Hi,
What is the most up-to-date method for thresholding clusters of adjacent
grayordinates using workbench, or which fsl tools are best to use with cifti
data. I saw that PALM by FSL was recommended in a previous thread. Is that
still recommended? Is that to be used in place of film or FEAT or
n approaches that of censoring when there is significant, uncorrectable
noise, but not otherwise. Movement regression is common to both approaches.
Peace,
Matt.
From: "Michael F.W. Dreyfuss"
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Wednesday, August 10
Thanks, are there any that are combined with some sort of subcortical
parcellation?
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Thursday, August 11, 2016 4:32:21 PM
To: Michael F.W. Dreyfuss; Harms, Michael
Cc: Burgess, Gregory; hcp
0.222537 0 0 0 0 0 0
Thank you very much,
Michael
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Tuesday, August 9, 2016 5:19:29 PM
To: Harms, Michael; Burgess, Gregory; Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Mo
From: Burgess, Gregory <gburg...@wustl.edu>
Sent: Tuesday, August 2, 2016 2:30:10 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Movement Confounds and Censoring
> On Aug 2, 2016, at 10:17 AM, Michael F.W. Dreyfuss <mid2...@med
afterward.
Thank you,
Michael
From: Burgess, Gregory <gburg...@wustl.edu>
Sent: Thursday, August 4, 2016 10:05:47 AM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] PALM for Cifti data
PALM isn’t intended to replace the l
74237 0.091615 -0.222537 0 00 0 0 0
Thank you very much,
Michael
From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Tuesday, August 9, 2016 5:19:29 PM
To: Harms, Michael; Burgess, Gregory; Michael F.W. Dreyfuss
Cc:
Thank you,
Michael
From: Burgess, Gregory <gburg...@wustl.edu>
Sent: Thursday, August 4, 2016 10:35:33 AM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Movement Confounds and Censoring
> On Aug 4, 2016, at 8:52 AM, Mi
ee them. I am also not familiar with palm_vestwrite, and I haven't been
able to any documentation online.
Thank you,
Michael
From: Burgess, Gregory <gburg...@wustl.edu>
Sent: Tuesday, September 13, 2016 10:24:14 AM
To: Michael F.W. Dreyfuss
Cc: hcp-users@hum
Hello, I am trying to run palm on cifti data with TFCE to find mean activation
across a group. When I use the -T flag, the program crashed with the error:
Command:
palm -i ${ContrastName}.dtseries.nii -transposedata -d
$LevelThreeFEATDir/design.mat -o $ContrastName -t
palm for a simple group average on cifti data like this?
Thanks again,
Michael
From: Dierker, Donna <do...@wustl.edu>
Sent: Thursday, September 8, 2016 10:00:58 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] PALM
can run TFCE with palm here? Or is
anything else recommended for identifying clusters of activation?
Thank you,
Michael
From: Michael F.W. Dreyfuss
Sent: Tuesday, September 13, 2016 12:25:03 PM
To: Burgess, Gregory
Cc: hcp-users@humanconnectome.org; Anderson M
urg...@wustl.edu>
Sent: Monday, September 12, 2016 2:50:41 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] PALM with cifti files
Hi Michael,
I just want to verify that you are trying to use PALM for “higher-level” group
analyses. PALM is not currentl
.ox.ac.uk>
Sent: Thursday, September 15, 2016 5:39:12 AM
To: Michael F.W. Dreyfuss
Cc: Dierker, Donna; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Palm with TFCE on Cifti data
Hi Michael,
Please see an example in this page:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/PALM/Ex
could isolate
that parcel to do an anlysis?
Thank you,
Michael
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Tuesday, September 20, 2016 11:06:10 AM
To: Michael F.W. Dreyfuss; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users
for neural
correlates of differences in response inhibition.
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Monday, September 26, 2016 6:22:50 PM
To: Michael F.W. Dreyfuss; hcp-users@humanconnectome.org; NEUROSCIENCE tim
Subject: Re: [HCP-Users] ROIs and Beta
, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Tuesday, September 20, 2016 11:06:10 AM
To: Michael F.W. Dreyfuss; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
As Tim m
Hello,
Is there anyway to include subject-level variance estimates when running palm
on a group level? Different subjects in my tfMRI study have different numbers
of correct trials modeled in their GLMs, so confidence around each subject's
estimate is variable. Seems it would be optimal to
Is that correct?
