Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

Unfortunately there isn't a particularly easy way to do this.  There is
-cifti-label-export-table, from which you'd need to strip out the color
information (every other line).  The label table of a dlabel file is also
shown in -file-information.  These will work as long as all of the labels
have nonzero extent.  If you want it to be safe against that possibility,
you can use -cifti-parcel-mapping-to-label on the parcellated file to
generate a dlabel file to get the label table from.

Tim


On Tue, May 9, 2017 at 6:11 PM, Astafiev, Serguei <astaf...@wustl.edu>
wrote:

> Hi, Tim,
>
> Thank you very much for your help! -cifti-parcellate and -cifti-convert
> -to-text works. What is the easiest way to output label names (i.e.
> PUTAMEN_RIGHT) into txt file using this approach?
>
>
>
> Best regards,
>
> Serguei Astafiev
>
>
>
> *From:* 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 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 you need that
> result as text, there is -cifti-convert -to-text.
>
>
>
> Tim
>
>
>
>
>
> On Tue, May 9, 2017 at 11:45 AM, Astafiev, Serguei <astaf...@wustl.edu>
> wrote:
>
> 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_ACCUMBENS_RIGHT.dscalar.nii
>
> /usr/local/pkg/workbench1.2.3/bin_rh_linux64/wb_command: line 15: 32654
> Segmentation fault  (core dumped) 
> "$directory"/../exe_rh_linux64/wb_command
> "$@"
>
> Can somebody tell me what is wrong?
>
>
>
> ## 1} Convert subcortical MNI ROIs to CIFTI
>
> wb_command -cifti-create-label 14035rois_subcort.dlabel.nii -volume
> Atlas_ROIs.2.nii.gz Atlas_ROIs.2.nii.gz
>
>
>
> ## 2} Select ACCUMBENS_RIGHT and create ROI for it
>
> wb_command -cifti-label-to-roi 14035rois_subcort.dlabel.nii
> 14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii -name ACCUMBENS_RIGHT
>
>
>
> ## 3} Match ROI dimensions to z-stat dimensions
>
> wb_command -cifti-create-dense-from-template 100307_zstat1.dtseries.nii
> 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii -cifti
> 14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii
>
>
>
> ## 4} Extract values from ROI
>
> wb_command ‐cifti‐stats 100307_zstat1.dtseries.nii ‐reduce MEAN ‐roi
> 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii
>
>
>
>
>
> ___
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> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
>
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Astafiev, Serguei]

Hi, Tim,
Thank you very much for your help! -cifti-parcellate and -cifti-convert 
-to-text works. What is the easiest way to output label names (i.e. 
PUTAMEN_RIGHT) into txt file using this approach?

Best regards,
Serguei Astafiev

From: 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 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 you need that result as 
text, there is -cifti-convert -to-text.

Tim


On Tue, May 9, 2017 at 11:45 AM, Astafiev, Serguei 
<astaf...@wustl.edu<mailto:astaf...@wustl.edu>> wrote:
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_ACCUMBENS_RIGHT.dscalar.nii
/usr/local/pkg/workbench1.2.3/bin_rh_linux64/wb_command: line 15: 32654 
Segmentation fault  (core dumped) "$directory"/../exe_rh_linux64/wb_command 
"$@"
Can somebody tell me what is wrong?

## 1} Convert subcortical MNI ROIs to CIFTI
wb_command -cifti-create-label 14035rois_subcort.dlabel.nii -volume 
Atlas_ROIs.2.nii.gz Atlas_ROIs.2.nii.gz

## 2} Select ACCUMBENS_RIGHT and create ROI for it
wb_command -cifti-label-to-roi 14035rois_subcort.dlabel.nii 
14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii -name ACCUMBENS_RIGHT

## 3} Match ROI dimensions to z-stat dimensions
wb_command -cifti-create-dense-from-template 100307_zstat1.dtseries.nii 
14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii -cifti 
14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii

## 4} Extract values from ROI
wb_command ‐cifti‐stats 100307_zstat1.dtseries.nii ‐reduce MEAN ‐roi 
14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii



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intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

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 you need that
result as text, there is -cifti-convert -to-text.

Tim


On Tue, May 9, 2017 at 11:45 AM, Astafiev, Serguei 
wrote:

> 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_ACCUMBENS_RIGHT.dscalar.nii
>
> /usr/local/pkg/workbench1.2.3/bin_rh_linux64/wb_command: line 15: 32654
> Segmentation fault  (core dumped) 
> "$directory"/../exe_rh_linux64/wb_command
> "$@"
>
> Can somebody tell me what is wrong?
>
>
>
> ## 1} Convert subcortical MNI ROIs to CIFTI
>
> wb_command -cifti-create-label 14035rois_subcort.dlabel.nii -volume
> Atlas_ROIs.2.nii.gz Atlas_ROIs.2.nii.gz
>
>
>
> ## 2} Select ACCUMBENS_RIGHT and create ROI for it
>
> wb_command -cifti-label-to-roi 14035rois_subcort.dlabel.nii
> 14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii -name ACCUMBENS_RIGHT
>
>
>
> ## 3} Match ROI dimensions to z-stat dimensions
>
> wb_command -cifti-create-dense-from-template 100307_zstat1.dtseries.nii
> 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii -cifti
> 14035rois_subcort_ACCUMBENS_RIGHT.dscalar.nii
>
>
>
> ## 4} Extract values from ROI
>
> wb_command ‐cifti‐stats 100307_zstat1.dtseries.nii ‐reduce MEAN ‐roi
> 14035rois_subcort_ACCUMBENS_RIGHT_f.dscalar.nii
>
>
>
>
>
> Best regards,
>
> Serguei Astafiev
>
> Department of Psychiatry
>
> Washington University School of Medicine
>
> Campus Box 8134,
>
> 660 S. Euclid Ave, St. Louis, MO 63110
>
> Phone: (314) 286-2205
>
> FAX: (314) 286-0091
>
> E-mail: astaf...@wustl.edu
>
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
>
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

___
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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

You can use -cifti-create-dense-from-template to create a new ROI cifti
file that avoids this problem, just specify the cifti file you want to get
the stats from as the template, and provide the current roi file to a
-cifti option.

To get the stats within a single label, first use -cifti-label-to-roi.  If
you want some statistic in each label separately, consider using
-cifti-parcellate with the -method option.

Tim


On Wed, Oct 26, 2016 at 5:38 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:

> The first issue is probably related to whether the medial wall is in place
> or not.
>
> The second is related to –roi expecting a binary ROI rather than a label
> file.
>
> Peace,
>
> Matt.
>
> From: <hcp-users-boun...@humanconnectome.org> on behalf of "Michael F.W.
> Dreyfuss" <mid2...@med.cornell.edu>
> Date: Wednesday, 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 mean value form a cifti file using -
>
> cifti-weighted-stats within an ROI I produced from the Brodmann area maps
> Human.Brodmann09.32k_fs_LR.dlabel.nii.
>
>
> I use the command
>
>
> wb_command -cifti-weighted-stats 
> results_merged_tfce_FLOB1_tstat_fwep.dscalar.nii
> -roi HCP_S900_GroupAvg_v1/BA47.dscalar.nii -match-maps -mean
> -spatial-weights -left-area-surf HCP_S900_GroupAvg_v1/S900.L.
> midthickness_MSMAll.32k_fs_LR.surf.gii -right-area-surf
> HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.surf.gii
>
>
> but I get the error:
>
>
> ERROR: roi cifti has incompatible mapping along column
>
>
> alternatively, I've looked just within the left hemispheric data using the
> command:
>
>
> wb_command -metric-weighted-stats results_R_cort_tfce_tstat_fwep.gii -roi
> HCP_S900_GroupAvg_v1/BA47_Right.label.gii -weight-metric
> NOGO-GO_results_R_cort_tfce_tstat_fwep.gii -mean
>
>
> With the result:
>
> WARNING: Metric File: HCP_S900_GroupAvg_v1/BA47_Right.label.gii contains
> data array with NIFTI_INTENT_LABEL !!!
>
>
> 0.4116454
>
>
> Do you know how I can extract mean values from an ROI like this? Is this
> the appropriate command to use when I have an ROI?
>
>
> Thank you,
>
> Michael
>
>
>
> --
> *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 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 do this on the restricted dlabel file before -cifti-math).
>
> Basically, there are several ways to go about the task, and you took a
> different path than I expected.  By starting with -cifti-label-to-roi, you
> can avoid the need to manually edit a text file for the purpose of
> extracting the labels you want (and it also avoids doing math on label
> files, which has some rough edges).
>
> Tim
>
>
> On Tue, Sep 27, 2016 at 5:29 PM, Timothy Coalson <tsc...@mst.edu> wrote:
>
>> 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.
>>
>> Tim
>>
>>
>> On Tue, Sep 27, 2016 at 5:26 PM, Michael F.W. Dreyfuss <
>> mid2...@med.cornell.edu> wrote:
>>
>>> 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, 2016, at 6:20 PM, Michael F.W. Dreyfuss <
>>> 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 ex

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Glasser, Matthew]

The first issue is probably related to whether the medial wall is in place or 
not.

