Tractography visualization is somewhat rough around the edges. What was
the full probtrackx command you used? Do you have bingham parameter
volumes for the fiber orientations (mean, stdev, theta, phi, psi, ka, kb),
or only the fiber orientation sample volumes?
Tim
On Fri, Jun 7, 2019 at 7:48
Good morning, I would like to transform my data obtained with fsl's probtackx,
to visualized them with wb_view. But the instructions to run the command is not
clear for me. I've tried several choices but there is always something missing
or nor recognized (I'm very naive with all this.. just
To: *"Glasser, Matthew"
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] wb_command -cifti-gradient
>
>
>
> A 32k fs_LR surface file with suffix of dscalar.nii, and a
> thickness.32k_fs_LR.dscalar.nii can be an example.
>
>
>
>
: Tuesday, June 4, 2019 at 9:32 PM
To: "hcp-users@humanconnectome.org"
Subject: [HCP-Users] wb_command -cifti-gradient
Dear professors,
When I used the wb_command -cifti-gradient for fs_LR 32k cifti file, I was
asked to input the left and right surface files, where can I find the left
You can use the midthickness surfaces .surf.gii in the same folder.
Matt.
From: 秦键
Date: Tuesday, June 4, 2019 at 10:02 PM
To: "Glasser, Matthew"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] wb_command -cifti-gradient
A 32k fs_LR surface file with s
What file did you try to run this on?
Matt.
From: on behalf of 秦键
Date: Tuesday, June 4, 2019 at 9:32 PM
To: "hcp-users@humanconnectome.org"
Subject: [HCP-Users] wb_command -cifti-gradient
Dear professors,
When I used the wb_command -cifti-gradient for fs_LR 32k cifti file, I
Dear professors,
When I used the wb_command -cifti-gradient for fs_LR 32k cifti file, I was
asked to input the left and right surface files, where can I find the left and
right surface files and what are the format of them? Can I have an example of
the use of the wb_command -cifti-gradient?
;.
>> Tel: 314-747-6173
>>
>> St. Louis, MO 63110 Email: mha...@wustl.edu
>>
>>
>>
>> *From: * on behalf of Reza
>> Rajimehr
>> *Date: *Saturday, April 20, 2019 at 7:18 PM
>> *To: *hcp-users
>> *Subject: *
x 8134
>
> 660 South Euclid Ave
> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173
>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
>
>
> *From: * on behalf of Reza
> Rajimehr
> *Date: *Saturday, A
of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: on behalf of Reza Rajimehr
Date: Saturday, April 20, 2019 at 7:18 PM
To: hcp-users
Subject: [HCP-Users] wb_command -metric-tfce
Hi
Hi,
We have curvature data from two groups of subjects in a common anatomical
space (MSMAll). We performed a univariate comparison between the two groups
using t-test. We now have a map, which shows vertex-wise curvature
difference between the two groups (the curvature difference is shown only
Thanks for letting us know.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, April 8, 2019 at 6:34 AM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: Matt Glasser mailto:glass...@wustl.edu>>, Ido Tavor
mailto:idota...@gmail.com>>
Subject: Re: [HCP-
I’d like Tim’s input on where to upload if you don’t have your own convenient
spot.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 10:58 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in
We need the input files to the command that is taking too long. Also, does the
problem happen reproducibly?
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Sunday, March 31, 2019 at 10:53 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_co
, 2019 at 10:32 AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing
taking suspiciously long while
Its 500 time points.
I'll have a look at the volume input tommorow when I get back to the office. I
ran them serial
Date: Sunday, March 31, 2019 at 8:27 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] wb_command -cifti-resample in sub-cortical processing
taking suspiciously long while
some furthe
some further information that might be useful - the output file
rfMRI_REST_AP_temp_atlas.dtseries.nii, has already been created. its in the
target folder. but the command won't stop "running"
On Sun, 31 Mar 2019 at 16:13, Shachar Gal wrote:
> Dear experts,
>
> while running the fMRISurface
Dear experts,
while running the fMRISurface pipeline (using the latest pipeline release)
I encountered an issue where the subcortical-processing script takes a
really long while (now running for more than 6 hours).
this is the command on which it is stuck
${CARET7DIR}/wb_command
nesday, September 05, 2018 5:11 PM
To: NEUROSCIENCE tim ; Eric Earl
Cc: Darrick Sturgeon ; hcp-users@humanconnectome.org; Anders
Perrone
Subject: Re: [HCP-Users] wb_command failed to convert text to number
Getting extremely large numbers like that suggests something may have gone
wrong wit
arl mailto:e...@ohsu.edu>>
Cc: Darrick Sturgeon mailto:sturg...@ohsu.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Anders
Perrone mailto:perro...@ohsu.edu>>
Subject: Re: [HCP-Users] wb_comma
I have modified -cifti-convert -from-text to now accept text numbers that
require double (float64) to represent them, warn about them, and replace
them with the maximum of float32 (or its negation). This should cover most
cases (to accept numbers that are too big even for double, I'd have to look
Those numbers are too large to be represented in single precision float
(float32), which stops at about 10^38 (wb_command uses float32 for
virtually all data values, and the default cifti output datatype is
float32). The command could be made to truncate large values at the
maximum of float32
Hi,
I am trying a command like this on ten different inputs and getting a similar
ERROR:
.../workbench-1.3.2/bin_rh_linux64/../exe_rh_linux64/wb_command -cifti-convert
-from-text .../DCANBOLDProc_v4.0.0/temp_cifti.txt
.../task-SST03_Atlas.dtseries.nii
@humanconnectome.org>"
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] wb_command error
Does anyone know why this error would be thrown?