Thanks again,
Michael
From: Timothy Coalson <tsc...@mst.edu>
Sent: Thursday, September 15, 2016 4:46:12 PM
To: Michael F.W. Dreyfuss
Cc: Anderson M. Winkler; hcp-users@humanconnectome.org; Dierker, Donna
Subject: Re: [HCP-Users] Palm wit
: Timothy Coalson <tsc...@mst.edu>
Sent: Monday, September 19, 2016 4:48:28 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
The wb_command -cifti-weighted-stats command with -mean is probably what you
want (outputs a
additional information this command is
looking for
As for the thresholding, I arbitrarily chose 1 just to get this running.
Thanks,
Michael
From: Glasser, Matthew <glass...@wustl.edu>
Sent: Tuesday, September 20, 2016 12:57:49 PM
To: Michael F.W. Dr
es the input data look like?
Peace,
Matt.
From: "Michael F.W. Dreyfuss"
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Tuesday, September 20, 2016 at 1:22 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "Michael F
From: andersonwink...@gmail.com <andersonwink...@gmail.com> on behalf of
Anderson M. Winkler <wink...@fmrib.ox.ac.uk>
Sent: Friday, September 16, 2016 11:35:44 AM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Palm with TFCE on Cifti data
Hi Mic
Hello, is there a template cifti brain that is recommended for viewing images
in wb_view, eventually for the purpose of making figures?
Thank you,
Michael
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
I agree, that’s why I was checking in to see if there was a sub parcel you had
identified as being involved in response inhibition from your tasks, such as
flanker. There is a lot of background of IFG being involved in response
inhibition, particularly on go/nogo tasks,, so I was wondering if
Sep 27, 2016 at 4:15 PM, Michael F.W. Dreyfuss
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:
Thank you,
The problem was that the computer I was using before had an older version of
workbench. It works on my current computer.
As far as using
-cifti-label-to-
, 2016, at 6:20 PM, Michael F.W. Dreyfuss
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:
I’m sorry, but this is still not clear to me. It seems this function is meant
to perform an operation to produce a scalar file, but what is produced when I
use MAX for exa
Greg Burgess, Ph.D.
Staff Scientist, Human Connectome Project
Washington University School of Medicine
Department of Psychiatry
Phone: 314-362-7864
Email: gburg...@wustl.edu<mailto:gburg...@wustl.edu>
On Sep 27, 2016, at 9:26 AM, Michael F.W. Dreyfuss
<mid2...@med.cornell.edu<mailto:mid2...
are directed to find out how I can easily
separate and combine labels from existing files.
Thank you,
Michael
From: Michael F.W. Dreyfuss
Sent: Tuesday, September 27, 2016 2:19:06 PM
To: hcp-users@humanconnectome.org
Subject: Label Import with -discard-others
Hello, I
Hello, I have been trying to make a file containing the parcellations for BA44
and BA45 using the Broadmann using the following command:
wb_command -cifti-label-import Human.Brodmann09.32k_fs_LR.dlabel.nii
BrodmannLabels.txt Brodmann_IFG.dlabel.nii -discard-others
Where BrodmannLabels.txt
:10:15 PM
To: Michael F.W. Dreyfuss
Cc: Burgess, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
The surface structures in -cifti-separate are much coarser, they represent the
cifti file organization, not the parcellation areas. You want CORTE
er, Matthew <glass...@wustl.edu>
Sent: Tuesday, October 25, 2016 7:07:57 PM
To: Michael F.W. Dreyfuss; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Connectivity Analysis with Cifti
If you weren't using CIFTI how would you do such an analysis?
Peace,
Matt.
From:
<hcp-users-
in the subject's
fsf file before running feat_model?
Thanks,
Michael
From: Burgess, Gregory <gburg...@wustl.edu>
Sent: Wednesday, October 26, 2016 12:41:47 PM
To: Michael F.W. Dreyfuss
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP
, 2016 1:39:33 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Connectivity Analysis with Cifti
If you know how to do it in ANFI, why not use AFNI?
—Greg
> On Oct 26, 2016, at 12:04 PM, Michael F.W. Dreyfuss <mid2...@med.cornell.edu>
> wr
From: Timothy Coalson <tsc...@mst.edu>
Sent: Tuesday, September 27, 2016 6:37:42 PM
To: Michael F.W. Dreyfuss
Cc: Burgess, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
Actually, -cifti-math will output a dlabe
Hi,
What is/are the recommended method(s) for performing connectivity analyses with
cifti data? If I want to look at Amygdala-NAcc or Amyg-cortical connectivity,
for example, during one condition of a task fMRI relative to baseline or
another condition, how can I do this?
Thank you,
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