The second is related to –roi expecting a binary ROI rather than a label file.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Wednesday, October 26, 2016 at 2:40 PM
To: 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 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 maps 
Human.Brodmann09.32k_fs_LR.dlabel.nii.


I use the command


wb_command -cifti-weighted-stats 
results_merged_tfce_FLOB1_tstat_fwep.dscalar.nii -roi 
HCP_S900_GroupAvg_v1/BA47.dscalar.nii -match-maps -mean -spatial-weights 
-left-area-surf 
HCP_S900_GroupAvg_v1/S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii 
-right-area-surf 
HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.surf.gii


but I get the error:


ERROR: roi cifti has incompatible mapping along column


alternatively, I've looked just within the left hemispheric data using the 
command:


wb_command -metric-weighted-stats results_R_cort_tfce_tstat_fwep.gii -roi 
HCP_S900_GroupAvg_v1/BA47_Right.label.gii -weight-metric 
NOGO-GO_results_R_cort_tfce_tstat_fwep.gii -mean


With the result:

WARNING: Metric File: HCP_S900_GroupAvg_v1/BA47_Right.label.gii contains data 
array with NIFTI_INTENT_LABEL !!!


0.4116454


Do you know how I can extract mean values from an ROI like this? Is this the 
appropriate command to use when I have an ROI?


Thank you,

Michael




From: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Sent: Tuesday, September 27, 2016 6:37:42 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

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 do this on the 
restricted dlabel file before -cifti-math).

Basically, there are several ways to go about the task, and you took a 
different path than I expected.  By starting with -cifti-label-to-roi, you can 
avoid the need to manually edit a text file for the purpose of extracting the 
labels you want (and it also avoids doing math on label files, which has some 
rough edges).

Tim


On Tue, Sep 27, 2016 at 5:29 PM, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
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.

Tim


On Tue, Sep 27, 2016 at 5:26 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:
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, 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 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 scalar file. so 
BA44 was 65, BA45 was 66, and now there are two regions with values 65 and 66.

What I am trying to do is to merge regions together into one region as a label 
file to use as a single mask. Is this possible with this function?

I’m sorry if I’m missing something here.

Thank you,
Michael


On Sep 27, 2016, at 5:57 PM, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:

http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-reduce<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanconnectome.org_software_workbench-2Dcommand.php-3Ffunction-3D-2Dcifti-2Dreduce=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Xs5Efvm

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

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 maps 
Human.Brodmann09.32k_fs_LR.dlabel.nii.


I use the command


wb_command -cifti-weighted-stats 
results_merged_tfce_FLOB1_tstat_fwep.dscalar.nii -roi 
HCP_S900_GroupAvg_v1/BA47.dscalar.nii -match-maps -mean -spatial-weights 
-left-area-surf 
HCP_S900_GroupAvg_v1/S900.L.midthickness_MSMAll.32k_fs_LR.surf.gii 
-right-area-surf 
HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.surf.gii


but I get the error:


ERROR: roi cifti has incompatible mapping along column


alternatively, I've looked just within the left hemispheric data using the 
command:


wb_command -metric-weighted-stats results_R_cort_tfce_tstat_fwep.gii -roi 
HCP_S900_GroupAvg_v1/BA47_Right.label.gii -weight-metric 
NOGO-GO_results_R_cort_tfce_tstat_fwep.gii -mean


With the result:

WARNING: Metric File: HCP_S900_GroupAvg_v1/BA47_Right.label.gii contains data 
array with NIFTI_INTENT_LABEL !!!


0.4116454


Do you know how I can extract mean values from an ROI like this? Is this the 
appropriate command to use when I have an ROI?


Thank you,

Michael




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 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 do this on the 
restricted dlabel file before -cifti-math).

Basically, there are several ways to go about the task, and you took a 
different path than I expected.  By starting with -cifti-label-to-roi, you can 
avoid the need to manually edit a text file for the purpose of extracting the 
labels you want (and it also avoids doing math on label files, which has some 
rough edges).

Tim


On Tue, Sep 27, 2016 at 5:29 PM, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:
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.

Tim


On Tue, Sep 27, 2016 at 5:26 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:
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, 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 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 scalar file. so 
BA44 was 65, BA45 was 66, and now there are two regions with values 65 and 66.

What I am trying to do is to merge regions together into one region as a label 
file to use as a single mask. Is this possible with this function?

I’m sorry if I’m missing something here.

Thank you,
Michael


On Sep 27, 2016, at 5:57 PM, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:

http://www.humanconnectome.org/software/workbench-command.php?function=-cifti-reduce<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.humanconnectome.org_software_workbench-2Dcommand.php-3Ffunction-3D-2Dcifti-2Dreduce=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Xs5EfvmcgCd1YzshFEix8oFIzx34876b06vXtA_UXVI=KS6IGgzKif6PPGEjorzvQDKDv09VSeiBIXSHw-xZrAI=>

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 is equivalent to 
boolean OR, which is what we want.

The commands are generally written to perform small, specific actions, such 
that they could be suitable for multiple tasks.

Tim


On Tue, Sep 27, 2016 at 4:49 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<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, how would 
-cifti-reduce do that? Wouldn’t it be more suited to ca

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

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 do this on the restricted dlabel file before -cifti-math).

Basically, there are several ways to go about the task, and you took a
different path than I expected.  By starting with -cifti-label-to-roi, you
can avoid the need to manually edit a text file for the purpose of
extracting the labels you want (and it also avoids doing math on label
files, which has some rough edges).

Tim


On Tue, Sep 27, 2016 at 5:29 PM, Timothy Coalson  wrote:

> 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.
>
> Tim
>
>
> On Tue, Sep 27, 2016 at 5:26 PM, Michael F.W. Dreyfuss <
> mid2...@med.cornell.edu> wrote:
>
>> 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, 2016, at 6:20 PM, Michael F.W. Dreyfuss <
>> 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 value
>> for the key each labeled region had in the label file is not the value in
>> that scalar file. so BA44 was 65, BA45 was 66, and now there are two
>> regions with values 65 and 66.
>>
>> What I am trying to do is to merge regions together into one region as a
>> label file to use as a single mask. Is this possible with this function?
>>
>> I’m sorry if I’m missing something here.
>>
>> Thank you,
>> Michael
>>
>>
>> On Sep 27, 2016, at 5:57 PM, Timothy Coalson  wrote:
>>
>> 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 is equivalent to boolean OR, which is what we want.
>>
>> The commands are generally written to perform small, specific actions,
>> such that they could be suitable for multiple tasks.
>>
>> Tim
>>
>>
>> On Tue, Sep 27, 2016 at 4:49 PM, Michael F.W. Dreyfuss <
>> 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, 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 Sep 27, 2016, at 5:40 PM, Timothy Coalson  wrote:
>>>
>>> wb_shortcuts
>>>
>>>
>>>
>>
>>
>>
>

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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

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.

