This means that the template is asymmetric, not symmetric, correct?
Thanks,
Xavier.
On Fri, Apr 5, 2019 at 5:48 PM Glasser, Matthew wrote:
> FSL’s MNI152.
>
> Matt.
>
> From: on behalf of Xavier Guell
> Paradis
> Date: Friday, April 5, 2019 at 4:46 PM
> To: "
Dear HCP experts,
I am interested in analyzing your group-averaged subcortical volumetric data.
My understanding is that your volumetric data is registered to MNI space. I was
wondering if you could let me know what specific MNI template you used. I am
especially interested in knowing whether
Hello HCP,
We are a team of researchers designing some deep learning tools we have created
for modality conversions, and wanting to test our library on the HCP dataset
(structural T1 and T2). We are having issues copying from the s3 bucket.
Currently after creating our credentials, running aws
Dear HCP experts,
Is it possible to download HCP data using ascp (the command line version of
aspera)?
If so, is there a list of [[user@]host:]PATH for each download package of HCP
data?
(We would like to download the 100 unrelated resting state compact package to
an online cluster, and the
, is there a different method you would
recommend?
Thank you very much,
Xavier.
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Monday, March 05, 2018 7:11 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Is surface myelin map the same
Dear HCP experts,
When trying to download the "structural preprocessed" data from a single
subject I get the following error in Aspera: "Error: No such file or directory
(Code: 4)".
I have made sure that the folder I am downloading the data to exists.
How could I solve this?
Thank you,
Xavier.
Dear HCP experts,
Is S1200.All.MyelinMap_BC_MSMAll.32k_fs_LR.dscalar.nii calculated in the same
way as the S1200_AverageT1wDividedByT2w_2mmResample.nii, with the only
difference that one file is surface and the other is volume?
Thank you very much,
Xavier.
Dear HCP experts,
I have a dscalar file (myfile.dscalar.nii), and I would like to restrict this
file so that it only contains data for CORTEX_LEFT and CORTEX_RIGHT.
If I do this right, CORTEX_LEFT and CORTEX_RIGHT should be a total number of
59412 data points.
I have tried this, which has not
Dear HCP experts,
I have a dlabel file that labels a particular nucleus of the left thalamus
(thalamusnucleus.dlabel.nii). I would like to convert this dlabel file to a
whole-brain dscalar file, so that this nucleus in the left thalamus has a value
of 1 and the rest of the brain has a value of
: Tuesday, December 12, 2017 7:37 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] -cifti-separate converts from dscalar to nifti: is it
possible to generate one nifti from each dscalar map?
wb_command -volume-merge allows you to select specific maps despite its
Dear HCP experts,
I have a dscalar file with 4 maps and would like to convert each map into one
separate nifti file. I am not worried about the problem of surface information
in a nifti file, because I am interested in subcortical data only.
I have been able to transform the dscalar into a nifti
Thank you very much, it works!
Xavier.
From: Timothy Coalson [tsc...@mst.edu]
Sent: Monday, November 27, 2017 7:39 PM
To: Xavier Guell Paradis
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Show outline of dscalar map at a given
:
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>>
Date: Monday, November 27, 2017 at 2:29 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@h
.
Thank you very much for your help,
Xavier.
From: Harms, Michael [mha...@wustl.edu]
Sent: Tuesday, November 21, 2017 7:29 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?
Hi
Dear HCP experts,
I was wondering if there is a publicly available, basic subcortical
parcellation (deliniating structures such as caudate and putamen) of the
standard volume structural file of HCP (such as S900_AverageT1w_restore.nii.gz).
Restated, is there a parcellation that deliniates
04, 2017 4:09 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How to transform all subcortical values to 0 in a
dscalar?
You can use -cifti-replace-structure with the -volume-all option and a volume
file of zeroes. If you have a lot of maps (or you want
Dear HCP experts,
I have a dscalar file with one map of cortical and subcortical data. I would
like to transform all subcortical values to 0, and leave the cortical surface
values intact. I have explored the -cifti-stats and -volume-stats options as
well as -cifti-create-dense-scalar but cannot
] on behalf of Xavier Guell Paradis
[xavie...@mit.edu]
Sent: Tuesday, September 12, 2017 2:05 PM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] Resampling freesurfer-HCP
Dear HCP experts,
I have an overlay freesurfer file (format is .w) which corresponds to a task
activity surface map (group
Dear HCP experts,
I have an overlay freesurfer file (format is .w) which corresponds to a task
activity surface map (group result). I have one .w file for each cerebral
hemisphere. I would like to visualize these maps using wb_view, and have tried
to follow the instructions you published
Thank you Matt and Tim for the very useful comments!
Xavier.
