Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

[Timothy Coalson]

The -cifti-convert command is not the correct command to map volume-based
data onto surfaces, its purpose is to take existing cifti data and convert
it to formats that can be used to a limited extent in utilities that don't
read cifti files (for instance, making what we have referred to as "fake
nifti" files).

The central command needed to do what you want is
-volume-to-surface-mapping, but you need to have generated individual
subject surfaces and ensured they are properly aligned to your volume files
before you can use it for its intended purpose.

Tim


On Wed, Mar 28, 2018 at 3:56 PM, Glasser, Matthew 
wrote:

> I think you might need to contact the Petersen lab for support for their
> code.  If you have T1w, T2w, field map and fMRI you could use the HCP
> Pipelines to get CIFTI timeseries.  If you don’t, you might be able to use
> CIFTIFY, a beta tool for mapping legacy fMRI data to CIFTI by Erin Dickie:
>
> https://edickie.github.io/ciftify
>
> Peace,
>
> Matt.
>
> From: Boukhdhir Amal 
> Reply-To: Boukhdhir Amal 
> Date: Wednesday, March 28, 2018 at 3:51 PM
> To: Matt Glasser 
> Subject: Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)
>
> Hello,
>
> I have preprocessed volume data (4D Nifti) from the CoRR HNU data and I
> want to convert these volumes into surface data
> to be able to run a Matlab-based parcellation algorithm from Gordon et al,
> 2016 (Resources )
> which is based on Cifti time series.
>
> Resources
>
> 
>
> Your help is truly appreciated ! Thank you !
>
>
>
>
> Cordialement,
>
> *Amal Boukhdhir, étudiante Doctorat*
> Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
> (SIMEXP
> lab )
> CIUSSS du Centre-Est-de-l’Île-de-Montréal
> Bureau M6808
> 4565, Chemin Queen-Mary
> 
> Montréal (Québec)
> H3W 1W5
>
> Département d'informatique et de Recherche opérationnelle (Computer
> Vision & Geometric Modeling Lab 
> )
> Université de Montréal
> CP 6128 Succ centre-ville
> Montréal (Québec)
> H3C 3J7
> 
>
>
>
> Le mercredi 28 mars 2018 à 12:16:53 UTC-4, Glasser, Matthew <
> glass...@wustl.edu> a écrit :
>
>
> I would need to know more about your study to best assist you.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Boukhdhir Amal
> 
> Reply-To: Boukhdhir Amal 
> Date: Wednesday, March 28, 2018 at 11:07 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)
>
> Hello,
>
> I am trying to convert a nifti 4D volume to cifti format but this command
> does not provide a useful image:
> *./wb_command -cifti-convert -to-nifti  path_to_cifti path_to_nifti*
>
> Is it possible to have a CIFTI version inclusing cortical and subcortical
> areas ?  Any insights related to that please ?
>
>
>
>
> Best Regards,
>
> *Amal Boukhdhir, étudiante Doctorat*
> Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
> (SIMEXP
> lab )
> CIUSSS du Centre-Est-de-l’Île-de-Montréal
> Bureau M6808
> 4565, Chemin Queen-Mary
> 
> Montréal (Québec)
> H3W 1W5
>
> Département d'informatique et de Recherche opérationnelle (Computer
> Vision & Geometric Modeling Lab 
> )
> Université de Montréal
> CP 6128 Succ centre-ville
> Montréal (Québec)
> H3C 3J7
>
>
>
>
> Cordialement,
>
> *Amal Boukhdhir, étudiante Doctorat*
> Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
> (SIMEXP
> lab )
> CIUSSS du Centre-Est-de-l’Île-de-Montréal
> Bureau M6808
> 4565, Chemin Queen-Mary
> 
> Montréal (Québec)
> H3W 1W5
>
> Département d'informatique et de Recherche opérationnelle (Computer
> Vision & Geometric Modeling Lab 
> )
> Université de Montréal
> CP 6128 Succ centre-ville
> Montréal (Québec)
> H3C 3J7
> 
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

[Erin W. E. Dickie]

Hi Amal,

Good to hear from somebody from the SIMEXP lab! I think the functions in
ciftify might work well for your use case. I presented to your lab a little
about this last year.