Tim


On Tue, Sep 27, 2016 at 5:26 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> 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, 2016, at 6:20 PM, Michael F.W. Dreyfuss <
> 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 value
> for the key each labeled region had in the label file is not the value in
> that scalar file. so BA44 was 65, BA45 was 66, and now there are two
> regions with values 65 and 66.
>
> What I am trying to do is to merge regions together into one region as a
> label file to use as a single mask. Is this possible with this function?
>
> I’m sorry if I’m missing something here.
>
> Thank you,
> Michael
>
>
> On Sep 27, 2016, at 5:57 PM, Timothy Coalson  wrote:
>
> 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 is
> equivalent to boolean OR, which is what we want.
>
> The commands are generally written to perform small, specific actions,
> such that they could be suitable for multiple tasks.
>
> Tim
>
>
> On Tue, Sep 27, 2016 at 4:49 PM, Michael F.W. Dreyfuss <
> 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, 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 Sep 27, 2016, at 5:40 PM, Timothy Coalson  wrote:
>>
>> wb_shortcuts
>>
>>
>>
>
>
>

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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

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 you are interested in, use -cifti-merge (or wb_shortcuts
-cifti-concatenate) to put all those binary ROIs as separate maps in a
single dscalar file, then use -cifti-reduce on that multi-ROI dscalar file
to get a single map with the combined binary ROI.

To then separate the ROI per-hemisphere, you can use -cifti-separate (on
the binary ROI dscalar file).

Tim


On Tue, Sep 27, 2016 at 5:20 PM, Michael F.W. Dreyfuss <
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 value
> for the key each labeled region had in the label file is not the value in
> that scalar file. so BA44 was 65, BA45 was 66, and now there are two
> regions with values 65 and 66.
>
> What I am trying to do is to merge regions together into one region as a
> label file to use as a single mask. Is this possible with this function?
>
> I’m sorry if I’m missing something here.
>
> Thank you,
> Michael
>
>
>
> On Sep 27, 2016, at 5:57 PM, Timothy Coalson  wrote:
>
> 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 is
> equivalent to boolean OR, which is what we want.
>
> The commands are generally written to perform small, specific actions,
> such that they could be suitable for multiple tasks.
>
> Tim
>
>
> On Tue, Sep 27, 2016 at 4:49 PM, Michael F.W. Dreyfuss <
> 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, 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 Sep 27, 2016, at 5:40 PM, Timothy Coalson  wrote:
>>
>> wb_shortcuts
>>
>>
>>
>
>

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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

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, 2016, at 6:20 PM, Michael F.W. Dreyfuss 
> 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 value for the key each 
labeled region had in the label file is not the value in that scalar file. so 
BA44 was 65, BA45 was 66, and now there are two regions with values 65 and 66.

What I am trying to do is to merge regions together into one region as a label 
file to use as a single mask. Is this possible with this function?

I’m sorry if I’m missing something here.

Thank you,
Michael


On Sep 27, 2016, at 5:57 PM, Timothy Coalson 
> wrote:

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 is equivalent to 
boolean OR, which is what we want.

The commands are generally written to perform small, specific actions, such 
that they could be suitable for multiple tasks.

Tim


On Tue, Sep 27, 2016 at 4:49 PM, Michael F.W. Dreyfuss 
> 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, 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 Sep 27, 2016, at 5:40 PM, Timothy Coalson 
> wrote:

wb_shortcuts





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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

The easier way is to use -cifti-merge (or wb_shortcuts -cifti-concatenate
for simpler syntax), then -cifti-reduce.  It is possible to do with
-cifti-math, but not as convenient.

Tim


On Tue, Sep 27, 2016 at 4:37 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> Thank you, that works. Then if I want multiple parcels to be collapsed
> into a single ROI to make a mask spanning several ROIs that are not
> considered separate keys, which command would do that.
>
> Thank you,
> Michael
>
>
> On Sep 27, 2016, at 5:26 PM, Timothy Coalson <tsc...@mst.edu> wrote:
>
> The easiest way to deal with this is probably to use -cifti-separate to
> get them as gifti label files, which are each single-hemisphere.  The use
> of the same key/name for both hemispheres was an unfortunate choice, which
> we intended to avoid in the future.
>
> Tim
>
>
> On Tue, Sep 27, 2016 at 4:15 PM, Michael F.W. Dreyfuss <
> 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 with files like Human.Brodmann09.32k_fs_LR.dlabel.nii
>> where the ROIs in both hemispheres are under the same key? If I want to
>> 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>
>> *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 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 that command to work.  However, the
>> outputs are gifti files, not cifti files - it is a format conversion
>> command, and probably not what you want to do.
>>
>> Instead of separating to gifti files, you should use -cifti-label-to-roi
>> on the dlabel file to get the areas by name as separate ROIs (as 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 <
>> mid2...@med.cornell.edu> wrote:
>>
>>> 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 -cifti-separate ToyNogo_GlasserParcellation_FL
>>> OBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii COLUMN -label
>>> R_IFSp_ROI ToyNogo_R_IFSp_Beta.pscalar.ni
>>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__ToyNogo-5FR-5FIFSp-5FBeta.pscalar.ni=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=RNChVFlNku6C4rq5ASbFdbABN7bwTnnLDhy6op63_hY=qzxt7r-90CndJvK0gVl2yx_UvsFswqgrT2CDYJdSaLM=>i
>>> -roi R_IFSp_ROI.plabel.nii
>>>
>>> ERROR: unrecognized structure type
>>>
>>> The problem seems to be in recognizing the structures name (i.e.
>>> R_IFSp_ROI). Do you know how I can reference a specific structure or
>>> structures with a command from a label file, or is there another comparable
>>> command you would suggest for isolating structures from a label file?
>>>
>>> Thank you,
>>> Michael
>>>
>>> On Sep 27, 2016, at 10:41 AM, Burgess, Gregory <gburg...@wustl.edu>
>>> wrote:
>>>
>>> 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-analysis as your guide (
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__neurosy
>>> nth.org_analyses_terms_response-2520inhibition_=DQIGaQ=
>>> lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_
>>> z1plf

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

Thank you, that works. Then if I want multiple parcels to be collapsed into a 
single ROI to make a mask spanning several ROIs that are not considered 
separate keys, which command would do that.

Thank you,
Michael

On Sep 27, 2016, at 5:26 PM, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:

The easiest way to deal with this is probably to use -cifti-separate to get 
them as gifti label files, which are each single-hemisphere.  The use of the 
same key/name for both hemispheres was an unfortunate choice, which we intended 
to avoid in the future.

Tim


On Tue, 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-roi

How would that work with files like Human.Brodmann09.32k_fs_LR.dlabel.nii where 
the ROIs in both hemispheres are under the same key? If I want to 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<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 -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 probably not what you 
want to do.

Instead of separating to gifti files, you should use -cifti-label-to-roi on the 
dlabel file to get the areas by name as separate ROIs (as 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 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:
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 -cifti-separate 
ToyNogo_GlasserParcellation_FLOBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii
 COLUMN -label R_IFSp_ROI 
ToyNogo_R_IFSp_Beta.pscalar.ni<https://urldefense.proofpoint.com/v2/url?u=http-3A__ToyNogo-5FR-5FIFSp-5FBeta.pscalar.ni=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=RNChVFlNku6C4rq5ASbFdbABN7bwTnnLDhy6op63_hY=qzxt7r-90CndJvK0gVl2yx_UvsFswqgrT2CDYJdSaLM=>i
 -roi R_IFSp_ROI.plabel.nii

ERROR: unrecognized structure type

The problem seems to be in recognizing the structures name (i.e. R_IFSp_ROI). 
Do you know how I can reference a specific structure or structures with a 
command from a label file, or is there another comparable command you would 
suggest for isolating structures from a label file?

