[HCP-Users] MEG sensor location file

2017-03-19 Thread Parnesh Raniga 
Hi,

I am trying to run the megconnectome pipelines on the preprocessed MEG
datasets. The icamne pipeline for example requires the MEG sensor locations
(read using ft_read_sens) and I am not sure if this information is meant to
be in the raw data, the preprocessed data or somewhere else. Any help would
be much appreciated.

Regards,
Parnesh

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

[HCP-Users] reference surface file for probtrackx2

2017-03-19 Thread Govinda Surampudi 
Hi all, 
I am running tractography on single subject bedpostX preprocessed data to 
generate structural connectivity matrices of the brain.
I refered to https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide for running 
the command.
It says "When using surfaces, the user must set the surface coordinate 
convention and provide a surface reference volume." and " Use the browse button 
to locate a reference image (e.g., subject1.bedpostX/struct.nii.gz if seed 
space is structral space).".
However, I am not able to find a surface reference image in the single subject 
bedpostX preprocessed data downloaded from connctomeDB.
Could you explain briefly what a surface reference file is and where would I 
find one ?
Thanks a lot !
Regards,
Govinda 
 
___
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users

Re: [HCP-Users] reference surface file for probtrackx2

2017-03-19 Thread Glasser, Matthew 
The appropriate image to use is:

${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_1.25.nii.gz.

Peace,

Matt.

On 3/19/17, 10:53 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Govinda Surampudi"  wrote:

>Hi all,
>I am running tractography on single subject bedpostX preprocessed data to
>generate structural connectivity matrices of the brain.
>I refered to https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide for
>running the command.
>It says "When using surfaces, the user must set the surface coordinate
>convention and provide a surface reference volume." and " Use the browse
>button to locate a reference image (e.g., subject1.bedpostX/struct.nii.gz
>if seed space is structral space).".
>However, I am not able to find a surface reference image in the single
>subject bedpostX preprocessed data downloaded from connctomeDB.
>Could you explain briefly what a surface reference file is and where
>would I find one ?
>Thanks a lot !
>Regards,
>Govinda
>
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>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 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] reference surface file for probtrackx2

2017-03-19 Thread Elam, Jennifer 
Hi Govinda,

Thanks, Matt. That file is in the structural preprocessed package, if you don't 
already have it for the subject you are working on.


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 Glasser, Matthew 

Sent: Sunday, March 19, 2017 11:27:22 AM
To: Govinda Surampudi; hcp-users
Subject: Re: [HCP-Users] reference surface file for probtrackx2

The appropriate image to use is:

${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_1.25.nii.gz.

Peace,

Matt.

On 3/19/17, 10:53 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Govinda Surampudi"  wrote:

>Hi all,
>I am running tractography on single subject bedpostX preprocessed data to
>generate structural connectivity matrices of the brain.
>I refered to https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide for
>running the command.
>It says "When using surfaces, the user must set the surface coordinate
>convention and provide a surface reference volume." and " Use the browse
>button to locate a reference image (e.g., subject1.bedpostX/struct.nii.gz
>if seed space is structral space).".
>However, I am not able to find a surface reference image in the single
>subject bedpostX preprocessed data downloaded from connctomeDB.
>Could you explain briefly what a surface reference file is and where
>would I find one ?
>Thanks a lot !
>Regards,
>Govinda
>
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>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 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

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

Re: [HCP-Users] reference surface file for probtrackx2

2017-03-19 Thread Elam, Jennifer 
Sorry, it's the diffusion preprocessed package you need.


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: Elam, Jennifer
Sent: Sunday, March 19, 2017 11:49:06 AM
To: Glasser, Matthew; Govinda Surampudi; hcp-users
Subject: Re: [HCP-Users] reference surface file for probtrackx2


Hi Govinda,

Thanks, Matt. That file is in the structural preprocessed package, if you don't 
already have it for the subject you are working on.


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 Glasser, Matthew 

Sent: Sunday, March 19, 2017 11:27:22 AM
To: Govinda Surampudi; hcp-users
Subject: Re: [HCP-Users] reference surface file for probtrackx2

The appropriate image to use is:

${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_1.25.nii.gz.

Peace,

Matt.

On 3/19/17, 10:53 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Govinda Surampudi"  wrote:

>Hi all,
>I am running tractography on single subject bedpostX preprocessed data to
>generate structural connectivity matrices of the brain.
>I refered to https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide for
>running the command.
>It says "When using surfaces, the user must set the surface coordinate
>convention and provide a surface reference volume." and " Use the browse
>button to locate a reference image (e.g., subject1.bedpostX/struct.nii.gz
>if seed space is structral space).".
>However, I am not able to find a surface reference image in the single
>subject bedpostX preprocessed data downloaded from connctomeDB.
>Could you explain briefly what a surface reference file is and where
>would I find one ?
>Thanks a lot !
>Regards,
>Govinda
>
>___
>HCP-Users mailing list
>HCP-Users@humanconnectome.org
>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 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

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

Re: [HCP-Users] reference surface file for probtrackx2

2017-03-19 Thread Govinda Surampudi 
Thank you all for your support.

