m:* Timothy Coalson [mailto:tsc...@mst.edu]
> *Sent:* Tuesday, May 09, 2017 4:49 PM
> *To:* Astafiev, Serguei
> *Cc:* hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] ROIs and Betas from Cifti Data
>
>
>
> There is a bug in that command in the current release (1.2.3). Try t
09, 2017 4:49 PM
To: Astafiev, Serguei
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
There is a bug in that command in the current release (1.2.3). Try the
"dev_latest" version matching your operating system here:
http://brainvis.wustl.edu
There is a bug in that command in the current release (1.2.3). Try the
"dev_latest" version matching your operating system here:
http://brainvis.wustl.edu/workbench/
You might also consider using -cifti-parcellate to get the average values
within all subcortical structures at the same time. If
, October 26, 2016 at 2:40 PM
> To: Timothy Coalson <tsc...@mst.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
>
> Hello,
>
> I am trying to extract the m
org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
Hello,
I am trying to extract the mean value form a cifti file using -
cifti-weighted-stats within an ROI I produced from the Brodmann area map
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
Actually, -cifti-math will output a dlabel file with an improper label
table, which will look empty (it is not a proper dlabel file, but it does
have the ROI you want in it). You should then use -cifti-change-mapping
with -scalar on that output to make it into a viewable ROI file (you could
also
If you already have a dlabel file that excludes the things you aren't
interested in, you don't need to bother with the -cifti-reduce I
described. Since "unlabeled" is generally represented as 0, you can use
-cifti-math with 'x > 0' to generate a combined binary ROI from that
restricted dlabel
To me, a mask is a binary ROI (1 where the stuff you want is, 0
elsewhere). This is quite different from a label file (lots of different
integers). I did not mean for you to run -cifti-reduce on a dlabel file.
I was suggesting that you use -cifti-label-to-roi to make a binary ROI from
each
The command I was using was :
wb_command -cifti-reduce Brodmann_Bilateral_IFG.dlabel.nii MAX
Brodmann_Bilateral_IFG_Merged.dscalar.nii
Where Brodmann_Bilateral_IFG.dlabel.nii contains two labels.
Again, this command does not seem to the production of a label file directly.
Thanks
On Sep 27,
; look at BA44 in the right hemisphere only, for example, how can I separate
>> it from BA44 in the left hemisphere to look at them separately?
>>
>> Thank you,
>> Michael
>>
>>
>> --------------
>> *From:* Timothy Coalson <tsc...@mst.edu>
&g
ely?
Thank you,
Michael
From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Sent: Tuesday, September 27, 2016 4:10:15 PM
To: Michael F.W. Dreyfuss
Cc: Burgess, Gregory;
hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subject: Re:
o look at them separately?
>
> Thank you,
> Michael
>
>
> --
> *From:* Timothy Coalson <tsc...@mst.edu>
> *Sent:* Tuesday, September 27, 2016 4:10:15 PM
> *To:* Michael F.W. Dreyfuss
> *Cc:* Burgess, Gregory; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Us
: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
The surface structures in -cifti-separate are much coarser, they represent
the cifti file organization, not the parcellation areas. You want
CORTEX_LEFT and CORTEX_RIGHT for that command to work. However, the
outputs are gifti files, not cifti files - it is a format conversion
command, and
I can get separate the volumetric part of cifti files with a command like:
wb_command -cifti-separate
ToyNogo_fdr_palm/ToyNogo_results_merged_tstat.dscalar.nii COLUMN -volume
ACCUMBENS_RIGHT R_Acc_Beta.nii.gz -roi R_NAcc_ROI.nii.gz
But when I try that on surface data I get the error:
HCP did not have a task that was geared toward response inhibition.
Furthermore, although it’s alluring to believe that a single parcel will
encapsulate all of response inhibition, it’s doubtful.
Why not select a set of parcels in and near IFG, and correct for multiple
comparisons? Use a
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
uot;Glasser, Matthew" <glass...@wustl.edu>
Date: Tuesday, September 27, 2016 at 4:52 AM
To: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>,
NEUROSCIENCE tim <tsc...@mst.edu&
9 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>, Timothy
Coalson <tsc...@mst.edu<mailto:tsc...
id2...@med.cornell.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
Thank you,
Are there any examples available for
W. Dreyfuss" <mid2...@med.cornell.edu>, Timothy Coalson <
> tsc...@mst.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
>
> OK, I tried this:
>
> wb_comm
.W. Dreyfuss"
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>, Timothy Coalson
<tsc...@mst.edu<mailto:tsc...@mst.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailt
Cc: "Michael F.W. Dreyfuss"
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>, Timothy Coalson
<tsc...@mst.edu<mailto:tsc...@mst.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:h
eyfuss; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
If you are getting error messages, I recommend posting them.
Peace,
Matt.
From: "Michael F.W. Dreyfuss"
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date:
ustl.edu>>, Timothy
Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas fro
s" <mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>, Timothy
Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
<hcp-users@humanconnectome.org<mailto:hcp-users@h
ome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
As Tim mentions, it sounds like you might want to use a parcellated analysis, as this will be more sensitive/powerful and you’ll know exactly what areas you are finding. The
, 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
ember 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
: 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
The wb_command -cifti-weighted-stats command with -mean is probably what
you want (outputs a number to the command line), though you'll need to have
each ROI as a separate file and run it separately for each of them.
Alternatively, if you turned the ROIs into a label file, you could get
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