Let me know if there is anything I can do to help.

Thanks,
Erin

On Wed, Mar 28, 2018 at 4:56 PM, Glasser, Matthew 
wrote:

> I think you might need to contact the Petersen lab for support for their
> code.  If you have T1w, T2w, field map and fMRI you could use the HCP
> Pipelines to get CIFTI timeseries.  If you don’t, you might be able to use
> CIFTIFY, a beta tool for mapping legacy fMRI data to CIFTI by Erin Dickie:
>
> https://edickie.github.io/ciftify
>
> Peace,
>
> Matt.
>
> From: Boukhdhir Amal 
> Reply-To: Boukhdhir Amal 
> Date: Wednesday, March 28, 2018 at 3:51 PM
> To: Matt Glasser 
> Subject: Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)
>
> Hello,
>
> I have preprocessed volume data (4D Nifti) from the CoRR HNU data and I
> want to convert these volumes into surface data
> to be able to run a Matlab-based parcellation algorithm from Gordon et al,
> 2016 (Resources )
> which is based on Cifti time series.
>
> Resources
>
> 
>
> Your help is truly appreciated ! Thank you !
>
>
>
>
> Cordialement,
>
> *Amal Boukhdhir, étudiante Doctorat*
> Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
> (SIMEXP
> lab )
> CIUSSS du Centre-Est-de-l’Île-de-Montréal
> Bureau M6808
> 4565, Chemin Queen-Mary
> 
> Montréal (Québec)
> H3W 1W5
>
> Département d'informatique et de Recherche opérationnelle (Computer
> Vision & Geometric Modeling Lab 
> )
> Université de Montréal
> CP 6128 Succ centre-ville
> Montréal (Québec)
> H3C 3J7
> 
>
>
>
> Le mercredi 28 mars 2018 à 12:16:53 UTC-4, Glasser, Matthew <
> glass...@wustl.edu> a écrit :
>
>
> I would need to know more about your study to best assist you.
>
> Peace,
>
> Matt.
>
> From:  on behalf of Boukhdhir Amal
> 
> Reply-To: Boukhdhir Amal 
> Date: Wednesday, March 28, 2018 at 11:07 AM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)
>
> Hello,
>
> I am trying to convert a nifti 4D volume to cifti format but this command
> does not provide a useful image:
> *./wb_command -cifti-convert -to-nifti  path_to_cifti path_to_nifti*
>
> Is it possible to have a CIFTI version inclusing cortical and subcortical
> areas ?  Any insights related to that please ?
>
>
>
>
> Best Regards,
>
> *Amal Boukhdhir, étudiante Doctorat*
> Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
> (SIMEXP
> lab )
> CIUSSS du Centre-Est-de-l’Île-de-Montréal
> Bureau M6808
> 4565, Chemin Queen-Mary
> 
> Montréal (Québec)
> H3W 1W5
>
> Département d'informatique et de Recherche opérationnelle (Computer
> Vision & Geometric Modeling Lab 
> )
> Université de Montréal
> CP 6128 Succ centre-ville
> Montréal (Québec)
> H3C 3J7
>
>
>
>
> Cordialement,
>
> *Amal Boukhdhir, étudiante Doctorat*
> Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
> (SIMEXP
> lab )
> CIUSSS du Centre-Est-de-l’Île-de-Montréal
> Bureau M6808
> 4565, Chemin Queen-Mary
> 
> Montréal (Québec)
> H3W 1W5
>
> Département d'informatique et de Recherche opérationnelle (Computer
> Vision & Geometric Modeling Lab 
> )
> Université de Montréal
> CP 6128 Succ centre-ville
> Montréal (Québec)
> H3C 3J7
> 
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

___
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Re: [HCP-Users] fMRISurface volume to surface mapping

[Timothy Coalson]

This is a little tricky, as v1.2.3's wb_command -metric-to-volume-mapping
does not reduce the mapped values by their partial voxel volumes.  The
dev_latest build available here should do this reduction by default (with
an option for the old behavior):

http://brainvis.wustl.edu/workbench/

With this version, you can map a metric file of all 1's to the volume with
the ribbon mapping method, and the results will be the estimated cortical
partial volume of each voxel.

