Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-27 Thread Timothy Coalson 
>
>>
>> --
>>
>> Michael Harms, Ph.D.
>>
>> ---
>>
>> Associate Professor of Psychiatry
>>
>> Washington University School of Medicine
>>
>> Department of Psychiatry, Box 8134
>>
>> 660 South Euclid Ave
>> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
>> Tel: 314-747-6173 <(314)%20747-6173>
>>
>> St. Louis, MO  63110  Email: mha...@wustl.edu
>>
>>
>>
>> *From: *Yassine Benhajali <yanama...@gmail.com>
>> *Date: *Tuesday, March 27, 2018 at 11:05 AM
>> *To: *"Harms, Michael" <mha...@wustl.edu>
>> *Cc: *NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users <
>> hcp-users@humanconnectome.org>
>>
>>
>> *Subject: *Re: [HCP-Users] Convert activation cifti data to volume nifti
>>
>>
>>
>> Ok, here te hole story behind what I try to achieve:
>>
>>
>>
>> - What I did?
>>
>> The surface maps you see on the figure is originally a volume based
>> activation maps that I mapped on surface. This map is generated from
>> unprocessed HCP data with our lab software NIAK
>> <http://niak.simexp-lab.org/>. My analysis consist of stacking volume
>> activation maps as vector of voxels, then correlate each subject vector
>> with the rest of the dataset to have a subject by subject correlation
>> matrix.
>>
>>
>>
>> - What I'm trying to do?
>>
>> My aim is to repeat the same process above but now with already computed
>> activation map from HCP pipeline. So i need a way to transform activation
>> surface map to a vector of voxels in order to correlate thse vector between
>> subjects.
>>
>>
>>
>> If you think that there is a way to correlate activation maps between
>> subject directly from surface, I would be happy to know how.
>>
>>
>>
>> Thanks
>>
>> Yassine
>>
>>
>>
>> Le mar. 27 mars 2018 à 10:04, Harms, Michael <mha...@wustl.edu> a écrit :
>>
>>
>>
>> For the surfaces, why not quantify the activation via the surface area,
>> rather than volume?
>>
>>
>>
>> Cheers,
>>
>> -MH
>>
>>
>>
>> --
>>
>> Michael Harms, Ph.D.
>>
>> ---
>>
>> Associate Professor of Psychiatry
>>
>> Washington University School of Medicine
>>
>> Department of Psychiatry, Box 8134
>>
>> 660 South Euclid Ave
>> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
>> Tel: 314-747-6173 <(314)%20747-6173>
>>
>> St. Louis, MO  63110  Email: mha...@wustl.edu
>>
>>
>>
>> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Yassine
>> Benhajali <yanama...@gmail.com>
>> *Date: *Tuesday, March 27, 2018 at 8:58 AM
>> *To: *NEUROSCIENCE tim <tsc...@mst.edu>
>> *Cc: *hcp-users <hcp-users@humanconnectome.org>
>> *Subject: *Re: [HCP-Users] Convert activation cifti data to volume nifti
>>
>>
>>
>> Thank you for your reply.
>>
>> I would like to extract the volume based activation maps from each
>> subject and put it as vector and do the same for each subject then stack
>> them all in one matrix like this figure. Then, I'll do some clustering on
>> that  stack.
>>
>> [image: age.png]
>>
>>
>>
>> If you have any hint on how to accomplish that without loosing the
>> benefit of surface based registration.
>>
>>
>>
>> Best,
>>
>> Yassine
>>
>>
>>
>> Le lun. 26 mars 2018 à 17:20, Timothy Coalson <tsc...@mst.edu> a écrit :
>>
>> For subcortical structures, it is as simple as wb_command -cifti-separate
>> using -volume-all.
>>
>>
>>
>> For surface data, you would need to map it back into volume, using that
>> subject's surfaces, thereby losing the advantages of surface registration
>> (for both analysis and display).  You would need to use -cifti-separate
>> with -metric, and then use -metric-to-volume-mapping.
>>
>>
>>
>> Why are you trying to do this?  We might have suggestions of other ways
>> to accomplish your task.
>>
>>
>>
>> Tim
>>
>>
>>
>>
>>
>> On Mon, Mar 26, 2018 at 12:37 PM, Yassine Benhajali <yanama...@gmail.com>
>> wrote:
>>
>> Hi all,

Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-27 Thread Yassine Benhajali 
Thank you!
Le mar. 27 mars 2018 à 14:15, Harms, Michael <mha...@wustl.edu> a écrit :

