chael
From: Timothy Coalson
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 dlabel file with an improper
: 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
> wrote:
>
> Thank you. Is there a recommended method for
the subject's
fsf file before running feat_model?
Thanks,
Michael
From: Burgess, Gregory
Sent: Wednesday, October 26, 2016 12:41:47 PM
To: Michael F.W. Dreyfuss
Cc: Glasser, Matthew; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Connectivity Ana
From: Glasser, Matthew
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:
mailto:hcp-users-boun.
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,
Michael
, 2016, at 6:20 PM, Michael F.W. Dreyfuss
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 example is just a scalar file where the
that they could be suitable for multiple tasks.
Tim
On Tue, Sep 27, 2016 at 4:49 PM, Michael F.W. Dreyfuss
mailto:mid2...@med.cornell.edu>> wrote:
How would this work with -cifti-reduce? If I have a cifti with BA44 and BA45
for example and I want those two regions to be merged into one, h
How would this work with -cifti-reduce? If I have a cifti with BA44 and BA45
for example and I want those two regions to be merged into one, how would
-cifti-reduce do that? Wouldn’t it be more suited to calculating something
(i.e. mean, mode, etc.) within each of those parcels?
Thank you
On S
:15 PM, Michael F.W. Dreyfuss
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-roi
How would that work wit
dscalar files), and
then use -cifti-merge and -cifti-reduce to combine them back into one larger
ROI.
Tim
On Tue, Sep 27, 2016 at 10:36 AM, Michael F.W. Dreyfuss
mailto:mid2...@med.cornell.edu>> wrote:
I can get separate the volumetric part of cifti files with a command like:
wb_command
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 con
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
mailto:mid2...@med.cornell.edu
> 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
>
>> On Sep 27, 2016, at 9:26 AM, Michael F.W. Dreyfuss
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 yo
k for neural
correlates of differences in response inhibition.
From: Glasser, Matthew
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 Betas from Cifti Data
Can’
how I could isolate
that parcel to do an anlysis?
Thank you,
Michael
From: Glasser, Matthew
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] ROIs and Betas from
From: andersonwink...@gmail.com on behalf of
Anderson M. Winkler
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 Michael,
No, I have no idea of what is going on. What was the
k like?
Peace,
Matt.
From: "Michael F.W. Dreyfuss"
mailto:mid2...@med.cornell.edu>>
Date: Tuesday, September 20, 2016 at 1:22 PM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Michael F.W. Dreyfuss"
mailto:mid2...@med.cornell.edu>>, Timothy C
OK, I tried this:
wb_command -cifti-find-clusters
FoodGo_HCP_mesh_TFCE_palm/FoodGo_results_merged_tfce_tstat_fwep.dscalar.nii 0 0
0 0 COLUMN FoodGo_results_merged_tfce_tstat_fwep_ROIs.dscalar.nii -left-surface
HCP_S900_GroupAvg_v1/S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii
-right-surface
H
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
Sent: Tuesday, September 20, 2016 12:57:49 PM
To: Michael F.W. Dreyfuss; NEUROSCIENCE tim
Cc: hcp-users
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 acc
asser, Matthew 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 mentions, it sounds like
thresholding method to
identify contiguous swaths of volumetric and surface activation.
Thank you very much again,
Michael
On Sep 19, 2016, at 6:41 PM, Timothy Coalson
mailto:tsc...@mst.edu>> wrote:
On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss
mailto:mid2...@med.cornell.edu&g
: Timothy Coalson
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 number to the command line
Hello, I have run palm with TFCE on my group level data successfully for a task
based fMRI study (yay!), and I would like to be able to identify ROIs from my
cifti data (both surface and volume). I then want to extract subject level beta
weights for a given condition from those ROIs to relate th
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
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HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailm
2016 11:33:51 AM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Palm with TFCE on Cifti data
Hi Michael,
This isn't correct I'm afraid. Even if PALM run to completion, with these
inputs it is shuffling the timeseries data within-subject, bu
f.gii
Is that correct?
