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,
I am trying to create ROI from FS parcellation and extract z-values from it.
Steps 1 and 2 works. Step 3 gives me error message (core dumped):
wb_command -cifti-create-dense-from-template 100307_zstat1.dtseries.nii
14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii -cifti
14035rois_subcort_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
-cifti-parc
: 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
9, 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), though you&
alysis instead of a cluster analysis.
Thank you,
Michael
From: Timothy Coalson mailto:tsc...@mst.edu>>
Sent: Monday, September 19, 2016 4:48:28 PM
To: Michael F.W. Dreyfuss
Cc: hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>
Subje
rnell.edu>>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "Michael F.W. Dreyfuss"
mailto:mid2...@med.cornell.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@h
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
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
hy
Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
As an aside, if the end-game of the analysis is a permutation a
t.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
Thank you for this. We had explored this option in the past and two issues were
1) there was not
@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"
mailto:mid2...@med.cornell.edu>>
Date: Tuesday, September 20, 2016 at 10:40 AM
To: Matt Glas
2016 at 12:55 PM
To: Matt Glasser mailto:glass...@wustl.edu>>, Timothy
Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas fro
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
u>>, Timothy Coalson
mailto:tsc...@mst.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
OK, I tried
oalson
mailto:tsc...@mst.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
OK, I tried this:
wb_command -cifti-find-clusters
FoodGo_HCP_mesh_TFC
Matthew wrote:
>
> What does the input data look like?
>
> Peace,
>
> Matt.
>
> From: "Michael F.W. Dreyfuss"
> Date: Tuesday, September 20, 2016 at 1:22 PM
> To: Matt Glasser
> Cc: "Michael F.W. Dreyfuss" , Timothy Coalson <
> tsc.
identify and extract beta weights from
>> each.
>>
>> Thank you,
>> Michael
>>
>> On Sep 20, 2016, at 2:26 PM, Glasser, Matthew wrote:
>>
>> What does the input data look like?
>>
>> Peace,
>>
>> Matt.
>>
>>
uot;
mailto:mid2...@med.cornell.edu>>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "Michael F.W. Dreyfuss"
mailto:mid2...@med.cornell.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
ass...@wustl.edu>>, Timothy
Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
Hi Matt, I'm interested in using pa
u>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Timothy
Coalson mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
Thank you,
I've attached an image with a dot
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’
ectome.org>"
mailto:hcp-users@humanconnectome.org>>, Timothy
Coalson mailto:tsc...@mst.edu>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
Yes, but none of these regions is exactly what's typically called IFG, so to
limit comparisons I was wondering if you kn
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&
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
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 meta-a
Thank you,
Yes, I wasn’t necessarily looking for one parcel, but any set of parcels that
may be implicated in response inhibition or considered to be part of IFG,
although the fewer the better for fewer comparisons.
If I want to follow the following steps, can you please recommend which
wb_com
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:
wb_command
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 probab
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 CORTEX_LEFT and
CORTEX_RIGHT for
o look at them separately?
>
> Thank you,
> Michael
>
>
> --
> *From:* Timothy Coalson
> *Sent:* Tuesday, September 27, 2016 4:10:15 PM
> *To:* Michael F.W. Dreyfuss
> *Cc:* Burgess, Gregory; hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] ROIs and Betas
othy Coalson 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: [HCP-Users] ROIs and Betas from Cifti Data
The surface structures in
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
>> *Sent:* Tuesday, September 27, 2016 4:10:
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
http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-reduce
It is a simple reduction across columns (by default, anyway) in the file.
For these kinds of files, that means it isn't reducing across space. MAX
is one of the options it can calculate, and for binary ROIs, that
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 value for the key each
labeled region had in the label file is not the value in that sca
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, 2
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 label
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 file
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 d
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
ot;
mailto:mid2...@med.cornell.edu>>
Date: Wednesday, October 26, 2016 at 2:40 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] ROIs and Beta
s related to –roi expecting a binary ROI rather than a label
> file.
>
> Peace,
>
> Matt.
>
> From: on behalf of "Michael F.W.
> Dreyfuss"
> Date: Wednesday, October 26, 2016 at 2:40 PM
> To: Timothy Coalson
> Cc: "hcp-users@humanconnectome.org&q
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
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
to: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). T
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