

[Aaron C]

Dear HCP experts,

I am looking for temporal signal to noise ratio of the resting state data of 
HCP subjects. Is that information available somewhere?

Also, is there any existing scene file to check GM/WM segmentation quality? 
Thank you.

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[HCP-Users] Software version for HCP Pipeline (v 3.27.0)

[Aaron C]

Dear HCP experts,


Would you please suggest FreeSurfer, FSL, and Connectome Workbench version for 
using HCP Pipeline v 3.27.0? Thank you.

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[HCP-Users] A question about white matter atlas for HCP diffusion data

[Aaron C]

Dear HCP experts,

I have a question about white matter atlas for TBSS analysis of the HCP 
diffusion data. Would you please suggest which atlas would be appropriate for 
this purpose? Do I still need to do any additional registration between the 
white matter atlas and the TBSS results? Thank you.


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[HCP-Users] A question HCP FIX-denoised resting-state data

[Aaron C]

Dear HCP experts,


I have a question about HCP FIX-denoised resting-state data. Could I still 
reasonably expect any high frequency correlations preserved in this dataset 
with ICA-FIX? Thank you.

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[HCP-Users] a question about *.dconn.nii files

[Aaron C]

Dear HCP experts,


I have a question about loading *.dconn.nii files. I am wondering if there is 
any way (using ciftiopen or other MATLAB tools) to only load a specific row of 
the connectivity matrix in the *.dconn.nii file without loading the whole 
matrix into the memory. Thank you.

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[HCP-Users] MSMSulc data

[Aaron C]

Dear HCP experts,


I tried to find the MSMSulc version of cortical thickness, myelin, and 
resting-state fMRI data in the HCP datasets but cannot find them. Are they 
available somewhere? Thank you.

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[HCP-Users] A question about the data in native space

[Aaron C]

Dear HCP experts,


I have a question about obtaining the data in native space. Could I get the 
rfMRI ICA-FIX cleaned data in each subject's native space (without 
cross-subject normalization)? Thank you.

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Re: [HCP-Users] A question about workbench command

[Aaron C]

Hi Tim,


Thank you for your reply. I was just trying to see if the pairwise geodesic 
distances would be interesting, but the current workbench command would 
generate thousands of files for doing this.


I also have a question about the discussions in the following thread:

https://www.mail-archive.com/hcp-users@humanconnectome.org/msg05759.html

If I have a scene file of a dtseries.nii and would like to save the different 
maps of this dtseries using workbench command line, will I need to use the 
commands of a "development" version of workbench? I didn't find it on the HCP 
website. Thank you.


Aaron


From: Timothy Coalson <tsc...@mst.edu>
Sent: Wednesday, February 14, 2018 4:53:54 PM
To: Aaron C
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A question about workbench command

Not currently, no, though it could be added.  It is undefined between left and 
right hemispheres, so the obvious format would be a metric file, rather than 
cifti grayordinates.  Our uses of geodesic distance are generally limited to a 
short distance, we haven't really found it useful to know the geodesic distance 
between vertices that are separated by multiple sulci.

What are you planning to do with the distances?

Tim


On Tue, Feb 13, 2018 at 11:10 PM, Aaron C 
<aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> wrote:

Dear HCP experts,


Is there a one-line workbench command that could extract the matrix of geodesic 
distances between every pair of cortical grayordinates for a given brain 
surface? Thank you.

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[HCP-Users] A question about workbench command

[Aaron C]

Dear HCP experts,


Is there a one-line workbench command that could extract the matrix of geodesic 
distances between every pair of cortical grayordinates for a given brain 
surface? Thank you.

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Re: [HCP-Users] A question about the geodesic distance

[Aaron C]

Hi Matt,


Thank you for looking into my question. I am trying to compare geodesic 
distance between a given pair of brain vertices across different subjects, so I 
hope I would be able to locate the same brain vertex in different subjects. Is 
this feasible using the data after MSM-All registration? Thank you.


Aaron

From: Glasser, Matthew <glass...@wustl.edu>
Sent: Wednesday, January 3, 2018 10:41 PM
To: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A question about the geodesic distance

This question appears to presume a standard mesh meaning some kind of 
registration has occurred.  I think you need to be a bit more specific about 
what you are wanting to do.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>>
Date: Wednesday, January 3, 2018 at 8:19 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] A question about the geodesic distance


Dear HCP experts,


I have a question about the geodesic distance with respect to the MSM-All 
registration. Given a pair of brain vertices, is the variance of their geodesic 
distance across different subjects still preserved after MSM-All registration? 
Thank you.

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[HCP-Users] A question about the geodesic distance

[Aaron C]

Dear HCP experts,


I have a question about the geodesic distance with respect to the MSM-All 
registration. Given a pair of brain vertices, is the variance of their geodesic 
distance across different subjects still preserved after MSM-All registration? 
Thank you.