Thanks again,
Michael
From: Timothy Coalson
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 with TFCE on Cifti data
_
From: Timothy Coalson
Sent: Thursday, September 15, 2016 4:05:19 PM
To: Michael F.W. Dreyfuss
Cc: Anderson M. Winkler; hcp-users@humanconnectome.org; Dierker, Donna
Subject: Re: [HCP-Users] Palm with TFCE on Cifti data
That .shape.gii file is not a surface file, you need .s
: 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/Examples<https://urldefense.proofpoint.com/v2/url?u=ht
for use on volumetric data?
Thanks a lot,
Michael
From: Dierker, Donna
Sent: Wednesday, September 14, 2016 11:09:04 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Palm with TFCE on Cifti data
Michael, if $ContrastName
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
/tmp/CtxFGNG/CtxFGNG_
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
to see 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
Sent: Tuesday, September 13, 2016 10:24:14 AM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org;
, 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 currently able to conduct “lower-level
Hello,
I am getting errors when I try to use palm with cifti files. Is there an option
or options that I need to use with palm for it to read dtseries.nii files
appropriately? Are there any examples of simple implementations of palm on
cifti type fMRI data (task based especially)?
Thanks you
palm for a simple group average on cifti data like this?
Thanks again,
Michael
From: Dierker, Donna
Sent: Thursday, September 8, 2016 10:00:58 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] PALM Errors
Did you try using
Hello,
I am trying to run PALM on subject level betas in cifti to get group means and
identify clusters of significant activation. I have tried two things so far,
and both have resulted in errors.
The first attempt was the following:
palm $COPE_INPUTS -d $LevelThreeFEATDir/design.mat -t
$L
Thanks, are there any that are combined with some sort of subcortical
parcellation?
From: Glasser, Matthew
Sent: Thursday, August 11, 2016 4:32:21 PM
To: Michael F.W. Dreyfuss; Harms, Michael
Cc: Burgess, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP
___
From: Harms, Michael
Sent: Thursday, August 11, 2016 9:45:01 AM
To: Michael F.W. Dreyfuss; Glasser, Matthew
Cc: Harms, Michael; Burgess, Gregory; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Movement Confounds and Censoring
BTW: You mentioned film_gls and flameo. Is this is task-base
g when there is significant, uncorrectable
noise, but not otherwise. Movement regression is common to both approaches.
Peace,
Matt.
From: "Michael F.W. Dreyfuss"
mailto:mid2...@med.cornell.edu>>
Date: Wednesday, August 10, 2016 at 6:58 PM
To: Matt Glasser mailto:glass...@
tivity, it would be a good idea to
use a parcellation to increase your sensitivity and power. As for movement
regressors and motion censoring, I don’t recommend that approach, but what you
have there looks okay aside from the 00, 10, and 01.
Peace,
Matt.
From: "Michael F.W. Dreyfuss&qu
15 -0.222537 0 0 0 0 0 0
Thank you very much,
Michael
From: Glasser, Matthew
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] Movement Confounds an
Thank you,
Michael
From: Burgess, Gregory
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, Michael F.W. Dreyfuss
>
afterward.
Thank you,
Michael
From: Burgess, Gregory
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 level 1 (timeseries) analysis
Hi, I am trying to adapt palm into my analysis scripts upon your recommendation
and I have a few questions:
1) Does this function essentially like FEAT/film_gls? That is, should I be
running PALM for level 1 (run), level 2 (subject) and level 3 (group) analyses,
or just at one of these levels?
From: Burgess, Gregory
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
> wrote:
>
> Hi, I have some bas
2016 8:07:15 AM
To: Glasser, Matthew; Harms, Michael; Michael F.W. Dreyfuss;
hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] Cluster Thresholding
And you can use PALM for a parcellated analysis as well. That will in fact be
an example during one of the "practical" sessions f
Hi, I have some basic questions about the movement parameters that are put out
by the HCP preprocessing scripts.
1) What is the difference between Movement_Regressors_dt.txt and
Movement_Regressors.txt? I would like to use one as a confound.
2) What does each column in these represent? I'm as
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
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