>
>
> That depends on which of the contrasts for the EMOTION you want to use.
> You can find a listing of them in the Contrasts.txt file.
>
>
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email: mha...@wustl.edu
>
>
>
> *From: *<hcp-users-boun...@humanconnectome.org> on behalf of Yassine
> Benhajali <yanama...@gmail.com>
> *Date: *Tuesday, March 27, 2018 at 12:08 PM
> *To: *"Harms, Michael" <mha...@wustl.edu>
>
>
> *Cc: *hcp-users <hcp-users@humanconnectome.org>
> *Subject: *Re: [HCP-Users] Convert activation cifti data to volume nifti
>
>
>
> Thank you for the clarification.
>
> Here is a tree structure of one subject folder
> "tfMRI_EMOTION_hp200_s2_level2.feat" , could you tell me which cope folder
> you are talking about? there is six of them, and which file to be read on
> matlab?
>
>
>
> .
>
> ├── 139435_tfMRI_EMOTION_level2_hp200_s2.dscalar.nii
>
> ├── Contrasts.txt
>
> ├── design.con
>
> ├── design_cov.png
>
> ├── design_cov.ppm
>
> ├── design.fsf
>
> ├── design.grp
>
> ├── design.mat
>
> ├── design.png
>
> ├── design.ppm
>
> └── GrayordinatesStats
>
> ├── cope1.feat
>
> │   ├── cope1.dtseries.nii
>
> │   ├── logfile
>
> │   ├── mask.dtseries.nii
>
> │   ├── mean_random_effects_var1.dtseries.nii
>
> │   ├── pe1.dtseries.nii
>
> │   ├── res4d.dtseries.nii
>
> │   ├── tdof_t1.dtseries.nii
>
> │   ├── tstat1.dtseries.nii
>
> │   ├── varcope1.dtseries.nii
>
> │   ├── weights1.dtseries.nii
>
> │   ├── zflame1lowertstat1.dtseries.nii
>
> │   ├── zflame1uppertstat1.dtseries.nii
>
> │   └── zstat1.dtseries.nii
>
> ├── cope2.feat
>
> │   ├── cope1.dtseries.nii
>
> │   ├── logfile
>
> │   ├── mask.dtseries.nii
>
> │   ├── mean_random_effects_var1.dtseries.nii
>
> │   ├── pe1.dtseries.nii
>
> │   ├── res4d.dtseries.nii
>
> │   ├── tdof_t1.dtseries.nii
>
> │   ├── tstat1.dtseries.nii
>
> │   ├── varcope1.dtseries.nii
>
> │   ├── weights1.dtseries.nii
>
> │   ├── zflame1lowertstat1.dtseries.nii
>
> │   ├── zflame1uppertstat1.dtseries.nii
>
> │   └── zstat1.dtseries.nii
>
> ├── cope3.feat
>
> │   ├── cope1.dtseries.nii
>
> │   ├── logfile
>
> │   ├── mask.dtseries.nii
>
> │   ├── mean_random_effects_var1.dtseries.nii
>
> │   ├── pe1.dtseries.nii
>
> │   ├── res4d.dtseries.nii
>
> │   ├── tdof_t1.dtseries.nii
>
> │   ├── tstat1.dtseries.nii
>
> │   ├── varcope1.dtseries.nii
>
> │   ├── weights1.dtseries.nii
>
> │   ├── zflame1lowertstat1.dtseries.nii
>
> │   ├── zflame1uppertstat1.dtseries.nii
>
> │   └── zstat1.dtseries.nii
>
> ├── cope4.feat
>
> │   ├── cope1.dtseries.nii
>
> │   ├── logfile
>
> │   ├── mask.dtseries.nii
>
> │   ├── mean_random_effects_var1.dtseries.nii
>
> │   ├── pe1.dtseries.nii
>
> │   ├── res4d.dtseries.nii
>
> │   ├── tdof_t1.dtseries.nii
>
> │   ├── tstat1.dtseries.nii
>
> │   ├── varcope1.dtseries.nii
>
> │   ├── weights1.dtseries.nii
>
> │   ├── zflame1lowertstat1.dtseries.nii
>
> │   ├── zflame1uppertstat1.dtseries.nii
>
> │   └── zstat1.dtseries.nii
>
> ├── cope5.feat
>
> │   ├── cope1.dtseries.nii
>
> │   ├── logfile
>
> │   ├── mask.dtseries.nii
>
> │   ├── mean_random_effects_var1.dtseries.nii
>
> │   ├── pe1.dtseries.nii
>
> │   ├── res4d.dtseries.nii
>
> │   ├── tdof_t1.dtseries.nii
>
> │   ├── tstat1.dtseries.nii
>
> │   ├── varcope1.dtseries.nii
>
> │   ├── weights1.dtseries.nii
>
> │   ├── zflame1lowertstat1.dtseries.nii
>
> │   ├── zflame1uppertstat1.dtseries.nii
>
> │   └── zstat1.dtseries.nii
>
> └── cope6.feat
>
> ├── cope1.dtseries.nii
>
> ├── logfile
>
> ├── mask.dtseries.nii
>
> ├── mean_random_effects_var1.dtserie

Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-27 Thread Harms, Michael 

That depends on which of the contrasts for the EMOTION you want to use.  You 
can find a listing of them in the Contrasts.txt file.