Thank you,
Michael

On Sep 27, 2016, at 10:41 AM, Burgess, Gregory 
<gburg...@wustl.edu<mailto:gburg...@wustl.edu>> wrote:

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-analysis as your guide 
(https://urldefense.proofpoint.com/v2/url?u=http-3A__neurosynth.org_analyses_terms_response-2520inhibition_=DQIGaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8=DxHCajoqQSf0nIWSDbUHyB6J7F2eax1NswvaNpprHaU=
 ). Your statistical power should still benefit from the parcellated analysis 
and reduced number of multiple comparisons, relative to a whole-brain analysis.

--Greg


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...@med.cornell.edu>> wrote:

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 you had any 
information on spec

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

The easiest way to deal with this is probably to use -cifti-separate to get
them as gifti label files, which are each single-hemisphere.  The use of
the same key/name for both hemispheres was an unfortunate choice, which we
intended to avoid in the future.

Tim


On Tue, Sep 27, 2016 at 4:15 PM, Michael F.W. Dreyfuss <
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 with files like Human.Brodmann09.32k_fs_LR.dlabel.nii
> where the ROIs in both hemispheres are under the same key? If I want to
> 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>
> *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 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 that command to work.  However, the
> outputs are gifti files, not cifti files - it is a format conversion
> command, and probably not what you want to do.
>
> Instead of separating to gifti files, you should use -cifti-label-to-roi
> on the dlabel file to get the areas by name as separate ROIs (as 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 <
> mid2...@med.cornell.edu> wrote:
>
>> 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 -cifti-separate ToyNogo_GlasserParcellation_FL
>> OBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii COLUMN -label
>> R_IFSp_ROI ToyNogo_R_IFSp_Beta.pscalar.nii -roi R_IFSp_ROI.plabel.nii
>>
>> ERROR: unrecognized structure type
>>
>> The problem seems to be in recognizing the structures name (i.e.
>> R_IFSp_ROI). Do you know how I can reference a specific structure or
>> structures with a command from a label file, or is there another comparable
>> command you would suggest for isolating structures from a label file?
>>
>> Thank you,
>> Michael
>>
>> On Sep 27, 2016, at 10:41 AM, Burgess, Gregory <gburg...@wustl.edu>
>> wrote:
>>
>> 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-analysis as your guide (
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__
>> neurosynth.org_analyses_terms_response-2520inhibition_=
>> DQIGaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=
>> rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Pb-
>> c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8=DxHCajoqQSf0nIWSD
>> bUHyB6J7F2eax1NswvaNpprHaU= ). Your statistical power should still
>> benefit from the parcellated analysis and reduced number of multiple
>> comparisons, relative to a whole-brain analysis.
>>
>> --Greg
>>
>> 
>> 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 <
>> mid2...@med.cornell.edu> wrote:
>>
>> 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 you had any information on specifically where within your parcellation
>> that may be most relevant.
>>
>> On Sep 27, 201

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

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 with files like Human.Brodmann09.32k_fs_LR.dlabel.nii where 
the ROIs in both hemispheres are under the same key? If I want to 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>
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 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 that command to work.  However, the outputs are gifti files, 
not cifti files - it is a format conversion command, and probably not what you 
want to do.

Instead of separating to gifti files, you should use -cifti-label-to-roi on the 
dlabel file to get the areas by name as separate ROIs (as 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 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:
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 -cifti-separate 
ToyNogo_GlasserParcellation_FLOBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii
 COLUMN -label R_IFSp_ROI ToyNogo_R_IFSp_Beta.pscalar.nii -roi 
R_IFSp_ROI.plabel.nii

ERROR: unrecognized structure type

The problem seems to be in recognizing the structures name (i.e. R_IFSp_ROI). 
Do you know how I can reference a specific structure or structures with a 
command from a label file, or is there another comparable command you would 
suggest for isolating structures from a label file?

Thank you,
Michael

On Sep 27, 2016, at 10:41 AM, Burgess, Gregory 
<gburg...@wustl.edu<mailto:gburg...@wustl.edu>> wrote:

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-analysis as your guide 
(https://urldefense.proofpoint.com/v2/url?u=http-3A__neurosynth.org_analyses_terms_response-2520inhibition_=DQIGaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8=DxHCajoqQSf0nIWSDbUHyB6J7F2eax1NswvaNpprHaU=
 ). Your statistical power should still benefit from the parcellated analysis 
and reduced number of multiple comparisons, relative to a whole-brain analysis.

--Greg


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...@med.cornell.edu>> wrote:

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 you had any 
information on specifically where within your parcellation that may be most 
relevant.

On Sep 27, 2016, at 9:57 AM, Harms, Michael 
<mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote:

Just a reminder to be careful here to avoid issues of 
circularity/double-dipping.  You indicated that you had a priori hypotheses 
about IFG involvement, but that doesn’t allow you to then select a particular 
IFG parcel based on your task activation map.  Ideally, you would have selected 
your parcel(s) for analysis prior to ever computing/viewing your activation map 
(unless what you showed was a map from an independent, unrelated set of 
subjects).


___
HCP-Users mailing list
HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers=DQIGaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdG

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

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 probably not what you want to do.

Instead of separating to gifti files, you should use -cifti-label-to-roi on
the dlabel file to get the areas by name as separate ROIs (as 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 <
mid2...@med.cornell.edu> wrote:

> 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 -cifti-separate ToyNogo_GlasserParcellation_
> FLOBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii COLUMN -label
> R_IFSp_ROI ToyNogo_R_IFSp_Beta.pscalar.nii -roi R_IFSp_ROI.plabel.nii
>
> ERROR: unrecognized structure type
>
> The problem seems to be in recognizing the structures name (i.e.
> R_IFSp_ROI). Do you know how I can reference a specific structure or
> structures with a command from a label file, or is there another comparable
> command you would suggest for isolating structures from a label file?
>
> Thank you,
> Michael
>
> On Sep 27, 2016, at 10:41 AM, Burgess, Gregory  wrote:
>
> 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-analysis as your guide (https://urldefense.
> proofpoint.com/v2/url?u=http-3A__neurosynth.org_analyses_
> terms_response-2520inhibition_=DQIGaQ=lb62iw4YL4RFalcE2hQUQealT9-
> RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYF
> Swg=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8=
> DxHCajoqQSf0nIWSDbUHyB6J7F2eax1NswvaNpprHaU= ). Your statistical power
> should still benefit from the parcellated analysis and reduced number of
> multiple comparisons, relative to a whole-brain analysis.
>
> --Greg
>
> 
> 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 <
> mid2...@med.cornell.edu> wrote:
>
> 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
> you had any information on specifically where within your parcellation that
> may be most relevant.
>
> On Sep 27, 2016, at 9:57 AM, Harms, Michael  wrote:
>
> Just a reminder to be careful here to avoid issues of
> circularity/double-dipping.  You indicated that you had a priori hypotheses
> about IFG involvement, but that doesn’t allow you to then select a
> particular IFG parcel based on your task activation map.  Ideally, you
> would have selected your parcel(s) for analysis prior to ever
> computing/viewing your activation map (unless what you showed was a map
> from an independent, unrelated set of subjects).
>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
> humanconnectome.org_mailman_listinfo_hcp-2Dusers=DQIGaQ&
> c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_
> z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Pb-c1m96L6xixMU-j16J-
> GkC6tGV5lAdGNKy-Tj1ht8=Kd8JGIfyDD_MWOgH24WZFrQNLqIT2e2KIaFCaLTw3PM=
>
>
>
>
> --Greg
>
> 
> 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
>
>
> 
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
>
> ___
> HCP-Users mailing list
> 

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

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 -cifti-separate 
ToyNogo_GlasserParcellation_FLOBS1_fdr_palm/ToyNogo_results_dat_tstat.pscalar.nii
 COLUMN -label R_IFSp_ROI ToyNogo_R_IFSp_Beta.pscalar.nii -roi 
R_IFSp_ROI.plabel.nii

ERROR: unrecognized structure type

The problem seems to be in recognizing the structures name (i.e. R_IFSp_ROI). 
Do you know how I can reference a specific structure or structures with a 
command from a label file, or is there another comparable command you would 
suggest for isolating structures from a label file?