Note that we do not recommend routine use of a dev_latest version,
particularly for wb_view, as we may change new features before the release,
resulting in undesirable interaction between a dev_latest and an official
release (palette names may change, resulting in resetting to default
palettes, scenes saved from dev_latest may give errors in release versions,
etc).

If you want more detail about the per-vertex mapping, then even in v1.2.3,
the -volume-to-surface-mapping command has an -output-weights-text
suboption to the -ribbon-constrained option, which dumps the voxel weights
used for mapping to a text format.  The order of fields is vertex number,
then groups of 4 representing voxel ijk indices and the weight for that
voxel.  These are simply used in a weighted average.

Tim


On Wed, Mar 28, 2018 at 10:59 AM, Thomas Kirk 
wrote:

> Dear all,
>
> I am writing to ask about the “novel partial volume weighted ribbon
> constrained volume to surface mapping algorithm” mentioned in the Glasser
> 2013 paper (p120, fMRISurface section).
>
> I am currently working on a similar tool to estimate partial volumes
> within the voxels of the cortical surface and I would like to compare my
> method to this part of the pipeline. As I am not interested in applying
> partial volume correction at this stage I need to extract just the partial
> volume estimates from the pipeline, ie, pre-correction. Does anyone know
> how I could go about this?
>
> Thank you in anticipation
> Tom Kirk
>
> Institute of Biomedical Engineering,
> University of Oxford, UK
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

[Glasser, Matthew]

I think you might need to contact the Petersen lab for support for their code.  
If you have T1w, T2w, field map and fMRI you could use the HCP Pipelines to get 
CIFTI timeseries.  If you don’t, you might be able to use CIFTIFY, a beta tool 
for mapping legacy fMRI data to CIFTI by Erin Dickie:

https://edickie.github.io/ciftify

Peace,

Matt.

From: Boukhdhir Amal >
Reply-To: Boukhdhir Amal >
Date: Wednesday, March 28, 2018 at 3:51 PM
To: Matt Glasser >
Subject: Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

Hello,

I have preprocessed volume data (4D Nifti) from the CoRR HNU data and I want to 
convert these volumes into surface data
to be able to run a Matlab-based parcellation algorithm from Gordon et al, 2016 
(Resources) which is 
based on Cifti time series.



Resources




Your help is truly appreciated ! Thank you !




Cordialement,

Amal Boukhdhir, étudiante Doctorat
Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
(SIMEXP lab)
CIUSSS du Centre-Est-de-l’Île-de-Montréal
Bureau M6808
4565, Chemin Queen-Mary
Montréal (Québec)
H3W 1W5

Département d'informatique et de Recherche opérationnelle (Computer Vision & 
Geometric Modeling Lab)
Université de Montréal
CP 6128 Succ centre-ville
Montréal (Québec)
H3C 3J7




Le mercredi 28 mars 2018 à 12:16:53 UTC-4, Glasser, Matthew 
> a écrit :


I would need to know more about your study to best assist you.

Peace,

Matt.

From: 
>
 on behalf of Boukhdhir Amal 
>
Reply-To: Boukhdhir Amal >
Date: Wednesday, March 28, 2018 at 11:07 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

Hello,

I am trying to convert a nifti 4D volume to cifti format but this command does 
not provide a useful image:
./wb_command -cifti-convert -to-nifti  path_to_cifti path_to_nifti

Is it possible to have a CIFTI version inclusing cortical and subcortical areas 
?  Any insights related to that please ?