Regards,
Govinda

> On 19-Mar-2017, at 10:25 PM, Elam, Jennifer  wrote:
> 
> Sorry, it's the diffusion preprocessed package you need.
> 
> 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: Elam, Jennifer
> Sent: Sunday, March 19, 2017 11:49:06 AM
> To: Glasser, Matthew; Govinda Surampudi; hcp-users
> Subject: Re: [HCP-Users] reference surface file for probtrackx2
>  
> Hi Govinda,
> Thanks, Matt. That file is in the structural preprocessed package, if you 
> don't already have it for the subject you are working on.
> 
> 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 Glasser, Matthew 
> 
> Sent: Sunday, March 19, 2017 11:27:22 AM
> To: Govinda Surampudi; hcp-users
> Subject: Re: [HCP-Users] reference surface file for probtrackx2
>  
> The appropriate image to use is:
> 
> ${StudyFolder}/${Subject}/T1w/T1w_acpc_dc_restore_1.25.nii.gz.
> 
> Peace,
> 
> Matt.
> 
> On 3/19/17, 10:53 AM, "hcp-users-boun...@humanconnectome.org on behalf of
> Govinda Surampudi"  govinda.suramp...@research.iiit.ac.in> wrote:
> 
> >Hi all,
> >I am running tractography on single subject bedpostX preprocessed data to
> >generate structural connectivity matrices of the brain.
> >I refered to https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide for
> >running the command.
> >It says "When using surfaces, the user must set the surface coordinate
> >convention and provide a surface reference volume." and " Use the browse
> >button to locate a reference image (e.g., subject1.bedpostX/struct.nii.gz
> >if seed space is structral space).".
> >However, I am not able to find a surface reference image in the single
> >subject bedpostX preprocessed data downloaded from connctomeDB.
> >Could you explain briefly what a surface reference file is and where
> >would I find one ?
> >Thanks a lot !
> >Regards,
> >Govinda
> >
> >___
> >HCP-Users mailing list
> >HCP-Users@humanconnectome.org
> >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 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

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

Re: [HCP-Users] MEG sensor location file

2017-03-19 Thread Georgios Michalareas 
The sensor locations originally are in the raw data files of each scan 
so you can read them from there with ft_read_sens.

But they are also in the processed data in the field .grad in the data 
structure.

For the icamne pipeline and other processing pipelines you only need to 
define the raw data file locations as variables before running the 
pipelines and then the pipelines read the sensor locations from there.

Let me know if you still have issues
Best
Giorgos

On 3/19/2017 1:26 PM, Parnesh Raniga wrote:
> Hi,
>
> I am trying to run the megconnectome pipelines on the preprocessed MEG 
> datasets. The icamne pipeline for example requires the MEG sensor 
> locations (read using ft_read_sens) and I am not sure if this 
> information is meant to be in the raw data, the preprocessed data or 
> somewhere else. Any help would be much appreciated.
>
> Regards,
> Parnesh
>
> ___
> 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] MEG sensor location file

2017-03-19 Thread Parnesh Raniga 
Thanks Georgios,

I was hoping to avoid downloading the raw data files and have modified the
scripts to read the grad structure from the icaclass outputs. Seems to work
well but I will certainly ask if I have an issue. Thanks for the great
resource!

Cheers,
Parnesh

On 20 March 2017 at 15:47, Georgios Michalareas <
giorgos.michalar...@esi-frankfurt.de> wrote:

> The sensor locations originally are in the raw data files of each scan
> so you can read them from there with ft_read_sens.
>
> But they are also in the processed data in the field .grad in the data
> structure.
>
> For the icamne pipeline and other processing pipelines you only need to
> define the raw data file locations as variables before running the
> pipelines and then the pipelines read the sensor locations from there.
>
> Let me know if you still have issues
> Best
> Giorgos
>
> On 3/19/2017 1:26 PM, Parnesh Raniga wrote:
> > Hi,
> >
> > I am trying to run the megconnectome pipelines on the preprocessed MEG
> > datasets. The icamne pipeline for example requires the MEG sensor
> > locations (read using ft_read_sens) and I am not sure if this
> > information is meant to be in the raw data, the preprocessed data or
> > somewhere else. Any help would be much appreciated.
> >
> > Regards,
> > Parnesh
> >
> > ___
> > 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
>

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