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Thursday, September 07, 2017 5:25 PM
To: NEUROSCIENCE tim; Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Table
Dear HCP experts,
I have a thresholded functional connectivity map (dscalar), and the dlabel
files from the Glasser 2016 multimodal cortical parcellation. I was wondering
whether there is a wb_command that would automatically generate a table
indicating which labels overlap with my functional
Dear HCP experts,
I have three subcortical ROIs (three dlabel files). I would like to obtain a
correlation value (r, or fisher z) of the resting-state time course between
each pair or ROIs (e.g. three r values, one for each pair: "ROI_1-ROI_2",
"ROI_1-ROI_3" and "ROI_2-ROI_3"). I would like to
Timothy Coalson [tsc...@mst.edu]
Sent: Wednesday, August 09, 2017 4:57 PM
To: Xavier Guell Paradis
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How can I convert subcortical nifti files to dlabel
files?
You need to have a dtseries (or dconn) file open before you can
information that might be useful: when I open the dlabel
file, I can see it listed in the "Labels" list of the "Features ToolBox".
Thank you very much,
Xavier.
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Wednesday, August 09, 2017 2:13
option of "Show Data/Time Series Graph" but not the option of "Show Cifti
Connectivity".
Thank you very much,
Xavier.
From: Timothy Coalson [tsc...@mst.edu]
Sent: Tuesday, August 08, 2017 4:39 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanc
Dear HCP experts,
I have several subcortical nifti files, each containing one cluster. I would
like to convert them to dlabel files, so that then I can use wb_view to see the
functional connectivity from each of these clusters (using your group .dconn
file).
How can I convert subcortical nifti
This is very useful, thank you very much for the quick and very helpful reply!
Xavier.
From: Elam, Jennifer [e...@wustl.edu]
Sent: Thursday, July 13, 2017 11:21 AM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] saving one
3, Structure: CORTEX_LEFT", but -cifti-separate seems to
require a lot of processing memory.
Thank you very much,
Xavier.
Xavier Guell Paradis, M.D.
Research Fellow
Massachusetts Institute of Technology
McGovern Institute for Brain Research
Office: 46-4033A
Phone: (617) 32
.
From: Harms, Michael [mha...@wustl.edu]
Sent: Wednesday, July 05, 2017 12:02 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Convert a .dscalar.nii to multiple nifti files?
Hi,
You can’t represent the surface information in a .dscalar.nii via
Thank you very much!
From: Timothy Coalson [tsc...@mst.edu]
Sent: Friday, May 05, 2017 4:58 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum
values?
The command to do
I do this?
Thank you very much,
Xavier.
From: Timothy Coalson [tsc...@mst.edu]
Sent: Friday, May 05, 2017 4:32 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum
values?
On Fri,
Dear HCP experts,
I am trying to modify the group average dconn file
(HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it only
includes data from the cerebellum (even though, of course, these data will
correspond to the connectivity of each cerebellum voxel to the rest of
Dear HCP experts,
Is there a way I can create a dscalar.nii file which contains four
cope.dtseries.nii files as four different maps?
I have been exploring different possibilities with wb_command but can't find
the way to do it.
Thank you very much,
Xavier.
Dear HCP experts,
If we reported in a publication the number of twins in a group of subjects,
would this be considered "publishing restricted data"? (e.g., "800 subjects
completed all tasks. This group included 100 pairs of twins")
Thank you,
Xavier.
Dear HCP experts,
I have been calculating group Cohen's d maps as follows:
1) -cifti-merge all level2 cope files of a task contrast
2) -cifti-reduce mean, -cifti-reduce stdev and -cifti-math mean/stdev
Is this the correct order, or should I have demeaned each individual subject
before using
onnectome.org/msg02548.html
John Harwell
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Xavier Guell Paradis <xavie...@mit.edu&l
m/hcp-users@humanconnectome.org/msg02548.html
John Harwell
From:
hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
on behalf
Dear HCP experts,
Is it possible to edit the colors of the palette in wb view? For example, is it
possible to define color A, color B and color C and tell wb view to show
values=1 in color A, values=2 in color B, values=3 in color C, etc.?
Thank you very much,
Xavier.
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: Expected date of 1,200 subjects release?
Hi Xavier,
Look for it in the next week or two, barring any last minute issues.
Best,
Jenn
Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School
Dear HCP tema,
Is there an expected date for the release of the 1,200 subjects data?
Thank you very much,
Xavier.
___
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
MINUSCUE.dscalar.nii
Thank you very much,
Xavier.
From: Burgess, Gregory [gburg...@wustl.edu]
Sent: Monday, February 06, 2017 5:18 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Motor task contrats: no RH-cue, LH-c
Dear HCP experts,
I was wondering if it is possible to download HCP data directly to a shared
computing cluster (e.g. the openmind.mit.edu cluster). Since data is downloaded
via Aspera Connect, there is no link that one can copy and paste to download
data directly to the cluster.
Thank you very
for another reason?
Thank you very much,
Xavier.
From: Elam, Jennifer [e...@wustl.edu]
Sent: Friday, February 03, 2017 11:12 AM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] 900 group average: are individual subjects the "S500
Re
Dear HCP experts,
In order to get the level2 data from the individual subjects which were
included in the 900 subjects group average, should we put together the subjects
of the "S500 Release Subjects" with the "S900 New Subjects"?