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[HCP-Users] A question about registering the HCP diffusion data to the standard space

[Aaron C]

Dear HCP experts,


I have a question about registering the HCP diffusion data to the standard 
space for cross-subject analysis. I see the file "acpc_dc2standard.nii.gz" in 
the folder ${StudyFolder}/${Subject}/MNINonLinear/xfms/


Would you please suggest if the following command would be appropriate:


applywarp --ref=MNI152_T1_1mm --in=dti_FA.nii.gz --warp=acpc_dc2standard.nii.gz 
--out=dti_FA_warped.nii.gz


Should I use any reference image specific for the HCP data instead of 
"MNI152_T1_1mm"? After this registration step, I guess the white matter voxels 
in the file "dti_FA_warped.nii.gz" should be comparable across different 
subjects? Thank you.

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[HCP-Users] A question about the unprocessed structural data

[Aaron C]

Dear HCP experts,


I have a question about the files in the unprocessed structural data. Could you 
please explain what are the following files in the subject folders? Thank you.


{Subject_ID}.strc_AFI.nii.gz

{Subject_ID}.BIAS_32CH.nii.gz

{Subject_ID}.BIAS_BC.nii.gz

{Subject_ID}.FieldMap_Magnitude.nii.gz

{Subject_ID}.FieldMap_Phase.nii.gz

{Subject_ID}.T1w_MPR1_reorient_sformMod.nii.gz

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[HCP-Users] Questions about saving cifti files

[Aaron C]

Dear HCP experts,

I have two questions about using "ciftisave" or "ciftisavereset".

1. I tried to reuse the header of an existing cifti file. But if I substitute 
its single-precision data matrix with my double-precision matrix and use 
"ciftisavereset" to save it, I notice that the new cifti file is still in 
single precision. Is there a way for me to change the precision specified in 
the header?

2. I see some cifti files such as 
"S900.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii" contain multiple maps and 
each of these maps has a different map name (subject IDs in this case). Is 
there a way for me to save a similar *.dscalar.nii file with my customized 
names?

Thank you.


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Re: [HCP-Users] A question about brain registration matrix

[Aaron C]

Hi Matt,

Thank you for your reply. I am looking for the file which provides me with the 
information to calculate how much deformation was done for some subjects. Will 
it possible for me to compute the displacements of vertices for the MSM-All 
registration using this file "${Subject}.L.sphere.MSMAll.native.surf.gii"? 
Thank you.

Aaron

From: Glasser, Matthew <glass...@wustl.edu>
Sent: Sunday, November 19, 2017 10:47 PM
To: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A question about brain registration matrix

This is a deformed spherical surface, not a warpfield or affine matrix as you 
might be used to using, however, we do provide this:

${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.L.sphere.MSMAll.native.surf.gii
${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.R.sphere.MSMAll.native.surf.gii

What is it specifically that you need to do?

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>>
Date: Sunday, November 19, 2017 at 9:38 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] A question about brain registration matrix


Dear HCP experts,

I have a question about the transformation matrix aligning the raw data to the 
MSM-All registered data. Could I find the file of this matrix in the 
preprocessed data? Thank you.


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Re: [HCP-Users] HCP-Users Digest, Vol 50, Issue 40

[Aaron C]

Dear HCP experts,


I have a question about the different reconstruction algorithms of the rfMRI 
data Jennifer mentioned in her previous email. Did the S900 group-average dense 
connectome (820 subjects) mix the subjects with different rfMRI reconstruction 
algorithms? Thank you.


From: hcp-users-boun...@humanconnectome.org 
 on behalf of 
hcp-users-requ...@humanconnectome.org 
Sent: Friday, January 27, 2017 1:00:01 PM
To: hcp-users@humanconnectome.org
Subject: HCP-Users Digest, Vol 50, Issue 40

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When replying, please edit your Subject line so it is more specific
than "Re: Contents of HCP-Users digest..."


Today's Topics:

   1. Re: Unrelated subjects (Elam, Jennifer)
   2. Very large z values for task contrasts in
  S900_ALLTASKS_level3_zstat file: what does this mean in terms of
  statistical significance? (Xavier Guell Paradis)
   3. Re: Very large z values for task contrasts in
  S900_ALLTASKS_level3_zstat file: what does this mean in terms of
  statistical significance? (Glasser, Matthew)
   4. Re: Very large z values for task contrasts in
  S900_ALLTASKS_level3_zstat file: what does this mean in terms of
  statistical significance? (David Van Essen)
   5. Re: Very large z values for task contrasts in
  S900_ALLTASKS_level3_zstat file: what does this mean in terms of
  statistical significance? (Xavier Guell Paradis)
   6. Re: Very large z values for task contrasts in
  S900_ALLTASKS_level3_zstat file: what does this mean in terms of
  statistical significance? (Glasser, Matthew)
   7. Re: Very large z values for task contrasts in
  S900_ALLTASKS_level3_zstat file: what does this mean in terms of
  statistical significance? (Xavier Guell Paradis)


--

Message: 1
Date: Thu, 26 Jan 2017 17:57:43 +
From: "Elam, Jennifer" 
Subject: Re: [HCP-Users] Unrelated subjects
To: "hcp-users@humanconnectome.org" 
Message-ID:



Content-Type: text/plain; charset="windows-1252"

It looks like the message I sent with the attached CSV of unrelated S900 
subjects with complete rfMRI and physio data did not go through to the list 
(likely blocked due to the attachment). The original message is pasted below. 
If you would like that file please email me directly and I will send it on.


