Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?

[Xavier Guell Paradis]

Thank you very much!

From: Timothy Coalson [tsc...@mst.edu]
Sent: Friday, May 05, 2017 4:58 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum 
values?

The command to do this is -cifti-separate with the -volume option and -roi 
suboption, and the CEREBELLUM_LEFT and CEREBELLUM_RIGHT structures (we don't 
use the CEREBELLUM label in the volume, instead we split the hemispheres), 
however, it always outputs the data from the requested structure also, so you 
don't want to run it on a dconn (especially not for volume structures).  
Instead, run it on any dscalar or small dtseries file you have lying around 
that uses the same dense mapping (or use -cifti-reduce to make one from the 
dconn).  Alternatively, if you are using a standard grayordinate space, you can 
extract the cerebellum halves from the volume label file in the Pipelines 
repository that defines the grayordinate voxels, with -volume-label-to-roi, 
like this:

wb_command -volume-label-to-roi 
Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz 
cerebellum_left_roi.nii.gz -name CEREBELLUM_LEFT
wb_command -volume-label-to-roi 
Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz 
cerebellum_right_roi.nii.gz -name CEREBELLUM_RIGHT

Since either way of getting these ROIs has the halves separate, you then need 
to combine them with -volume-math:

wb_command -volume-math 'x || y' cerebellum_all_roi.nii.gz -var x 
cerebellum_left_roi.nii.gz -var y cerebellum_right_roi.nii.gz

Tim


On Fri, May 5, 2017 at 3:42 PM, Xavier Guell Paradis 
> wrote:
Thank you for your reply.
Runing -cifti-restrict-dense-map again with ROW direction has worked; now I see 
cerebellum data only. However, I think it would be "cleaner" to do as you 
suggested and "get the ROI of where cerebellum data exists from the cifti 
file". How could I do this?
Thank you very much,
Xavier.

From: Timothy Coalson [tsc...@mst.edu]
Sent: Friday, May 05, 2017 4:32 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum 
values?

On Fri, May 5, 2017 at 3:09 PM, Xavier Guell Paradis 
> wrote:
Dear HCP experts,
I am trying to modify the group average dconn file 
(HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it only 
includes data from the cerebellum (even though, of course, these data will 
correspond to the connectivity of each cerebellum voxel to the rest of the 
brain).
I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile -vol-roi 
cerebellumatlas.nii
("cerebellumatlas.nii" is a cerebellum volume atlas which contains values for 
the cerebellum only)
This has not worked.

That should work, but you need to run it again on the output of that, this time 
with the ROW direction, so that both directions are cerebellum-only.  Please be 
more specific than "has not worked", did you get an error (and if so, copy the 
error message), or did its output not match what you expected?

I have also tried to use the -cerebellum-roi option of 
-cifti-restrict-dense-map, without writing any metric file after 
-cerebellum-roi. This also doesn't work.

This should have caused an error, as the current grayordinates space doesn't 
use surfaces for cerebellum.  Additionally, if you don't provide a required 
argument to an option, you will get a different kind of error.

Is there any way to tell wb_command that I only want to keep the cerebellar 
data, without having to include any file which indicates where the cerebellum 
is?

No, this isn't a use case we expected, normally we want to match existing cifti 
mappings (for instance, 91k grayordinates), not make new ones.  It is possible 
to get the ROI of where cerebellum data exists from the cifti file, but since 
you say you already have that ROI...on the other hand, if the specific error 
you got was something like "volume space doesn't match", then you actually 
should derive the ROI from the cifti file, rather than using whatever you have.

Thank you very much,
Xavier.

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Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?

[Timothy Coalson]

The command to do this is -cifti-separate with the -volume option and -roi
suboption, and the CEREBELLUM_LEFT and CEREBELLUM_RIGHT structures (we
don't use the CEREBELLUM label in the volume, instead we split the
hemispheres), however, it always outputs the data from the requested
structure also, so you don't want to run it on a dconn (especially not for
volume structures).  Instead, run it on any dscalar or small dtseries file
you have lying around that uses the same dense mapping (or use
-cifti-reduce to make one from the dconn).  Alternatively, if you are using
a standard grayordinate space, you can extract the cerebellum halves from
the volume label file in the Pipelines repository that defines the
grayordinate voxels, with -volume-label-to-roi, like this:

wb_command -volume-label-to-roi
Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz
cerebellum_left_roi.nii.gz -name CEREBELLUM_LEFT
wb_command -volume-label-to-roi
Pipelines/global/templates/91282_Greyordinates/Atlas_ROIs.2.nii.gz
cerebellum_right_roi.nii.gz -name CEREBELLUM_RIGHT

Since either way of getting these ROIs has the halves separate, you then
need to combine them with -volume-math:

wb_command -volume-math 'x || y' cerebellum_all_roi.nii.gz -var
x cerebellum_left_roi.nii.gz -var y cerebellum_right_roi.nii.gz

