[HCP-Users] Downloading HCP data to a shared computing cluster

2017-02-03 Thread Xavier Guell Paradis
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

Re: [HCP-Users] 900 group average: are individual subjects the "S500 Release Subjects" + the "S900 New Subjects"

2017-02-03 Thread Xavier Guell Paradis
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

[HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.?

2017-02-03 Thread Xavier Guell Paradis
Dear HCP experts, I was wondering if there is any reason why motor contrasts of one motor task minus cue (e.g. RH-Cue) were not calculated. Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org

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?

2017-01-31 Thread Xavier Guell Paradis
-SHAPES is the third contrast listed in the Contrasts.txt file)? Thank you, Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Monday, January 30, 2017 9:11 PM To: Xavier Guell Paradis; Glasser, Matthew; Elam, Jennifer; hcp-users@humanconnectome.org Cc: Burgess

Re: [HCP-Users] How many voxels in the cerebellum?

2017-02-02 Thread Xavier Guell Paradis
This one: HCP_S900_787_tfMRI_ALLTASKS_level3_zstat1_hp200_s2_MSMAll.dscalar Thanks, Xavier. From: Glasser, Matthew [glass...@wustl.edu] Sent: Thursday, February 02, 2017 11:28 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How

Re: [HCP-Users] How many voxels in the cerebellum?

2017-02-02 Thread Xavier Guell Paradis
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

[HCP-Users] How many voxels in the cerebellum?

2017-02-02 Thread Xavier Guell Paradis
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. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] Motor task contrats: no RH-cue, LH-cue, etc.?

2017-02-07 Thread Xavier Guell Paradis
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

[HCP-Users] 900 group average: are individual subjects the "S500 Release Subjects" + the "S900 New Subjects"

2017-02-03 Thread Xavier Guell Paradis
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.

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?

2017-02-01 Thread Xavier Guell Paradis
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

Re: [HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters

2017-02-02 Thread Xavier Guell Paradis
[tsc...@mst.edu] Sent: Monday, January 30, 2017 6:18 PM To: Xavier Guell Paradis Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters The -cifti-find-clusters command assigns a separate integer within each cluster. You

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?

2017-01-27 Thread Xavier Guell Paradis
: 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

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?

2017-01-27 Thread Xavier Guell Paradis
, 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

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?

2017-01-27 Thread Xavier Guell Paradis
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

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?

2017-01-30 Thread Xavier Guell Paradis
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

[HCP-Users] How to know cluster size (number of voxels) after -cifti-find-clusters

2017-01-30 Thread Xavier Guell Paradis
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?

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?

2017-01-30 Thread Xavier Guell Paradis
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

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?

2017-01-30 Thread Xavier Guell Paradis
m: Glasser, Matthew [glass...@wustl.edu] Sent: Monday, January 30, 2017 6:51 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

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?

2017-01-30 Thread Xavier Guell Paradis
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

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?

2017-01-30 Thread Xavier Guell Paradis
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

[HCP-Users] Very large z values for task contrasts in S900_ALLTASKS_level3_zstat file: what does this mean in terms of statistical significance?

2017-01-26 Thread Xavier Guell Paradis
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

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?

2017-01-26 Thread Xavier Guell Paradis
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

[HCP-Users] Memory required for -cifti-correlation of 700 subjects?

2017-02-24 Thread Xavier Guell Paradis
Dear HCP experts, After demeaning and merging resting-state files of 700 subjects (resulting in a 1200GB file), I would like to do -cifti-correlation to get a .dconn file. I am using a computational cluster, and even by using a node with 300GB of memory the command does not seem to work (I get

Re: [HCP-Users] Memory required for -cifti-correlation of 700 subjects?

2017-02-24 Thread Xavier Guell Paradis
: Harms, Michael [mha...@wustl.edu] Sent: Friday, February 24, 2017 9:44 AM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Memory required for -cifti-correlation of 700 subjects? Hi, Let’s step back. Why can’t you use the group dense connectome that we’ve already

Re: [HCP-Users] Expected date of 1,200 subjects release?

2017-02-11 Thread Xavier Guell Paradis
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

Re: [HCP-Users] Edit colors of palette in wb view?

2017-02-13 Thread Xavier Guell Paradis
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

[HCP-Users] Edit colors of palette in wb view?

2017-02-13 Thread Xavier Guell Paradis
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.

Re: [HCP-Users] Edit colors of palette in wb view?

2017-02-13 Thread Xavier Guell Paradis
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

[HCP-Users] d maps from cope files: first merge and then demean, or first demean and then merge?

2017-02-15 Thread Xavier Guell Paradis
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

[HCP-Users] Expected date of 1,200 subjects release?