Best,

Jenn


Hi Siobhan,
Here is a csv spreadsheet we pulled together for another user that has 339 
unrelated subjects from the S900 release with a T1, a T2, complete rfMRI, and 
physiological data.

If you end up using the fMRI data for these subjects, please note that two 
different image reconstruction algorithms were used on this data (r177 early in 
the project, r227 later) and data from the different reconstructions shouldn't 
be mixed in an analysis. The structural data should be unaffected by this and 
all the diffusion data was reconstructed using the r227 algorithm.

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: Elam, Jennifer
Sent: Thursday, January 26, 2017 10:30 AM
To: Ewert, Siobhan Geraldine; hcp-users@humanconnectome.org
Subject: Re: Unrelated subjects


I forgot to mention for everyone's benefit that you can find the reconstruction 
version for 3T dMRI and fMRI in the dMRI_3T_ReconVrs and fMRI_3T_ReconVrs 
columns in the CSV (these are columns W and X when viewed in Excel) of 
unrelated subjects attached to the previous message. These are also something 
you can filter for in ConnectomeDB to make sure you are using subjects with 
compatible data.


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: Elam, Jennifer
Sent: Thursday, 

[HCP-Users] A question about calculating dense connectome for individual subject

[Aaron C]

Dear HCP experts,


I have a question about calculating dense connectome for individual subject 
using HCP resting-state data. Should I calculate a dense connectome for each 
run of the subject and then average them? Or, should I demean, variance 
normalize, and concatenate the four runs and then calculate a dense connectome 
for the subject? Thank you.

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[HCP-Users] A question about multi-modal parcellation

[Aaron C]

Dear HCP experts,


I have a question about Dr. Glasser's multi-modal parcellation. Could I find a 
figure of the parcellation with its each parcel annotated with the 
corresponding parcel index from Table 1 of Supplementary Neuroanatomical 
Results of the multi-modal parcellation paper? Thank you.

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[HCP-Users] HCP script for probabilistic tractography

[Aaron C]

Dear HCP experts,


I am interested to calculate dense grayordinate-wise structural connectivity 
matrices for each subject using HCP diffusion data. I am wondering if there is 
an existing HCP script for this. If so, could you please advise me where to 
find this script? Thank you.

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[HCP-Users] A question about the order of cortical vertices

[Aaron C]

Dear HCP experts,


I have a question about the order of 59412 cortical vertices. Given a cortical 
vertex in the left hemisphere, how could I identify its homotopic counterpart 
in the right hemisphere? Thank you.

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[HCP-Users] A question about 164k data

[Aaron C]

Dear HCP experts,


I have a question about 164k data. Is there a computational less expensive way 
to calculate MSMAll-registered 164k individual myelin maps from the existing 
data? There were only MSMAll-registered 164k myelin maps with bias field 
corrected there in the existing data, but I am looking for MSMAll-registered 
individual maps without this correction.


Also, could I find S900 group-average 164k data somewhere or are there any 
existing scripts for this purpose? Thank you.

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[HCP-Users] A question about twins' zygosity

[Aaron C]

Dear HCP experts,


I have a question about twins' zygosity. I saw the HCP manual mentioned that 
the zygosity information in ConnectomeDB is self-reported. Will the genetic 
confirmed zygosity information be released sometime this year or later? Thank 
you.

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[HCP-Users] A question about the group-average tfMRI data in HCP_S900_GroupAvg_v1 Dataset

[Aaron C]

Dear HCP experts,


I have a question about the group-average tfMRI data in HCP_S900_GroupAvg_v1 
Dataset. The file 
"HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s4_MSMAll.dscalar.nii" has 
multiple contrast maps, but I didn't find an explanation for the labels of 
these maps. For example, for the motor mapping task of right hand, there are 
maps called "tfMRI_MOTOR_RH", "tfMRI_MOTOR_RH-AVG", "tfMRI_MOTOR_neg_RH", and 
"tfMRI_MOTOR_AVG-RH". And there is also a one called "tfMRI_MOTOR_AVG". I'd 
like to know what do they mean. Thank you.

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[HCP-Users] A question about multi-modal parcellation

[Aaron C]

Dear HCP experts,

I have a question about a detail of the methods of multi-modal parcellation. 
Were age and gender regressed out from the data? Thank you.


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[HCP-Users] A question about importing the entire label table of *.dlabel.nii file into the MATLAB

[Aaron C]

Dear HCP experts,


When I am using "wb_command -file-information" to display the information of a 
*.dlabel.nii file, I see there are six fields there in the label table:


Label table for ALL maps
   KEY   NAME RED   GREENBLUE   ALPHA
 0   ???1.000   1.000   1.000   0.000
 1   R_V1_ROI   0.298   0.020   1.000   1.000
 2   R_MST_ROI  0.204   0.424   0.518   1.000
 3   R_V6_ROI   0.263   0.369   0.671   1.000
... ...

But when I am trying to use either "ciftiopen" or "ft_read_cifti" to import 
this table into the MATLAB, only the values in the first field "KEY" can be 
loaded into the MATLAB. Is there a convenient way for me to load the values of 
all the other fields of this label table into the MATLAB? Thank you.

