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.
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.
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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
, 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
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.
___
HCP-Users
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
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 tr
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",
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 ma
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
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
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
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”?
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
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
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
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
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.
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.
___
Dear HCP experts,
Would you please suggest FreeSurfer, FSL, and Connectome Workbench version for
using HCP Pipeline v 3.27.0? Thank you.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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
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.
___
HCP-Users mailing list
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.
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.
___
HCP-Users mailing list
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.
___
HCP-Users mailing list
P
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 i
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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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 som
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.
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
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
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
bject}.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
Th
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.
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
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
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.
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.
___
HCP-Users mailing list
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
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.
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
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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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
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.
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
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
S
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
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
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
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.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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.
___
HCP-Users mailing list
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
.
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 time
Dear HCP experts,
>From 59412 grayordinates of the cortex, how could I identify the grayordinates
>adjacent to the medial wall? Thank you.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
Dear HCP experts,
I noticed that subject #599065's gender information is missing. Could anyone
please provide this information? Thank you.
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
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
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
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.
meseries 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.
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
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
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
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
, 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
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
65 matches
Mail list logo