Thank you,
Michael

On Sep 27, 2016, at 10:41 AM, Burgess, Gregory 
> wrote:

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-analysis as your guide 
(https://urldefense.proofpoint.com/v2/url?u=http-3A__neurosynth.org_analyses_terms_response-2520inhibition_=DQIGaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8=DxHCajoqQSf0nIWSDbUHyB6J7F2eax1NswvaNpprHaU=
 ). Your statistical power should still benefit from the parcellated analysis 
and reduced number of multiple comparisons, relative to a whole-brain analysis.

--Greg


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 
> wrote:

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 you had any 
information on specifically where within your parcellation that may be most 
relevant.

On Sep 27, 2016, at 9:57 AM, Harms, Michael 
> wrote:

Just a reminder to be careful here to avoid issues of 
circularity/double-dipping.  You indicated that you had a priori hypotheses 
about IFG involvement, but that doesn’t allow you to then select a particular 
IFG parcel based on your task activation map.  Ideally, you would have selected 
your parcel(s) for analysis prior to ever computing/viewing your activation map 
(unless what you showed was a map from an independent, unrelated set of 
subjects).


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers=DQIGaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=Pb-c1m96L6xixMU-j16J-GkC6tGV5lAdGNKy-Tj1ht8=Kd8JGIfyDD_MWOgH24WZFrQNLqIT2e2KIaFCaLTw3PM=




--Greg


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



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Burgess, Gregory]

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-analysis as your guide 
(http://neurosynth.org/analyses/terms/response%20inhibition/). Your statistical 
power should still benefit from the parcellated analysis and reduced number of 
multiple comparisons, relative to a whole-brain analysis.

--Greg


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  
> wrote:
>
> 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 you had any 
> information on specifically where within your parcellation that may be most 
> relevant.
>
>> On Sep 27, 2016, at 9:57 AM, Harms, Michael  wrote:
>>
>> Just a reminder to be careful here to avoid issues of 
>> circularity/double-dipping.  You indicated that you had a priori hypotheses 
>> about IFG involvement, but that doesn’t allow you to then select a 
>> particular IFG parcel based on your task activation map.  Ideally, you would 
>> have selected your parcel(s) for analysis prior to ever computing/viewing 
>> your activation map (unless what you showed was a map from an independent, 
>> unrelated set of subjects).
>>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>



--Greg


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



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] ROIs and Betas from Cifti Data

[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 you had any 
information on specifically where within your parcellation that may be most 
relevant.

On Sep 27, 2016, at 9:57 AM, Harms, Michael 
> wrote:

Just a reminder to be careful here to avoid issues of 
circularity/double-dipping.  You indicated that you had a priori hypotheses 
about IFG involvement, but that doesn’t allow you to then select a particular 
IFG parcel based on your task activation map.  Ideally, you would have selected 
your parcel(s) for analysis prior to ever computing/viewing your activation map 
(unless what you showed was a map from an independent, unrelated set of 
subjects).



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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Harms, Michael]

Hi Michael,
Just a reminder to be careful here to avoid issues of circularity/double-dipping.  You indicated that you had a priori hypotheses about IFG involvement, but that doesn’t allow you to then select a particular IFG parcel based on your task activation map.
  Ideally, you would have selected your parcel(s) for analysis prior to ever computing/viewing your activation map (unless what you showed was a map from an independent, unrelated set of subjects).


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu







From: <hcp-users-boun...@humanconnectome.org> on behalf of "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>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data





I clicked in a corresponding location and your activation appears to fall within area IFSp.  The inferior frontal gyrus contains multiple areas, as does the inferior frontal sulcus.  We have only directly commented on the function of the areas in relation
 to the 7 HCP acquired tasks (See the supplementary neuroanatomical results).


Peace,


Matt.




From: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>
Date: Monday, September 26, 2016 at 5:59 PM
To: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>,
 Timothy Coalson <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 knew of a reason that one of them should be considered a locus of response inhibition based on your data that would warrant using that region
 as an a priori ROI to look 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 Betas from Cifti Data
 


Can’t you just click which area is under that cluster?  I didn’t realize you already had the data registered.


Peace,


Matt.




From: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>
Date: Monday, September 26, 2016 at 4:09 PM
To: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>,
 Timothy Coalson <tsc...@mst.edu>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data







Thank you,


I've attached an image with a dot on the cluster I'm interested in. I could send you the dscalar file too, but prefer not to distribute to the whole listserv. 


Since we have a priori hypotheses about the IFG being involved in this task (it is a go/nogo task), I want test for an effect specifically in that region similar to the one shown that I am seeing. In volumetric analysis I would use an anatomically or functionally
 defined mask and either A) look for a region within that mask that survives cluster thresholding to localize where in that region is involved or B) test if average betas are different within that region between conditions. I was wondering if one of the parcels
 from your parcellation was something you know to be where response inhibition on tasks like go/nogo may be localized as a reason for using that parcellation or set of parcellations. Otherwise I would be interested in something like a combined mask of BA44
 and BA45 as representing IFG.


Also, is it possible to do something like TFCE or fdr correction within a region like this within palm as that would reduce the area I am looking over for an effect and reduce the cluster size needed compared to a whole brain analysis?


Thank you,
Michael


From: Glasser, Matthew <glass...@wustl.edu>
Sent: Monday, September 26, 2016 2:18:26 PM
To: Michael F.W. Dreyfuss; NEUROSCIENCE tim
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data
 


Is there a surface-based map of this task contrast somewhere that I could look at?  Without that I would just be guessing…


Peace,


Matt.




From: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>
Date: Monday, September 26, 2016 at 1:13 PM
To: Matt Glasser <glass...@wustl.edu>, Timothy Coalson <tsc...@mst.edu>
Cc: "hcp-users@humanconnectome.org" <hcp-

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

Yes, but none of these regions is exactly what's typically called IFG, so to 
limit comparisons I was wondering if you knew of a reason that one of them 
should be considered a locus of response inhibition based on your data that 
would warrant using that region as an a priori ROI to look 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 Betas from Cifti Data

Can’t you just click which area is under that cluster?  I didn’t realize you 
already had the data registered.

Peace,

Matt.

From: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Monday, September 26, 2016 at 4:09 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...@mst.edu>>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data


Thank you,


I've attached an image with a dot on the cluster I'm interested in. I could 
send you the dscalar file too, but prefer not to distribute to the whole 
listserv.


Since we have a priori hypotheses about the IFG being involved in this task (it 
is a go/nogo task), I want test for an effect specifically in that region 
similar to the one shown that I am seeing. In volumetric analysis I would use 
an anatomically or functionally defined mask and either A) look for a region 
within that mask that survives cluster thresholding to localize where in that 
region is involved or B) test if average betas are different within that region 
between conditions. I was wondering if one of the parcels from your 
parcellation was something you know to be where response inhibition on tasks 
like go/nogo may be localized as a reason for using that parcellation or set of 
parcellations. Otherwise I would be interested in something like a combined 
mask of BA44 and BA45 as representing IFG.


Also, is it possible to do something like TFCE or fdr correction within a 
region like this within palm as that would reduce the area I am looking over 
for an effect and reduce the cluster size needed compared to a whole brain 
analysis?


Thank you,

Michael


From: Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Sent: Monday, September 26, 2016 2:18:26 PM
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

Is there a surface-based map of this task contrast somewhere that I could look 
at?  Without that I would just be guessing…

Peace,

Matt.

From: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Monday, September 26, 2016 at 1:13 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.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 from Cifti Data


Hi Matt, I'm interested in using part of your parcellation to look at response 
inhibition on a go/nogo task. Do you have a sense of which region in your 
parcellation corresponds best to the part of inferior frontal gyrus typically 
implemented in successful nogo response inhibition, and how I could isolate 
that parcel to do an anlysis?