Best Regards,

Amal Boukhdhir, étudiante Doctorat
Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
(SIMEXP lab)
CIUSSS du Centre-Est-de-l’Île-de-Montréal
Bureau M6808
4565, Chemin Queen-Mary
Montréal (Québec)
H3W 1W5

Département d'informatique et de Recherche opérationnelle (Computer Vision & 
Geometric Modeling Lab)
Université de Montréal
CP 6128 Succ centre-ville
Montréal (Québec)
H3C 3J7




Cordialement,

Amal Boukhdhir, étudiante Doctorat
Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
(SIMEXP lab)
CIUSSS du Centre-Est-de-l’Île-de-Montréal
Bureau M6808
4565, Chemin Queen-Mary
Montréal (Québec)
H3W 1W5

Département d'informatique et de Recherche opérationnelle (Computer Vision & 
Geometric Modeling Lab)
Université de Montréal
CP 6128 Succ centre-ville
Montréal (Québec)
H3C 3J7



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[HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

[Boukhdhir Amal]

Hello, 
I am trying to convert a nifti 4D volume to cifti format but this command does 
not provide a useful image: ./wb_command -cifti-convert -to-nifti  
path_to_cifti path_to_nifti
Is it possible to have a CIFTI version inclusing cortical and subcortical areas 
?  Any insights related to that please ?




Best Regards,

Amal Boukhdhir, étudiante Doctorat 
Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
(SIMEXP lab)
CIUSSS du Centre-Est-de-l’Île-de-Montréal
Bureau M6808
4565, Chemin Queen-Mary
Montréal (Québec)
H3W 1W5

Département d'informatique et de Recherche opérationnelle (Computer Vision & 
Geometric Modeling Lab)
Université de Montréal
CP 6128 Succ centre-ville
Montréal (Québec)
H3C 3J7




Cordialement,

Amal Boukhdhir, étudiante Doctorat 
Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
(SIMEXP lab)
CIUSSS du Centre-Est-de-l’Île-de-Montréal
Bureau M6808
4565, Chemin Queen-Mary
Montréal (Québec)
H3W 1W5

Département d'informatique et de Recherche opérationnelle (Computer Vision & 
Geometric Modeling Lab)
Université de Montréal
CP 6128 Succ centre-ville
Montréal (Québec)
H3C 3J7



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Re: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

[Glasser, Matthew]

I would need to know more about your study to best assist you.

Peace,

Matt.

From: 
>
 on behalf of Boukhdhir Amal 
>
Reply-To: Boukhdhir Amal >
Date: Wednesday, March 28, 2018 at 11:07 AM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] Conversion from 4D data to Cifti (.dtseries.nii)

Hello,

I am trying to convert a nifti 4D volume to cifti format but this command does 
not provide a useful image:
./wb_command -cifti-convert -to-nifti  path_to_cifti path_to_nifti

Is it possible to have a CIFTI version inclusing cortical and subcortical areas 
?  Any insights related to that please ?




Best Regards,

Amal Boukhdhir, étudiante Doctorat
Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
(SIMEXP lab)
CIUSSS du Centre-Est-de-l’Île-de-Montréal
Bureau M6808
4565, Chemin Queen-Mary
Montréal (Québec)
H3W 1W5

Département d'informatique et de Recherche opérationnelle (Computer Vision & 
Geometric Modeling Lab)
Université de Montréal
CP 6128 Succ centre-ville
Montréal (Québec)
H3C 3J7




Cordialement,

Amal Boukhdhir, étudiante Doctorat
Centre de recherche de l’Institut Universitaire de gériatrie de Montréal 
(SIMEXP lab)
CIUSSS du Centre-Est-de-l’Île-de-Montréal
Bureau M6808
4565, Chemin Queen-Mary
Montréal (Québec)
H3W 1W5

Département d'informatique et de Recherche opérationnelle (Computer Vision & 
Geometric Modeling Lab)
Université de Montréal
CP 6128 Succ centre-ville
Montréal (Québec)
H3C 3J7



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[HCP-Users] fMRISurface volume to surface mapping

[Thomas Kirk]

Dear all, 

I am writing to ask about the “novel partial volume weighted ribbon constrained 
volume to surface mapping algorithm” mentioned in the Glasser 2013 paper (p120, 
fMRISurface section).

I am currently working on a similar tool to estimate partial volumes within the 
voxels of the cortical surface and I would like to compare my method to this 
part of the pipeline. As I am not interested in applying partial volume 
correction at this stage I need to extract just the partial volume estimates 
from the pipeline, ie, pre-correction. Does anyone know how I could go about 
this?

Thank you in anticipation 
Tom Kirk

Institute of Biomedical Engineering, 
University of Oxford, UK

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