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[HCP-Users] Export the colormaps of Connectome Workbench into the MATLAB

[Aaron C]

Dear HCP experts,


I see the colormaps used in Connectome Workbench are very nice. I am wondering 
if there is a way to export the colormaps of Connectome Workbench into the 
MATLAB. I am particularly interested in using the Workbench colormap 
"videen_style" in the MATLAB. Thank you.

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[HCP-Users] A question about ROI full names in multi-modal parcellation

[Aaron C]

Dear HCP experts,

Where could I find the full name for each of ROI acronyms used in Dr. Glasser's 
multi-modal parcellation? I tried "wb_command -file-information" but there were 
only ROI acronyms in the output. For example, for ROI 330, its acronym is 
"L_PGi_ROI", but I need to find out the full name of "PGi". And I need to do so 
for all ROIs. Thank you.


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Re: [HCP-Users] HCP script used for residual bias field correction on myelin maps

[Aaron C]

One more question. Is it necessary to also do residual bias field correction 
for resting-state data? Thank you.


From: Glasser, Matthew <glass...@wustl.edu>
Sent: Sunday, August 28, 2016 9:37 PM
To: Aaron C; Harms, Michael; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] HCP script used for residual bias field correction on 
myelin maps

No.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>>
Date: Sunday, August 28, 2016 at 5:02 PM
To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, 
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] HCP script used for residual bias field correction on 
myelin maps


Dear HCP experts,


I saw that Dr. Glasser et al.'s paper mentioned that the residual bias field of 
HCP Skyra data was caused by "the positioning of the head is ~ 5cm above 
isocenter and because of the smaller (customized 56 cm) body transmit coil 
making it more difficult to achieve the kind of B1 transmit homogeneity found 
in other whole body scanners". Are there any subjects from HCP 900 Subjects 
release scanned using other whole body scanners instead of this 3T Skyra 
system, which may not need this mandatory residual bias field correction? Thank 
you.


From: Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Sent: Sunday, August 28, 2016 1:52 PM
To: Aaron C; hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] HCP script used for residual bias field correction on 
myelin maps


Hi,
It's in the PostFreeSurfer/scripts/CreateMyelinMaps.sh script.
Look for the stuff related to "MyelinMap_BC".

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
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: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>>
Date: Sunday, August 28, 2016 at 11:25 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP script used for residual bias field correction on 
myelin maps


Dear HCP experts,


Could I find the shell or MATLAB script used for performing residual bias field 
correction on myelin maps somewhere online? It's described in Fig 18 of Dr. 
Glasser's 2013 paper "The minimal preprocessing pipelines for the Human 
Connectome Project", but I cannot find the actual script from HCP pipeline 
scripts. Thank you.

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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 
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Re: [HCP-Users] HCP script used for residual bias field correction on myelin maps

[Aaron C]

Dear HCP experts,


I saw that Dr. Glasser et al.'s paper mentioned that the residual bias field of 
HCP Skyra data was caused by "the positioning of the head is ~ 5cm above 
isocenter and because of the smaller (customized 56 cm) body transmit coil 
making it more difficult to achieve the kind of B1 transmit homogeneity found 
in other whole body scanners". Are there any subjects from HCP 900 Subjects 
release scanned using other whole body scanners instead of this 3T Skyra 
system, which may not need this mandatory residual bias field correction? Thank 
you.


From: Harms, Michael <mha...@wustl.edu>
Sent: Sunday, August 28, 2016 1:52 PM
To: Aaron C; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] HCP script used for residual bias field correction on 
myelin maps


Hi,
It's in the PostFreeSurfer/scripts/CreateMyelinMaps.sh script.
Look for the stuff related to "MyelinMap_BC".

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
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: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Aaron C <aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>>
Date: Sunday, August 28, 2016 at 11:25 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP script used for residual bias field correction on 
myelin maps


Dear HCP experts,


Could I find the shell or MATLAB script used for performing residual bias field 
correction on myelin maps somewhere online? It's described in Fig 18 of Dr. 
Glasser's 2013 paper "The minimal preprocessing pipelines for the Human 
Connectome Project", but I cannot find the actual script from HCP pipeline 
scripts. Thank you.

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[HCP-Users] A question about saving *.pconn.nii file

[Aaron C]

Dear HCP experts,


I have a question about saving *.pconn.nii file. I have a *.dlabel.nii file 
(for example, N ROIs) and a pre-computed parcellated connectome matrix (N x N). 
They are in the same order that the connectivity profile of ROI i (with its 
label i in the *.dlabel file) is in the row i (or column i) of the parcellated 
connectome matrix.


How could I save this parcellated connectome matrix into a *.pconn.nii file 
using any Connectome Workbench command? I need this *.pconn.nii" file to be 
compatible with Connectome Workbench so that I can display it using the scene 
similar to Scene 8 of Connectome Workbench Tutorial.


Thank you!

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[HCP-Users] Multi-modal parcellation *.dlabel files

[Aaron C]

Dear HCP experts,


I have a question about the *.dlabel files of multi-modal parcellation. I saw 
there were multiple *.dlabel files in the dataset from the BALSA site and I am 
wondering which *.dlabel file I should use. Should I use the file 
"Q1-Q6_RelatedParcellation210.CorticalAreas_dil_Final_Final_Areas_Group_Colors.32k_fs_LR.dlabel.nii"?
 Thank you.