Thank you,

Michael


From: Glasser, 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 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 HCP’s multi-modal parcellation is available here:

https://balsa.wustl.edu/study/show/RVVG<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_study_show_RVVG=DQMF-g=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=41tIMVdkyw4FbaKBCuAemq30kaX7FtpSn1fT4mnNgb4=LSobQp1e_k82tOjzxrgaFuayanqOIOB0FPCI128My64=>

Also, the HCP’s task analysis pipeline will allow you to parcellate before 
fitting the GLM, rather than afterwards to get the addition SNR benefits from 
averaging across a parcel.

Peace,

Matt.

From: 

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

Hi Matt, I'm interested in using part of your parcellation to look at response 
inhibition on a go/nogo task. Do you have a sense of which region in your 
parcellation corresponds best to the part of inferior frontal gyrus typically 
implemented in successful nogo response inhibition, and how I 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] 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 HCP’s multi-modal parcellation is available here:

https://balsa.wustl.edu/study/show/RVVG<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_study_show_RVVG=DQMF-g=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=41tIMVdkyw4FbaKBCuAemq30kaX7FtpSn1fT4mnNgb4=LSobQp1e_k82tOjzxrgaFuayanqOIOB0FPCI128My64=>

Also, the HCP’s task analysis pipeline will allow you to parcellate before 
fitting the GLM, rather than afterwards to get the addition SNR benefits from 
averaging across a parcel.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@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 how to use this, possibly? I have been 
trying to figure these out, but there are a lot of options and  I am just not 
able to decipher how to use these from the help page alone. The errors I am 
getting also do not clarify what I need to do to get the output I am looking 
for.

Before using this kind of multi-band data I had been using afni. To give an 
example of what I would want to do in terms of afni commands (if that’s any 
help), I would have saved all ROIs and then used 3dmaskave to extract mean beta 
weights for a given GLM beta for each subject and then I would relate those 
beta weights so subject’s behavior in R or another stats package.

Definitely agree that there’s not much meaning to a peak coordinate per se. I’m 
just trying to figure out how to report the clusters I am finding. In previous 
reports we would typically focus on broadmann areas or more general regional 
nomenclature (i.e. vmPFC, mid temporal lobe, etc.). Some of the clusters I’m 
finding also cover large areas from motor to visual cortex, so I am trying to 
consider good ways to report that.

At this point I would prefer to use TFCE or some other 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 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:


On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:

Thank you,


How can I turn the ROIs into a label file?

You can use -cifti-find-clusters if you just want spatial contiguity to define 
where ROIs should be considered separate, then use -cifti-label-import to make 
them into a dlabel file.

Also, how can I simply get a list of the ROIs with some information like 
cluster extent and peak voxel to be able to identify what part(s) of the brain 
each ROI is covering?

A single coordinate isn't a faithful representation of the cluster.  You can 
make a figure showing the clusters displayed on the brain (for instance, choose 
two of: beta maps, significance outlines, area outlines), and hopefully also 
provide the unthresholded beta and z maps for others to use.

You can get cluster extent info with -cifti-weighted-stats.

If the question you want to ask is "which areas are involved", you could do a 
parcellated analysis instead of a cluster analysis.

Thank you,

Michael


From: Timothy Coalson <tsc...@mst.edu<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>
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 y

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

I should probably rephrase some of -cifti-label-import help.  When it says:

"The label list file must have lines of the following format:

  
  "

It means 2 lines per label: the first line is the label name, the second
line is the numeric stuff, where  is an integer that you will find in
the data file you are importing to label.

If you don't need to assign names to your labels, just specify '' as the
filename - a pair of quotes with nothing inside them (double quotes will
also work) - quoting from the help:

"You may specify the empty string ('' will work on linux/mac) for
, which will be treated as if it is an empty file."

Then it will just assign names based on what value it found in the file
being imported:

"By default, it will set new label names with names of LABEL_# for any
values encountered that are not mentioned in the list file, specify
-discard-others to instead set these to the "unlabeled" key."

You do want these imported, rather than zeroed out, so you don't want to
use -discard-others.

Tim



On Tue, Sep 20, 2016 at 3:00 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> Thank you, I was using a bad input file. The command works now.
>
> for -cifti-label-import however, I am no sure how the label file is
> supposed to look. I get a malformed error:
>
> ERROR: label list file is malformed for entry #1: test 255 255 255 255
>
> I have 4 cortical and 1 subcortical ROIs which are colored differently on
> viewing, but the cifti file contains only 1 map.
>
> Ultimately I’d like to be able to identify and extract beta weights from
> each.
>
> Thank you,
> Michael
>
> On Sep 20, 2016, at 2:26 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> What does the input data look like?
>
> Peace,
>
> Matt.
>
> From: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>
> Date: Tuesday, September 20, 2016 at 1:22 PM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "Michael F.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_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 HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.
> surf.gii
>
> Where now I am using these 900 subject average files as templates. I
> though the -left-surface it was looking for was with the statistics run
>
> The output of this is null, however. Nothing shows up on wb_view and
> -file-information gives:
>
> Map   Minimum   MaximumMean   Sample Dev   % Positive   % Negative
> Inf/NaN   Map Name
>   1 0.000 0.000   0.0000.0000.0000.000
> 0   #1
>
> Am I doing something wrong still?
>
> Thanks,
> Michael
>
>
> On Sep 20, 2016, at 1:59 PM, Glasser, Matthew <glass...@wustl.edu> wrote:
>
> Presumably you have some of these if you have gotten this far?
>
>
>
>
> --
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
>
>

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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

Thank you, I was using a bad input file. The command works now.

for -cifti-label-import however, I am no sure how the label file is supposed to 
look. I get a malformed error:

ERROR: label list file is malformed for entry #1: test 255 255 255 255

I have 4 cortical and 1 subcortical ROIs which are colored differently on 
viewing, but the cifti file contains only 1 map.

Ultimately I’d like to be able to identify and extract beta weights from each.

Thank you,
Michael

On Sep 20, 2016, at 2:26 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

What does 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.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: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_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 
HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.surf.gii

Where now I am using these 900 subject average files as templates. I though the 
-left-surface it was looking for was with the statistics run

The output of this is null, however. Nothing shows up on wb_view and 
-file-information gives:

Map   Minimum   MaximumMean   Sample Dev   % Positive   % Negative   
Inf/NaN   Map Name
  1 0.000 0.000   0.0000.0000.0000.000 
0   #1

Am I doing something wrong still?

Thanks,
Michael


On Sep 20, 2016, at 1:59 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Presumably you have some of these if you have gotten this far?




The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.


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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Glasser, Matthew]

What does 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.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: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_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 
HCP_S900_GroupAvg_v1/S900.R.midthickness_MSMAll.32k_fs_LR.surf.gii

Where now I am using these 900 subject average files as templates. I though the 
-left-surface it was looking for was with the statistics run

The output of this is null, however. Nothing shows up on wb_view and 
-file-information gives:

Map   Minimum   MaximumMean   Sample Dev   % Positive   % Negative   
Inf/NaN   Map Name
  1 0.000 0.000   0.0000.0000.0000.000 
0   #1

Am I doing something wrong still?

Thanks,
Michael


On Sep 20, 2016, at 1:59 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:

Presumably you have some of these if you have gotten this far?



The materials in this message are private and may contain Protected Healthcare 
Information or other information of a sensitive nature. If you are not the 
intended recipient, be advised that any unauthorized use, disclosure, copying 
or the taking of any action in reliance on the contents of this information is 
strictly prohibited. If you have received this email in error, please 
immediately notify the sender via telephone or return mail.

___
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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

When I run


wb_command -cifti-find-clusters 
FoodNogo_results_merged_tfce_tstat_fwep.dscalar.nii 1 1 1 1 COLUMN 
FoodNogo_results_merged_tfce_tstat_fwep_ROIs.dscalar.nii


I get the error:

ERROR: left surface required but not provided


Then if I add the option:

-left-surface FoodNogo_results_L_cort_tfce_tstat_fwep.gii


I get

ERROR: Number of data arrays MUST be two in a SurfaceFile.