Thank you,
Xavier.
Great, thank you very much!!
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Thursday, February 02, 2017 11:34 AM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] How many voxels in the cerebellum?
2mm standard CIFTI files
Dear HCP experts,
Is there a way to know how many voxels does the cerebellum have in a given file?
Thank you very much,
Xavier.
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Hi Michael,
This has worked wonderfully.
Thank you all for your very helpful messages.
Xavier.
From: Harms, Michael [mha...@wustl.edu]
Sent: Tuesday, January 31, 2017 11:01 AM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Very
m: Glasser, Matthew [glass...@wustl.edu]
Sent: Monday, January 30, 2017 7:26 PM
To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer;
hcp-users@humanconnectome.org
Cc: Burgess, Gregory
Subject: Re: [HCP-Users] Very large z values for task contrasts in
S900_ALLTASKS_level3_zstat file: what does
To: Xavier Guell Paradis; Harms, Michael; Elam, Jennifer;
hcp-users@humanconnectome.org
Cc: Burgess, Gregory
Subject: Re: [HCP-Users] Very large z values for task contrasts in
S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical
significance?
Those are the level 2 copes
from cope1 files?
Thanks,
Xavier.
From: Harms, Michael [mha...@wustl.edu]
Sent: Monday, January 30, 2017 12:30 PM
To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis;
hcp-users@humanconnectome.org
Cc: Burgess, Gregory
Subject: Re: [HCP-Users] Very large z value
Dear HCP experts,
After using -cifti-find-clusters, is there a way to know the size of the
clusters that the command has found? We know that the clusters will be larger
than the specified volume-value-threshold, but is there a way to know the mm^3
or number of voxels of the clusters identified?
Dear Michael and Matthew,
Thank you very much for all your replies, your comments were extremely helpful.
Xavier.
From: Harms, Michael [mha...@wustl.edu]
Sent: Monday, January 30, 2017 12:30 PM
To: Elam, Jennifer; Glasser, Matthew; Xavier Guell Paradis;
hcp-users
Thank you again for the reply.
Is there a way to access data that was produced but not packaged up?
Thank you for your help,
Xavier.
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Friday, January 27, 2017 3:21 PM
To: Xavier Guell Paradis; hcp-users
, Matthew [glass...@wustl.edu]
Sent: Friday, January 27, 2017 3:01 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Very large z values for task contrasts in
S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical
significance?
I assume
: Thursday, January 26, 2017 6:53 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Very large z values for task contrasts in
S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical
significance?
The files called cope1 or beta are an effect size
to effect size values without having to go back to the individual subjects.
Thank you very much,
Xavier.
From: Glasser, Matthew [glass...@wustl.edu]
Sent: Thursday, January 26, 2017 5:33 PM
To: Xavier Guell Paradis; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users
Dear HCP team,
I have seen that the zstat values for tasks contrasts are very large in the
HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar.nii file, to
the point that one can observe areas of activation in task contrasts by setting
very high z value thresholds (e.g., a z
loading the UCTconn1003072BKseed.dconn.nii file.
I would be grateful if you could tell me whether there is something wrong in
the code I wrote.
Thank you very much,
Xavier.
Xavier Guell Paradis, M.D.
Visiting Scientist
Massachusetts Institute of Technology
McGovern Institute for Brain Research
very much,
Xavier.
Xavier Guell Paradis, M.D.
Visiting Scientist
Massachusetts Institute of Technology
McGovern Institute for Brain Research
Office: 46-4033A
Phone: (617) 324-4355
Email: xavie...@mit.edu
___
HCP-Users mailing list
HCP-Users@humanconn
Dear HCP team,
I am using wb_view version 1.2.3. I have noticed that it is not possible to
draw a continuous line by holding down the alt/option key and the left mouse
button while dragging the mouse. Drawing a border is possible only by drawing
multiple points.
Is this a known issue, or am I
es to p values using the
wb_command. Is this explained in the wustl.box link that you sent?
Thank you,
Xavier.
From: Dierker, Donna [do...@wustl.edu]
Sent: Wednesday, December 28, 2016 10:11 AM
To: Xavier Guell Paradis
Subject: Re: [HCP-Users] Threshold p val
data using p
values.
Thank you very much,
Xavier.
Xavier Guell Paradis, M.D.
Visiting Scientist
Massachusetts Institute of Technology
McGovern Institute for Brain Research
Office: 46-4033A
Phone: (617) 324-4355
Email: xavie...@mit.edu
___
HCP-Users mai
ctory (Code: 43)".
The same thing happens when I try to download the "900 Subjects Group Average
Data" or the "500 Subjects Group Average Data" or the "820 Subjects, MSM-All
Registered, Dense Connectome".
How could I solve this?
Thank you very much,
Xavier.
Xavier Gue
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