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[HCP-Users] Connectome workbench 1.2.2 doesn't work under Win 8

[Aaron C]

Dear HCP experts,


I tried to use the newly release version (1.2.2) of Connectome workbench, but 
it doesn't work under Win 8. Could anyone please check this problem? Thank you.

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[HCP-Users] HCP script used for generating group-averaged dense connectome

[Aaron C]

Dear HCP experts,

Could I find the shell or MATLAB script used for generating group-averaged 
dense connectome 
("HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii") somewhere 
online? Thank you.


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Re: [HCP-Users] HCP-Users Digest, Vol 44, Issue 3

[Aaron C]

Dear HCP experts,


I have a question about the recently released 7T REST denoised volume data. 
Have white matter/ventricle or global signals been removed from these 7T REST 
denoised volume data? Thank you.


From: hcp-users-boun...@humanconnectome.org 
 on behalf of 
hcp-users-requ...@humanconnectome.org 
Sent: Tuesday, July 5, 2016 1:00:01 PM
To: hcp-users@humanconnectome.org
Subject: HCP-Users Digest, Vol 44, Issue 3

Send HCP-Users mailing list submissions to
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than "Re: Contents of HCP-Users digest..."


Today's Topics:

   1. Error downloading 7T_REST_Volume_fix dataset (Parnesh Raniga)
   2. Re: Error downloading 7T_REST_Volume_fix dataset (Hodge, Michael)


--

Message: 1
Date: Tue, 5 Jul 2016 11:34:27 +1000
From: Parnesh Raniga 
Subject: [HCP-Users] Error downloading 7T_REST_Volume_fix dataset
To: hcp-users@humanconnectome.org
Message-ID:

Re: [HCP-Users] A question about R820 MSM-All registered dense connectome

[Aaron C]

Dear HCP experts,


Could anyone please provide a list of subjects used for the group-average dense 
connectome? I cannot figure out which 820 subjects were used, because there are 
832 subjects with the complete set of 4 rsfMRI scans in the database. Thank you 
very much.


From: Stephen Smith <st...@fmrib.ox.ac.uk>
Sent: Saturday, June 4, 2016 8:06:24 AM
To: Aaron C
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A question about R820 MSM-All registered dense 
connectome

Hi - we used the 820 subjects with the absolutely complete set of timepoints 
from all 4 runs, for the group-average dense connectome and group-ICA stuff.
Cheers


On 3 Jun 2016, at 19:16, Aaron C 
<aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>> wrote:

I checked the number of subjects which completed all four resting-state scans, 
but found this number was 832 instead of 820. Therefore, I cannot figure out 
which subjects were used for generating R820 MSM-All registered dense 
connectome of group-averaged functional connectivity file 
“HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii”. Could anyone 
please help me with my question? Thank you.


From: aaroncr...@outlook.com<mailto:aaroncr...@outlook.com>
To: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: A question about R820 MSM-All registered dense connectome
Date: Mon, 30 May 2016 21:03:33 -0400

Dear HCP experts,

Where could I find the subject ID number list of 820 subjects used for 
generating R820 MSM-All registered dense connectome of group-averaged 
functional connectivity “HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr”? 
Thank you.
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---
Stephen M. Smith, Professor of Biomedical Engineering
Head of Analysis,  Oxford University FMRIB Centre

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

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






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[HCP-Users] The grayordinates adjacent to the medial wall

[Aaron C]

Dear HCP experts,
>From 59412 grayordinates of the cortex, how could I identify the grayordinates 
>adjacent to the medial wall? Thank you. 
  
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[HCP-Users] One subject information missing

[Aaron C]

Dear HCP experts,

I noticed that subject #599065's gender information is missing. Could anyone 
please provide this information? Thank you.
  
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[HCP-Users] The computation of geodesic distance across hemispheres using the Connectome Workbench

[Aaron C]

Dear HCP experts,

Is it possible to compute the geodesic distance between two vertices on 
different hemispheres using any commands of the Connectome Workbench? It looks 
like that the command "-surface-geodesic-distance" could only compute geodesic 
distance from one vertex to all the other vertices on the ipsilateral 
hemisphere. Thank you.
  
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Re: [HCP-Users] A question about R820 MSM-All registered dense connectome

[Aaron C]

I checked the number of subjects which completed all four resting-state scans, 
but found this number was 832 instead of 820. Therefore, I cannot figure out 
which subjects were used for generating R820 MSM-All registered dense 
connectome of group-averaged functional connectivity file 
“HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii”. Could anyone 
please help me with my question? Thank you.
 
From: aaroncr...@outlook.com
To: hcp-users@humanconnectome.org
Subject: A question about R820 MSM-All registered dense connectome
Date: Mon, 30 May 2016 21:03:33 -0400




Dear HCP experts,

Where could I find the subject ID number list of 820 subjects used for 
generating R820 MSM-All registered dense connectome of group-averaged 
functional connectivity “HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr”? 
Thank you.