Tim


On Fri, May 5, 2017 at 3:42 PM, Xavier Guell Paradis 
wrote:

> Thank you for your reply.
> Runing -cifti-restrict-dense-map again with ROW direction has worked; now
> I see cerebellum data only. However, I think it would be "cleaner" to do as
> you suggested and "get the ROI of where cerebellum data exists from the
> cifti file". How could I do this?
> Thank you very much,
> Xavier.
> --
> *From:* Timothy Coalson [tsc...@mst.edu]
> *Sent:* Friday, May 05, 2017 4:32 PM
> *To:* Xavier Guell Paradis
> *Cc:* hcp-users@humanconnectome.org
> *Subject:* Re: [HCP-Users] modify dconn file so that it only includes
> cerebellum values?
>
> On Fri, May 5, 2017 at 3:09 PM, Xavier Guell Paradis 
> wrote:
>
>> Dear HCP experts,
>> I am trying to modify the group average dconn file
>> (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it
>> only includes data from the cerebellum (even though, of course, these data
>> will correspond to the connectivity of each cerebellum voxel to the rest of
>> the brain).
>> I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile
>> -vol-roi cerebellumatlas.nii
>> ("cerebellumatlas.nii" is a cerebellum volume atlas which contains values
>> for the cerebellum only)
>> This has not worked.
>>
>
> That should work, but you need to run it again on the output of that, this
> time with the ROW direction, so that both directions are cerebellum-only.
> Please be more specific than "has not worked", did you get an error (and if
> so, copy the error message), or did its output not match what you expected?
>
>>
>
>> I have also tried to use the -cerebellum-roi option of
>> -cifti-restrict-dense-map, without writing any metric file after
>> -cerebellum-roi. This also doesn't work.
>>
>
> This should have caused an error, as the current grayordinates space
> doesn't use surfaces for cerebellum.  Additionally, if you don't provide a
> required argument to an option, you will get a different kind of error.
>
> Is there any way to tell wb_command that I only want to keep the
>> cerebellar data, without having to include any file which indicates where
>> the cerebellum is?
>>
>
> No, this isn't a use case we expected, normally we want to match existing
> cifti mappings (for instance, 91k grayordinates), not make new ones.  It is
> possible to get the ROI of where cerebellum data exists from the cifti
> file, but since you say you already have that ROI...on the other hand, if
> the specific error you got was something like "volume space doesn't match",
> then you actually should derive the ROI from the cifti file, rather than
> using whatever you have.
>
>
>> Thank you very much,
>> Xavier.
>>
>> ___
>> HCP-Users mailing list
>> HCP-Users@humanconnectome.org
>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>
>
>

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Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?

[Xavier Guell Paradis]

Thank you for your reply.
Runing -cifti-restrict-dense-map again with ROW direction has worked; now I see 
cerebellum data only. However, I think it would be "cleaner" to do as you 
suggested and "get the ROI of where cerebellum data exists from the cifti 
file". How could I do this?
Thank you very much,
Xavier.

From: Timothy Coalson [tsc...@mst.edu]
Sent: Friday, May 05, 2017 4:32 PM
To: Xavier Guell Paradis
Cc: hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] modify dconn file so that it only includes cerebellum 
values?

On Fri, May 5, 2017 at 3:09 PM, Xavier Guell Paradis 
> wrote:
Dear HCP experts,
I am trying to modify the group average dconn file 
(HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it only 
includes data from the cerebellum (even though, of course, these data will 
correspond to the connectivity of each cerebellum voxel to the rest of the 
brain).
I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile -vol-roi 
cerebellumatlas.nii
("cerebellumatlas.nii" is a cerebellum volume atlas which contains values for 
the cerebellum only)
This has not worked.

That should work, but you need to run it again on the output of that, this time 
with the ROW direction, so that both directions are cerebellum-only.  Please be 
more specific than "has not worked", did you get an error (and if so, copy the 
error message), or did its output not match what you expected?

I have also tried to use the -cerebellum-roi option of 
-cifti-restrict-dense-map, without writing any metric file after 
-cerebellum-roi. This also doesn't work.

This should have caused an error, as the current grayordinates space doesn't 
use surfaces for cerebellum.  Additionally, if you don't provide a required 
argument to an option, you will get a different kind of error.

Is there any way to tell wb_command that I only want to keep the cerebellar 
data, without having to include any file which indicates where the cerebellum 
is?

No, this isn't a use case we expected, normally we want to match existing cifti 
mappings (for instance, 91k grayordinates), not make new ones.  It is possible 
to get the ROI of where cerebellum data exists from the cifti file, but since 
you say you already have that ROI...on the other hand, if the specific error 
you got was something like "volume space doesn't match", then you actually 
should derive the ROI from the cifti file, rather than using whatever you have.

Thank you very much,
Xavier.

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Re: [HCP-Users] modify dconn file so that it only includes cerebellum values?