I understand that this is a metric file and not a surface file, but 1) I do not 
know how to convert it, and 2) all the information is contained within the 
cifti file anyway, so I am unsure what 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. Dreyfuss; 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: Tuesday, September 20, 2016 at 10:40 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.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 from Cifti Data


Thank you for this. We had explored this option in the past and two issues were 
1) there was not a parcellation readily available with subcortical structures 
and 2) I do not feel a need to constrain activation to parcels rather than 
swaths of signal as they appear to cluster themselves.


I'm sure parcellation is a valid approach, but I would really like to be able 
to simply report activation as it appears to cluster such as with TFCE, fdr or 
cluster thresholding (although that is less favored now) as has been typical in 
fMRI reporting. Are there examples available for these kinds of analysis to 
eventually relate activation to behavior or other measures?


I am grateful for all the help you have all provided. Things are quite close, 
and I hope to be able to be able to get through these last steps as quickly as 
possible.





From: Glasser, 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 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 HCP’s multi-modal parcellation is available here:

https://balsa.wustl.edu/study/show/RVVG<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_study_show_RVVG=DQMF-g=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=41tIMVdkyw4FbaKBCuAemq30kaX7FtpSn1fT4mnNgb4=LSobQp1e_k82tOjzxrgaFuayanqOIOB0FPCI128My64=>

Also, the HCP’s task analysis pipeline will allow you to parcellate before 
fitting the GLM, rather than afterwards to get the addition SNR benefits from 
averaging across a parcel.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@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 how to use this, possibly? I have been 
trying to figure these out, but there are a lot of options and  I am just not 
able to decipher how to use these from the help page alone. The errors I am 
getting also do not clarify what I need to do to get the output I am looking 
for.

Before using this kind of multi-band data I had been using afni. To give an 
example of what I would want to do in terms of afni commands (if that’s any 
help), I would have saved all ROIs and then used 3dmaskave to extract mean beta 
weights for a given GLM beta for each subject and then I would relate those 
beta weights so subject’s behavior in R or another stats package.

Definitely agree that there’s not much meaning to a peak coordinate 

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Glasser, Matthew]

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: Tuesday, September 20, 2016 at 10:40 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.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 from Cifti Data


Thank you for this. We had explored this option in the past and two issues were 
1) there was not a parcellation readily available with subcortical structures 
and 2) I do not feel a need to constrain activation to parcels rather than 
swaths of signal as they appear to cluster themselves.


I'm sure parcellation is a valid approach, but I would really like to be able 
to simply report activation as it appears to cluster such as with TFCE, fdr or 
cluster thresholding (although that is less favored now) as has been typical in 
fMRI reporting. Are there examples available for these kinds of analysis to 
eventually relate activation to behavior or other measures?


I am grateful for all the help you have all provided. Things are quite close, 
and I hope to be able to be able to get through these last steps as quickly as 
possible.





From: Glasser, 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 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 HCP’s multi-modal parcellation is available here:

https://balsa.wustl.edu/study/show/RVVG<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_study_show_RVVG=DQMF-g=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=41tIMVdkyw4FbaKBCuAemq30kaX7FtpSn1fT4mnNgb4=LSobQp1e_k82tOjzxrgaFuayanqOIOB0FPCI128My64=>

Also, the HCP’s task analysis pipeline will allow you to parcellate before 
fitting the GLM, rather than afterwards to get the addition SNR benefits from 
averaging across a parcel.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@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 how to use this, possibly? I have been 
trying to figure these out, but there are a lot of options and  I am just not 
able to decipher how to use these from the help page alone. The errors I am 
getting also do not clarify what I need to do to get the output I am looking 
for.

Before using this kind of multi-band data I had been using afni. To give an 
example of what I would want to do in terms of afni commands (if that’s any 
help), I would have saved all ROIs and then used 3dmaskave to extract mean beta 
weights for a given GLM beta for each subject and then I would relate those 
beta weights so subject’s behavior in R or another stats package.

Definitely agree that there’s not much meaning to a peak coordinate per se. I’m 
just trying to figure out how to report the clusters I am finding. In previous 
reports we would typically focus on broadmann areas or more general regional 
nomenclature (i.e. vmPFC, mid temporal lobe, etc.). Some of the clusters I’m 
finding also cover large areas from motor to visual cortex, so I am trying to 
consider good ways to report that.

At this point I would prefer to use TFCE or some other 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 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:


On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:

Thank you,


How can I turn the ROIs into a label file?

You can use -cifti-find-clusters if you just want spatial contiguity to define 
where ROIs should be considered separate, then use -cifti-label-import to

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Glasser, Matthew]

That makes sense if Z stats are not involved.

Matt.

From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>
Date: Tuesday, September 20, 2016 at 11:00 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "Michael F.W. 
Dreyfuss" <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@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 approach (e.g,. 
PALM) applied to GLM betas, then I wouldn’t expect it to make much difference 
in terms of power to detect an effect if you parcellate before fitting the 
Level 1 GLM, or if you simply average the betas from the dense maps within each 
parcel (and then use those average betas as input to the permutation testing).  
The latter approach would allow one to simply run -cifti-parcellate on the 
dense task maps that HCP has already pre-computed.

cheers,
-MH

--
Michael Harms, Ph.D.
---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mha...@wustl.edu<mailto:mha...@wustl.edu>

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Date: Tuesday, September 20, 2016 at 10:06 AM
To: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>, NEUROSCIENCE tim 
<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 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 HCP’s multi-modal parcellation is available here:

https://balsa.wustl.edu/study/show/RVVG

Also, the HCP’s task analysis pipeline will allow you to parcellate before 
fitting the GLM, rather than afterwards to get the addition SNR benefits from 
averaging across a parcel.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@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 how to use this, possibly? I have been 
trying to figure these out, but there are a lot of options and  I am just not 
able to decipher how to use these from the help page alone. The errors I am 
getting also do not clarify what I need to do to get the output I am looking 
for.

Before using this kind of multi-band data I had been using afni. To give an 
example of what I would want to do in terms of afni commands (if that’s any 
help), I would have saved all ROIs and then used 3dmaskave to extract mean beta 
weights for a given GLM beta for each subject and then I would relate those 
beta weights so subject’s behavior in R or another stats package.

Definitely agree that there’s not much meaning to a peak coordinate per se. I’m 
just trying to figure out how to report the clusters I am finding. In previous 
reports we would typically focus on broadmann areas or more general regional 
nomenclature (i.e. vmPFC, mid temporal lobe, etc.). Some of the clusters I’m 
finding also cover large areas from motor to visual cortex, so I am trying to 
consider good ways to report that.

At this point I would prefer to use TFCE or some other 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 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:


On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:

Thank you,


How can I turn the ROIs into a label file?

You can use -cifti-find-cluste

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Harms, Michael]

As an aside, if the end-game of the analysis is a permutation approach (e.g,. PALM) applied to GLM betas, then I wouldn’t expect it to make much difference in terms of power to detect an effect if you parcellate before fitting the Level 1 GLM, or if you
 simply average the betas from the dense maps within each parcel (and then use those average betas as input to the permutation testing).  The latter approach would allow one to simply run -cifti-parcellate on the dense task maps that HCP has already pre-computed.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From: <hcp-users-boun...@humanconnectome.org> on behalf of "Glasser, Matthew" <glass...@wustl.edu>
Date: Tuesday, September 20, 2016 at 10:06 AM
To: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>, NEUROSCIENCE tim <tsc...@mst.edu>
Cc: "hcp-users@humanconnectome.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 HCP’s multi-modal parcellation is available here:


https://balsa.wustl.edu/study/show/RVVG  


Also, the HCP’s task analysis pipeline will allow you to parcellate before fitting the GLM, rather than afterwards to get the addition SNR benefits from averaging across a parcel.  


Peace,


Matt.