  
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[HCP-Users] A question about R820 MSM-All registered dense connectome

[Aaron C]

Dear HCP experts,

Where could I find the subject ID number list of 820 subjects used for 
generating R820 MSM-All registered dense connectome of group-averaged 
functional connectivity “HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr”? 
Thank you.
  
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Re: [HCP-Users] Some questions about the usage of CIFTI files

[Aaron C]

Thank Tim and Matt very much for your answers! 

I tried the function "ciftisavereset" using the following test code but 
encountered an error.

Test code:

% try to use the CIFTI header of the file 
"rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii" (91282*1200)
cii = 
ciftiopen('C:\cifti_test\rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii','wb_command.exe');
newcii = cii;
% test ciftisavereset to see if it can save the data of different number of 
maps/columns using the existing CIFTI header
simulate_data=rand(59412,1000);
newcii.cdata=simulate_data;
ciftisavereset(newcii,'C:\cifti_test\test.dtseries','wb_command.exe');


Output and error:

Qt: Untested Windows version 6.2 detected! 
Elapsed time is 0.153600 seconds.
Qt: Untested Windows version 6.2 detected! 
 
While running: 
wb_command.exe -cifti-convert -from-gifti-ext C:\cifti_test\test.dtseries.gii 
C:\cifti_test\test.dtseries 
 
ERROR: Parse error while reading: Tried to read 237648000 from Elapsed time is 
0.319364 seconds.
The system cannot find the path specified. 



I also tried to use "ciftisave" to save the data read directly from an existing 
*.dtseries.nii CIFTI file, but I also encountered an error.

Test code:

cii = 
ciftiopen('C:\cifti_test\rfMRI_REST1_LR_Atlas_hp2000_clean.dtseries.nii','wb_command.exe');
ciftisave(cii,'C:\cifti_test\test.dtseries.nii','wb_command.exe');


Output and error:

Qt: Untested Windows version 6.2 detected! 
Qt: Untested Windows version 6.2 detected! 
 
While running: 
wb_command.exe -cifti-convert -from-gifti-ext 
C:\cifti_test\test.dtseries.nii.gii C:\cifti_test\test.dtseries.nii 
 
ERROR: Parse error while reading: Tried to read 438153600 from>> 


It seems that I cannot save *.dtseries.nii using either "ciftisavereset" or 
"ciftisave". Would you please give me some hints how to fix this problem?

Thank you very much!

From: glass...@wustl.edu
To: tsc...@mst.edu; aaroncr...@outlook.com
CC: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Some questions about the usage of CIFTI files
Date: Fri, 13 May 2016 21:24:08 +






The mismatch is because the medial wall is not excluded from that particular 
file.  The HCP data files (e.g. dense timeseries files) have the medial wall 
excluded.



Peace,



Matt.





From:  on behalf of Timothy Coalson 

Date: Friday, May 13, 2016 at 3:09 PM

To: Aaron C 

Cc: "hcp-users@humanconnectome.org" 

Subject: Re: [HCP-Users] Some questions about the usage of CIFTI files







Inline replies.



Tim





On Fri, May 13, 2016 at 1:20 PM, Aaron C 
 wrote:


Dear HCP experts,



I have some questions about the usage of CIFTI files.



1. I checked the number of grayordinates of the following files using the 
command “wb_command -file-information”, and I noticed some of them have 
different number of grayordinates:



“Parcels_LR.dlabel.nii” from Gordon et al.’s parcellation: 64984 grayordinates 
(32492 left cortex vertices and 32492 right cortex vertices).

“100206.aparc.a2009s.32k_fs_LR.dlabel.nii”: 59412 grayordinates (29696 left 
cortex vertices and 29716 right cortex vertices)

“100206.MyelinMap.32k_fs_LR.dscalar.nii”: 59412 grayordinates (29696 left 
cortex vertices and 29716 right cortex vertices)

“HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii”: 91282 
grayordinates (29696 left cortex vertices, 29716 right cortex vertices and 
31870 subcortical voxels)





Probably the easiest way to fix this is to use 
-cifti-create-dense-from-template to make cifti files that do have matching 
indices.  Modifying a dconn is a bit trickier, and will also need to involve 
-cifti-transpose and -cifti-copy-mapping, and may use
 a lot of memory, so you may simply want to use the 91282 space as the template.
 

If two CIFTI files are with different number of grayordinates (e.g., 
“Parcels_LR.dlabel.nii” and “100206.MyelinMap.32k_fs_LR.dscalar.nii”), when 
both loaded into the MATLAB using "ciftiopen", then the first file will be just 
a 64984x1 array, and the second
 file will be just a 59412x1 array, but there is no other information about the 
correspondence of the same grayordinate between these two files. My question is 
how could I locate the same brain grayordinate from them?





You can also use -cifti-export-dense-mapping to get the mapping from matrix 
index to vertex/voxel + structure, but this is likely to be more involved.  
However, since you are interested in spatial neighbor information, you'll need 
this to figure that out

[HCP-Users] Some questions about the usage of CIFTI files

[Aaron C]

Dear HCP experts,

I have some questions about the usage of CIFTI files.