[Timothy Coalson]

On Fri, May 5, 2017 at 3:09 PM, Xavier Guell Paradis 
wrote:

> Dear HCP experts,
> I am trying to modify the group average dconn file
> (HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it
> only includes data from the cerebellum (even though, of course, these data
> will correspond to the connectivity of each cerebellum voxel to the rest of
> the brain).
> I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile
> -vol-roi cerebellumatlas.nii
> ("cerebellumatlas.nii" is a cerebellum volume atlas which contains values
> for the cerebellum only)
> This has not worked.
>

That should work, but you need to run it again on the output of that, this
time with the ROW direction, so that both directions are cerebellum-only.
Please be more specific than "has not worked", did you get an error (and if
so, copy the error message), or did its output not match what you expected?

>

> I have also tried to use the -cerebellum-roi option of
> -cifti-restrict-dense-map, without writing any metric file after
> -cerebellum-roi. This also doesn't work.
>

This should have caused an error, as the current grayordinates space
doesn't use surfaces for cerebellum.  Additionally, if you don't provide a
required argument to an option, you will get a different kind of error.

Is there any way to tell wb_command that I only want to keep the cerebellar
> data, without having to include any file which indicates where the
> cerebellum is?
>

No, this isn't a use case we expected, normally we want to match existing
cifti mappings (for instance, 91k grayordinates), not make new ones.  It is
possible to get the ROI of where cerebellum data exists from the cifti
file, but since you say you already have that ROI...on the other hand, if
the specific error you got was something like "volume space doesn't match",
then you actually should derive the ROI from the cifti file, rather than
using whatever you have.


> Thank you very much,
> Xavier.
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] modify dconn file so that it only includes cerebellum values?

[Xavier Guell Paradis]

Dear HCP experts,
I am trying to modify the group average dconn file 
(HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii) so that it only 
includes data from the cerebellum (even though, of course, these data will 
correspond to the connectivity of each cerebellum voxel to the rest of the 
brain).
I have tried -cifti-restrict-dense-map inputfile COLUMN outputfile -vol-roi 
cerebellumatlas.nii
("cerebellumatlas.nii" is a cerebellum volume atlas which contains values for 
the cerebellum only)
This has not worked.
I have also tried to use the -cerebellum-roi option of 
-cifti-restrict-dense-map, without writing any metric file after 
-cerebellum-roi. This also doesn't work.

Is there any way to tell wb_command that I only want to keep the cerebellar 
data, without having to include any file which indicates where the cerebellum 
is?

Thank you very much,
Xavier.

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Re: [HCP-Users] hcp publications

[Elam, Jennifer]

Hi Joelle,

You can look here for a mostly up to date listing (especially of within 
consortium publications) of pubs that use HCP data or methods: 
https://wiki.humanconnectome.org/pages/viewpage.action?pageId=63504481




You can also search Pubmed for the grant number MH091657 and get a current list 
of most of them: https://www.ncbi.nlm.nih.gov/pubmed/?term=MH091657


Best,

Jenn

Jennifer Elam, Ph.D.
Scientific Outreach, Human Connectome Project
Washington University School of Medicine
Department of Neuroscience, Box 8108
660 South Euclid Avenue
St. Louis, MO 63110
314-362-9387
e...@wustl.edu
www.humanconnectome.org



From: hcp-users-boun...@humanconnectome.org 
 on behalf of Joelle Zimmermann 

Sent: Friday, May 5, 2017 11:39:48 AM
To: hcp-users@humanconnectome.org
Subject: [HCP-Users] hcp publications

Hi HCPers,

Is there a list out there of publications with HCP data ? I'm aware of the few 
main reference HCP publications, but looking beyond that...

Thanks,
Joelle

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[HCP-Users] regression of potentially confounding variables

[Joelle Zimmermann]

Hi HCPers,

My goal is to look at variability of SC and FC across subject... I was
wondering what would be recommended as regressors?

In Stephen Smith's Nature Neuroscience 2015 paper looking at FC and
cognition, the following was regressed:
1.
Acquisition reconstruction software version (as an improved MRI
reconstruction method was implemented in the third quarter of acquisition
year 1).
2.
A summary statistic quantifying average subject head motion during the
resting-state fMRI acquisitions (this is the average, across all
timepoints, of the timepoint-to-timepoint head motion, that measure being
the linear distance moved, averaged across the head).
3.
Weight.
4.
Height.
5.
Blood pressure – systolic.
6.
Blood pressure – diastolic.
7.
Hemoglobin A1C measured in blood.
8.
The cube-root of total brain volume (including ventricles), as estimated by
FreeSurfer.
9.
The cube-root of total intracranial volume, as estimated by FreeSurfer.

I'm thinking of going along those lines any thoughts?

Thanks,
Joelle

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[HCP-Users] hcp publications

[Joelle Zimmermann]

Hi HCPers,

Is there a list out there of publications with HCP data ? I'm aware of the
few main reference HCP publications, but looking beyond that...

Thanks,
Joelle

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