2017-02-11 Thread Xavier Guell Paradis
Dear HCP tema, Is there an expected date for the release of the 1,200 subjects data? Thank you very much, Xavier. ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users

[HCP-Users] Seed-based RS functional connectivity for individual subject

2017-01-03 Thread Xavier Guell Paradis
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

[HCP-Users] Problem downloading data: "Destination path directory does not exist (Code: 6)"

2017-01-03 Thread Xavier Guell Paradis
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

Re: [HCP-Users] Problem downloading data: "Destination path directory does not exist (Code: 6)"

2017-01-03 Thread Xavier Guell Paradis
ychiatry Phone: 314-362-7864 Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu> On Jan 3, 2017, at 9:31 AM, Xavier Guell Paradis <xavie...@mit.edu<mailto:xavie...@mit.edu>> wrote: Dear HCP team, I am trying to download individual subject data (100307_3T_tfMRI_MOTOR_anal

[HCP-Users] Continuous border drawing holding "alt/option" key does not work

2016-12-29 Thread Xavier Guell Paradis
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

[HCP-Users] Workbench tutorial data download: "No such file or directory"

2016-12-23 Thread Xavier Guell Paradis
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

Re: [HCP-Users] Threshold p value in workbench view

2016-12-28 Thread Xavier Guell Paradis
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

[HCP-Users] Threshold p value in workbench view

2016-12-27 Thread Xavier Guell Paradis
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

[HCP-Users] Number of twins in group of subjects: would this be considered "publishing restricted data"?

2017-03-08 Thread Xavier Guell Paradis
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.

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-10 Thread Xavier Guell Paradis
...@mst.edu] Sent: Wednesday, August 09, 2017 6:55 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? If your "mycluster.nii" is in a different volume space than 222 MNI

Re: [HCP-Users] saving one of the .dconn maps as a separate cifti?

2017-07-13 Thread Xavier Guell Paradis
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

[HCP-Users] saving one of the .dconn maps as a separate cifti?

2017-07-13 Thread Xavier Guell Paradis
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

[HCP-Users] Convert a .dscalar.nii to multiple nifti files?

2017-07-05 Thread Xavier Guell Paradis
Dear HCP experts, Is it possible to convert a .dscalar.nii which contains 4 different maps to 4 different nifti files (one for each map)? I have tried -cifti-convert -to-nifti but the output was a very strange nifti file. Thank you very much, Xavier.

Re: [HCP-Users] Convert a .dscalar.nii to multiple nifti files?

2017-07-05 Thread Xavier Guell Paradis
. 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

Re: [HCP-Users] Convert a .dscalar.nii to multiple nifti files?

2017-07-05 Thread Xavier Guell Paradis
It works, thank you very much! Xavier. From: Harms, Michael [mha...@wustl.edu] Sent: Wednesday, July 05, 2017 12:09 PM To: Xavier Guell Paradis; hcp-users@humanconnectome.org Subject: Re: [HCP-Users] Convert a .dscalar.nii to multiple nifti files? In that case, I

[HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-08 Thread Xavier Guell Paradis
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

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
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

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
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

Re: [HCP-Users] How can I convert subcortical nifti files to dlabel files?

2017-08-09 Thread Xavier Guell Paradis
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

Re: [HCP-Users] merge multiple dtseries.nii into one dscalar.nii?

2017-05-05 Thread Xavier Guell Paradis
It worked, thank you very much. Xavier. From: Timothy Coalson [tsc...@mst.edu] Sent: Thursday, May 04, 2017 5:42 PM To: Xavier Guell Paradis Cc: hcp-users@humanconnectome.org Subject: Re: [HCP-Users] merge multiple dtseries.nii into one dscalar.nii? Use -cifti

[HCP-Users] modify dconn file so that it only includes cerebellum values?

2017-05-05 Thread Xavier Guell Paradis
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

Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?

2017-05-05 Thread Xavier Guell Paradis
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

Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?

2017-05-05 Thread Xavier Guell Paradis
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,

[HCP-Users] merge multiple dtseries.nii into one dscalar.nii?

2017-05-04 Thread Xavier Guell Paradis
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.

[HCP-Users] How to transform all subcortical values to 0 in a dscalar?

2017-10-04 Thread Xavier Guell Paradis
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

Re: [HCP-Users] How to transform all subcortical values to 0 in a dscalar?

2017-10-09 Thread Xavier Guell Paradis
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

[HCP-Users] Table indicating location of clusters according to a dlabel file?

2017-09-07 Thread Xavier Guell Paradis
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

Re: [HCP-Users] Table indicating location of clusters according to a dlabel file?

2017-09-07 Thread Xavier Guell Paradis
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

Re: [HCP-Users] Resampling freesurfer-HCP

2017-09-12 Thread Xavier Guell Paradis
] 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

[HCP-Users] Resampling freesurfer-HCP

2017-09-12 Thread Xavier Guell Paradis
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

[HCP-Users] Calculate resting-state correlation (r or fisher-z) between two ROIs

2017-08-23 Thread Xavier Guell Paradis
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

[HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

2017-11-21 Thread Xavier Guell Paradis
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

Re: [HCP-Users] Subcortical atlas of S900_AverageT1w_restore.nii.gz?

2017-11-22 Thread Xavier Guell Paradis
. 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