1. I checked the number of grayordinates of the following files using the 
command “wb_command -file-information”, and I noticed some of them have 
different number of grayordinates:

“Parcels_LR.dlabel.nii” from Gordon et al.’s parcellation: 64984 grayordinates 
(32492 left cortex vertices and 32492 right cortex vertices).
“100206.aparc.a2009s.32k_fs_LR.dlabel.nii”: 59412 grayordinates (29696 left 
cortex vertices and 29716 right cortex vertices)
“100206.MyelinMap.32k_fs_LR.dscalar.nii”: 59412 grayordinates (29696 left 
cortex vertices and 29716 right cortex vertices)
“HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii”: 91282 
grayordinates (29696 left cortex vertices, 29716 right cortex vertices and 
31870 subcortical voxels)

If two CIFTI files are with different number of grayordinates (e.g., 
“Parcels_LR.dlabel.nii” and “100206.MyelinMap.32k_fs_LR.dscalar.nii”), when 
both loaded into the MATLAB using "ciftiopen", then the first file will be just 
a 64984x1 array, and the second file will be just a 59412x1 array, but there is 
no other information about the correspondence of the same grayordinate between 
these two files. My question is how could I locate the same brain grayordinate 
from them?

2. I have the time series of only a subset of cortical surface vertices in a 
MATLAB matrix (e.g., a 59412x1200 matrix). How could I save the time series of 
the subset of cortical surface vertices in a CIFTI *.dtseries.nii file? The 
header of existing CIFTI *.dtseries.nii file cannot be used directly since I 
didn’t find such *.dtseries.nii file with a dimensionality of 59412x1200.
  
Similarly, I also have the pairwise correlations between only a subset of 
cortical surface vertices in a MATLAB matrix (e.g., just a 59412x59412 matrix, 
not like a 91282x91282 matrix which also includes subcortical voxels). How 
could I save it in a CIFTI *.dconn.nii file? The header of existing CIFTI 
*.dconn.nii file cannot be used directly since I didn’t find such *.dconn.nii 
file with a dimensionality of 59412x59412.  

3. How could I obtain surface vertex adjacencies of the fs_LR 32k surface using 
wb_command? I am looking for some commands in Connectome Workbench equivalent 
to the command “caret_command -surface-topology-neighbors” in the Caret 
software.

Thank you very much!

  
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[HCP-Users] Question about myelin maps in HCP S900 data

[Aaron C]

Dear HCP experts,

I have some questions about the myelin maps in HCP S900 distribution. In the 
folder 100307\MNINonLinear\fsaverage_LR32k, I see there are seven *.dscalar.nii 
files of myelin maps:

100307.MyelinMap.32k_fs_LR.dscalar.nii
100307.MyelinMap_BC.32k_fs_LR.dscalar.nii
100307.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii
100307.MyelinMap_MSMAll.32k_fs_LR.dscalar.nii
100307.SmoothedMyelinMap.32k_fs_LR.dscalar.nii
100307.SmoothedMyelinMap_BC.32k_fs_LR.dscalar.nii
100307.SmoothedMyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii

>From these names, I guess the files with “BC” are residual bias field 
>corrected myelin maps, and the files with “MSMAll” are MSMAll-registered 
>myelin maps. Am I correct?
 
For any group analysis, should I use MSMAll-registered myelin map from each 
individual for better registration between subjects?

Thank you.
  
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Re: [HCP-Users] A question about saving custom parcellation label map in a CIFTI *.dlabel.nii file

[Aaron C]

This works great! Thank you!
From: glass...@wustl.edu
To: aaroncr...@outlook.com; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] A question about saving custom parcellation label map 
in a CIFTI *.dlabel.nii file
Date: Sun, 8 May 2016 19:13:07 +






Save the matrix data as dscalar and then make the label table as an 
appropriately formatted text file and combine them with wb_command 
-cifti-label-import.



Peace,



Matt.





From: <hcp-users-boun...@humanconnectome.org> on behalf of Aaron C 
<aaroncr...@outlook.com>

Date: Sunday, May 8, 2016 at 2:07 PM

To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>

Subject: [HCP-Users] A question about saving custom parcellation label map in a 
CIFTI *.dlabel.nii file








Dear HCP experts,



I have a question about saving my custom parcellation label map in a CIFTI 
*.dlabel.nii file. I can now save the labels in a *.dscalar.nii file by using 
the CIFTI header of an existing *.dscalar.nii file, but I cannot do the same 
for saving my labels in *.dlabel.nii
 file directly by using the CIFTI header of an existing *.dlabel.nii file,  
because I need to use my own label table for defining label color scheme 
different from the one used in the CIFTI header of the existing *.dlabel.nii 
file.



Would you please advise how can I create a custom *.dlabel.nii file with my own 
ROI names, key values, and corresponding RGB color values from a vector of 
labels for each vertex (32k mesh)?



Many thanks!



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The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended
 recipient, be advised that any unauthorized use, disclosure, copying or the 
taking of any action in reliance on the contents of this information is 
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[HCP-Users] A question about saving custom parcellation label map in a CIFTI *.dlabel.nii file

[Aaron C]

Dear HCP experts,

I have a question about saving my custom parcellation label map in a CIFTI 
*.dlabel.nii file. I can now save the labels in a *.dscalar.nii file by using 
the CIFTI header of an existing *.dscalar.nii file, but I cannot do the same 
for saving my labels in *.dlabel.nii file directly by using the CIFTI header of 
an existing *.dlabel.nii file,  because I need to use my own label table for 
defining label color scheme different from the one used in the CIFTI header of 
the existing *.dlabel.nii file.