From: <hcp-users-boun...@humanconnectome.org> on behalf of "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson <tsc...@mst.edu>
Cc: "Michael F.W. Dreyfuss" <mid2...@med.cornell.edu>, "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] ROIs and Betas from Cifti Data





Thank you,


Are there any examples available for how to use this, possibly? I have been trying to figure these out, but there are a lot of options and  I am just not able to decipher how to use these from the help page alone. The errors I am getting also
 do not clarify what I need to do to get the output I am looking for.


Before using this kind of multi-band data I had been using afni. To give an example of what I would want to do in terms of afni commands (if that’s any help), I would have saved all ROIs and then used 3dmaskave to extract mean beta weights for
 a given GLM beta for each subject and then I would relate those beta weights so subject’s behavior in R or another stats package. 


Definitely agree that there’s not much meaning to a peak coordinate per se. I’m just trying to figure out how to report the clusters I am finding. In previous reports we would typically focus on broadmann areas or more general regional nomenclature
 (i.e. vmPFC, mid temporal lobe, etc.). Some of the clusters I’m finding also cover large areas from motor to visual cortex, so I am trying to consider good ways to report that.


At this point I would prefer to use TFCE or some other 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 <tsc...@mst.edu> wrote:




On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu> wrote:



Thank you,


How can I turn the ROIs into a label file?



You can use -cifti-find-clusters if you just want spatial contiguity to define where ROIs should be considered separate, then use -cifti-label-import to make them into a dlabel file.



Also, how can I simply get a list of the ROIs with some information like cluster extent and peak voxel to be able to identify what part(s) of the brain each ROI is covering?



A single coordinate isn't a faithful representation of the cluster.  You can make a figure showing the clusters displayed on the brain (for instance, choose two of: beta maps, significance outlines, area outlines), and hopefully also provide the
 unthresholded beta and z maps for others to use.


You can get cluster extent info with -cifti-weighted-stats.


If the question you want to ask is "which areas are involved", you could do a parcellated analysis instead of a cluster analysis.



Thank you,
Michael


From: 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_co

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

Thank you for this. We had explored this option in the past and two issues were 
1) there was not a parcellation readily available with subcortical structures 
and 2) I do not feel a need to constrain activation to parcels rather than 
swaths of signal as they appear to cluster themselves.


I'm sure parcellation is a valid approach, but I would really like to be able 
to simply report activation as it appears to cluster such as with TFCE, fdr or 
cluster thresholding (although that is less favored now) as has been typical in 
fMRI reporting. Are there examples available for these kinds of analysis to 
eventually relate activation to behavior or other measures?


I am grateful for all the help you have all provided. Things are quite close, 
and I hope to be able to be able to get through these last steps as quickly as 
possible.





From: Glasser, 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 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 HCP’s multi-modal parcellation is available here:

https://balsa.wustl.edu/study/show/RVVG<https://urldefense.proofpoint.com/v2/url?u=https-3A__balsa.wustl.edu_study_show_RVVG=DQMF-g=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=41tIMVdkyw4FbaKBCuAemq30kaX7FtpSn1fT4mnNgb4=LSobQp1e_k82tOjzxrgaFuayanqOIOB0FPCI128My64=>

Also, the HCP’s task analysis pipeline will allow you to parcellate before 
fitting the GLM, rather than afterwards to get the addition SNR benefits from 
averaging across a parcel.

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>>
Date: Monday, September 19, 2016 at 9:40 PM
To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: "Michael F.W. Dreyfuss" 
<mid2...@med.cornell.edu<mailto:mid2...@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 how to use this, possibly? I have been 
trying to figure these out, but there are a lot of options and  I am just not 
able to decipher how to use these from the help page alone. The errors I am 
getting also do not clarify what I need to do to get the output I am looking 
for.

Before using this kind of multi-band data I had been using afni. To give an 
example of what I would want to do in terms of afni commands (if that’s any 
help), I would have saved all ROIs and then used 3dmaskave to extract mean beta 
weights for a given GLM beta for each subject and then I would relate those 
beta weights so subject’s behavior in R or another stats package.

Definitely agree that there’s not much meaning to a peak coordinate per se. I’m 
just trying to figure out how to report the clusters I am finding. In previous 
reports we would typically focus on broadmann areas or more general regional 
nomenclature (i.e. vmPFC, mid temporal lobe, etc.). Some of the clusters I’m 
finding also cover large areas from motor to visual cortex, so I am trying to 
consider good ways to report that.

At this point I would prefer to use TFCE or some other 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 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> wrote:


On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:

Thank you,


How can I turn the ROIs into a label file?

You can use -cifti-find-clusters if you just want spatial contiguity to define 
where ROIs should be considered separate, then use -cifti-label-import to make 
them into a dlabel file.

Also, how can I simply get a list of the ROIs with some information like 
cluster extent and peak voxel to be able to identify what part(s) of the brain 
each ROI is covering?

A single coordinate isn't a faithful representation of the cluster.  You can 
make a figure showing the clusters displayed on the brain (for instance, choose 
two of: beta maps, significance outlines, area outlines), and hopefully also 
provide the unthresholded beta and z maps for others to use.

You can get cluster extent info with -cifti-weighted-stats.

If the question you want to ask is "which

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

On Mon, Sep 19, 2016 at 4:51 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> Thank you,
>
>
> How can I turn the ROIs into a label file?
>
You can use -cifti-find-clusters if you just want spatial contiguity to
define where ROIs should be considered separate, then use
-cifti-label-import to make them into a dlabel file.

> Also, how can I simply get a list of the ROIs with some information like
> cluster extent and peak voxel to be able to identify what part(s) of the
> brain each ROI is covering?
>
A single coordinate isn't a faithful representation of the cluster.  You
can make a figure showing the clusters displayed on the brain (for
instance, choose two of: beta maps, significance outlines, area outlines),
and hopefully also provide the unthresholded beta and z maps for others to
use.

You can get cluster extent info with -cifti-weighted-stats.

If the question you want to ask is "which areas are involved", you could do
a parcellated analysis instead of a cluster analysis.

> Thank you,
>
> Michael
> --
> *From:* 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 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-parcellate to make a file where each parcel contains the answer for
> an ROI.
>
> Tim
>
>
> On Mon, Sep 19, 2016 at 3:26 PM, Michael F.W. Dreyfuss <
> mid2...@med.cornell.edu> wrote:
>
>> 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 those betas to behavior (offline). Are there simple ways to: 1)
>> identify regions implicated on the group level and 2) extract subject-level
>> beta weights from them, such as with wb_command?
>>
>>
>> Thank you,
>>
>> Michael
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers=DQMFaQ=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg=owdejnaklI6Db2XSiTgha_Wfo4am5eKBMJpc1pFzI1A=Ia4QB3ti2OENrr5FEZXT5gcngkIh2Yh34e_N0EOpfFI=>
>>
>
>

___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] ROIs and Betas from Cifti Data

[Michael F.W. Dreyfuss]

Thank you,


How can I turn the ROIs into a label file?


Also, how can I simply get a list of the ROIs with some information like 
cluster extent and peak voxel to be able to identify what part(s) of the brain 
each ROI is covering?


Thank you,

Michael


From: 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 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-parcellate to 
make a file where each parcel contains the answer for an ROI.

Tim


On Mon, Sep 19, 2016 at 3:26 PM, Michael F.W. Dreyfuss 
<mid2...@med.cornell.edu<mailto:mid2...@med.cornell.edu>> wrote:

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 those betas to behavior 
(offline). Are there simple ways to: 1) identify regions implicated on the 
group level and 2) extract subject-level beta weights from them, such as with 
wb_command?


Thank you,

Michael

___
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Re: [HCP-Users] ROIs and Betas from Cifti Data

[Timothy Coalson]

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-parcellate to make a file where each parcel contains the answer for
an ROI.

Tim


On Mon, Sep 19, 2016 at 3:26 PM, Michael F.W. Dreyfuss <
mid2...@med.cornell.edu> wrote:

> 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
> those betas to behavior (offline). Are there simple ways to: 1) identify
> regions implicated on the group level and 2) extract subject-level beta
> weights from them, such as with wb_command?
>
>
> Thank you,
>
> Michael
>
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