/usr/local/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command -metric-merge /
opt/data/build/TestUmass/20180718_021040/P01_M
Does anyone know why this error would be thrown?
/usr/local/workbench/bin_rh_linux64/../exe_rh_linux64/wb_command
-metric-merge /
opt/data/build/TestUmass/20180718_021040/P01_MR1/MNINonLinear/Native/P01_MR1.L.S
trainR_FS.native.shape.gii -metric
/opt/data/build/TestUmass/20180718_021040/P01
VPIA Lab
>
> Department of Electrical and Computer Engineering
>
> The University of Memphis
>
> Email: ralfa...@memphis.edu
>
>
>
>
>
> *From: *"Harms, Michael"
> *Date: *Tuesday, June 12, 2018 at 12:25 PM
> *To: *"Rakib Al-Fahad (ralfa
ot;Rakib Al-Fahad (ralfahad)"
<mailto:ralfa...@memphis.edu>,
"hcp-users@humanconnectome.org"<mailto:hcp-users@humanconnectome.org>
<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] wb_command help
Hi,
See the "HCP1200 Parcellation+Timeseries
...@memphis.edu
From: "Harms, Michael"
Date: Tuesday, June 12, 2018 at 12:25 PM
To: "Rakib Al-Fahad (ralfahad)" ,
"hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] wb_command help
Hi,
See the “HCP1200 Parcellation+Timeseries+Netmats (PTN)” packages hosted at
...@wustl.edu
From: on behalf of "Rakib Al-Fahad
(ralfahad)"
Date: Tuesday, June 12, 2018 at 11:58 AM
To: "hcp-users@humanconnectome.org"
Subject: [HCP-Users] wb_command help
Hello,
I am a student of machine learning. I want to study structural and functional
brain connec
Hello,
I am a student of machine learning. I want to study structural and functional
brain connectivity from HCP data. Is there any way to get ROI based time series
and structural connectivity using wb_command ? I am not sure about which ROI
atlas should I use. I need suggestion for specific
eas) is what you want.
>>
>> Peace,
>>
>> Matt.
>>
>> From: on behalf of Xinyang Liu <
>> xinyang_ie...@163.com>
>> Date: Thursday, June 7, 2018 at 8:33 AM
>> To: HCP 讨论组
>> Subject: [HCP-Users] wb_command -metric-rois-from-extr
ce,
Matt.
From: on behalf of Xinyang Liu
Date: Thursday, June 7, 2018 at 8:33 AM
To: HCP 讨论组
Subject: [HCP-Users] wb_command -metric-rois-from-extrema
Dear HCP experts,
Hi. I have some confusions when using the workbench command
-metric-rois-from-extrema. When using it to draw ROIs
correction for
shrinkage by vertex areas) is what you want.
Peace,
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Xinyang Liu mailto:xinyang_ie...@163.com>>
Date: Thursday, June 7, 2018 at 8:33 AM
To: HCP 讨论组
mailto:hcp-users@humanconnectome.org>>
S
lf of Mohana Ramaratnam
<mohanakann...@gmail.com<mailto:mohanakann...@gmail.com>>
Date: Thursday, February 8, 2018 at 8:16 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanco
I am using wb_command version 1.2.3 and HCP-Pipelines version 3.23.0.
Has anybody encountered the error:
Unexpected parameter -local-affine-method?
This flag is passed by the call to
FreeSurfer2CaretConvertAndRegisterNonlinear.sh
in the PostFreesurfer step
(Ref:
Hi! I had a question about -cifti-roi-average. I can only make it work with a
metric ROI file, like this:
-cifti-roi-average ${subj}.MyelinMap_BC.native.dscalar.nii ROI_mm_avg.txt
-left-roi ROI_23.L.native.func.gii
but not a cifti ROI file, regardless if it is a 1 ROI file or has multiple
This feature has already been requested for this command.
Peace,
Matt.
On 5/2/14, 3:21 PM, Gaurav Patel gauravpa...@gmail.com wrote:
Hi! I had a question about -cifti-roi-average. I can only make it work
with a metric ROI file, like this:
-cifti-roi-average
Ok thanks!
_
gaurav patel
gauravpa...@gmail.com
www.neurofreak.com
On May 2, 2014, at 4:24 PM, Glasser, Matthew glass...@wusm.wustl.edu
wrote:
This feature has already been requested for this command.
Peace,
Matt.
On 5/2/14, 3:21 PM, Gaurav Patel
38 matches
Mail list logo