Would you please advise how can I create a custom *.dlabel.nii file with my own 
ROI names, key values, and corresponding RGB color values from a vector of 
labels for each vertex (32k mesh)?

Many thanks!

  
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Re: [HCP-Users] Questions about the extensively processed rfMRI data

[Aaron C]

Thank Dr. Smith very much for his very helpful answers.
 
I have one more question about the extensively processed rfMRI data of 
“parcellation-timeseries-netmats”. I think I saw the vitamin E capsule in the 
left side of the unprocessed structural image, which should be the subject’s 
right side, based on the description in the HCP manual. Will the HCP 
preprocessing and parcellation-timeseries-netmats extensively processing 
pipeline keep the left and right? For these ICA spatial maps in the volumetric 
file “melodic_IC_sum.nii.gz”, may I confirm that the left side of the ICA 
spatial maps displayed in FSLView is still the subject’s right side?
 
Thanks again.
 
Subject: Re: [HCP-Users] Questions about the extensively processed rfMRI data
From: st...@fmrib.ox.ac.uk
Date: Wed, 25 Feb 2015 06:21:36 +0100
CC: hcp-users@humanconnectome.org
To: aaroncr...@outlook.com

Hi
On 25 Feb 2015, at 03:39, Aaron C aaroncr...@outlook.com wrote:Dear HCP 
users,I have some questions about the extensively processed rfMRI data of 
“parcellation-timeseries-netmats”. Their filenames are 
“groupICA_3T_Q1-Q6related468_MSMsulc.tar.gz”, 
“NodeTimeseries_3T_Q1-Q6related468_MSMsulc_ICAd*_ts*.tar.gz”, and 
“netmats_3T_Q1-Q6related468_MSMsulc_ICAd*_ts*.tar.gz”. 1. For nodes, is there 
any specific threshold applied to the ICA spatial map to obtain the parcel?
No - thresholding was only used to generate the thumbnail overlays.
 I see from an old message of this mailing list that the thumbnail images were 
obtained by thresholding the ICA spatial map at Z6. But how about the 
threshold for obtaining that parcellation? Is that also Z6?
2. These ICA spatial maps were obtained from the ICA+FIX preprocessed data, 
therefore, given the dimensionality of 100 as an example, are all these 100 
components non- artifactual?

Not necessarily; there can still be some artefactual processes left in the 
data, and out of (eg) 100 components there can possibly be a few artefactual 
ones.   We have not attempted to classify those group-level components in the 
PTN release.
3. For these netmat *.pconn.nii files, are the first column corresponded to the 
first ICA component shown in the thumbnail image “.png” in the folder 
“melodic_IC_sum.sum”, the second column corresponded to the second thumbnail 
image “0001.png” in the folder, and so on? 

Yes
4. For these thumbnail PNG images, could I find any annotation regarding the 
corresponding dominant brain region on the HCP website (e.g., something similar 
to the annotations in Figure 4(A) of Dr. Smith et al.’s paper 
http://www.ncbi.nlm.nih.gov/pubmed/24238796)?

Sorry - we haven't tried to annotate the PTN components.
5. Have these data ever been global signal regressed?
No.  
Cheers, Steve.


 Many thanks!
 
  
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---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

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




  
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[HCP-Users] Questions about the extensively processed rfMRI data

[Aaron C]

Dear HCP users,
I have some questions about the extensively processed rfMRI data of 
“parcellation-timeseries-netmats”. Their filenames are 
“groupICA_3T_Q1-Q6related468_MSMsulc.tar.gz”, 
“NodeTimeseries_3T_Q1-Q6related468_MSMsulc_ICAd*_ts*.tar.gz”, and 
“netmats_3T_Q1-Q6related468_MSMsulc_ICAd*_ts*.tar.gz”. 1. For nodes, is there 
any specific threshold applied to the ICA spatial map to obtain the parcel? I 
see from an old message of this mailing list that the thumbnail images were 
obtained by thresholding the ICA spatial map at Z6. But how about the 
threshold for obtaining that parcellation? Is that also Z6?
2. These ICA spatial maps were obtained from the ICA+FIX preprocessed data, 
therefore, given the dimensionality of 100 as an example, are all these 100 
components non- artifactual?
3. For these netmat *.pconn.nii files, are the first column corresponded to the 
first ICA component shown in the thumbnail image “.png” in the folder 
“melodic_IC_sum.sum”, the second column corresponded to the second thumbnail 
image “0001.png” in the folder, and so on? 
4. For these thumbnail PNG images, could I find any annotation regarding the 
corresponding dominant brain region on the HCP website (e.g., something similar 
to the annotations in Figure 4(A) of Dr. Smith et al.’s paper 
http://www.ncbi.nlm.nih.gov/pubmed/24238796)?
5. Have these data ever been global signal regressed? Many thanks!
 
  
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