--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
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 Yassine Benhajali 
<yanama...@gmail.com>
Date: Tuesday, March 27, 2018 at 12:08 PM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Convert activation cifti data to volume nifti

Thank you for the clarification.
Here is a tree structure of one subject folder  
"tfMRI_EMOTION_hp200_s2_level2.feat" , could you tell me which cope folder you 
are talking about? there is six of them, and which file to be read on matlab?

.
├── 139435_tfMRI_EMOTION_level2_hp200_s2.dscalar.nii
├── Contrasts.txt
├── design.con
├── design_cov.png
├── design_cov.ppm
├── design.fsf
├── design.grp
├── design.mat
├── design.png
├── design.ppm
└── GrayordinatesStats
├── cope1.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope2.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope3.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope4.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope5.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
└── cope6.feat
├── cope1.dtseries.nii
├── logfile
├── mask.dtseries.nii
├── mean_random_effects_var1.dtseries.nii
├── pe1.dtseries.nii
├── res4d.dtseries.nii
├── tdof_t1.dtseries.nii
├── tstat1.dtseries.nii
├── varcope1.dtseries.nii
├── weights1.dtseries.nii
├── zflame1lowertstat1.dtseries.nii
├── zflame1uppertstat1.dtseries.nii
└── zstat1.dtseries.nii

 Cheers,
Yassine


Le mar. 27 mars 2018 à 12:18, Harms, Michael 
<mha...@wustl.edu<mailto:mha...@wustl.edu>> a écrit :

Certainly that can be done.  Take the beta (cope) maps from the CIFTI data, 
load them into (e.g., matlab), and correlate those vectors across subjects.  If 
you specifically want only the cortex, you’d need to exclude the subcortical 
voxels from the grayordinates.

There is no need to go back to voxels for what you are trying to do.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid 
Ave<https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.  
  Tel: 314-747-6173<tel:(314)%20747-6173>
St. Louis, MO  63110  Email: 
mha...@wustl.edu<mailto:mha...@wustl.edu>

From

Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-27 Thread Yassine Benhajali 
Thank you for the clarification.
Here is a tree structure of one subject folder
"tfMRI_EMOTION_hp200_s2_level2.feat" , could you tell me which cope folder
you are talking about? there is six of them, and which file to be read on
matlab?

.
├── 139435_tfMRI_EMOTION_level2_hp200_s2.dscalar.nii
├── Contrasts.txt
├── design.con
├── design_cov.png
├── design_cov.ppm
├── design.fsf
├── design.grp
├── design.mat
├── design.png
├── design.ppm
└── GrayordinatesStats
├── cope1.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope2.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope3.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope4.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
├── cope5.feat
│   ├── cope1.dtseries.nii
│   ├── logfile
│   ├── mask.dtseries.nii
│   ├── mean_random_effects_var1.dtseries.nii
│   ├── pe1.dtseries.nii
│   ├── res4d.dtseries.nii
│   ├── tdof_t1.dtseries.nii
│   ├── tstat1.dtseries.nii
│   ├── varcope1.dtseries.nii
│   ├── weights1.dtseries.nii
│   ├── zflame1lowertstat1.dtseries.nii
│   ├── zflame1uppertstat1.dtseries.nii
│   └── zstat1.dtseries.nii
└── cope6.feat
├── cope1.dtseries.nii
├── logfile
├── mask.dtseries.nii
├── mean_random_effects_var1.dtseries.nii
├── pe1.dtseries.nii
├── res4d.dtseries.nii
├── tdof_t1.dtseries.nii
├── tstat1.dtseries.nii
├── varcope1.dtseries.nii
├── weights1.dtseries.nii
├── zflame1lowertstat1.dtseries.nii
├── zflame1uppertstat1.dtseries.nii
└── zstat1.dtseries.nii

 Cheers,
Yassine


Le mar. 27 mars 2018 à 12:18, Harms, Michael <mha...@wustl.edu> a écrit :

>
>
> Certainly that can be done.  Take the beta (cope) maps from the CIFTI
> data, load them into (e.g., matlab), and correlate those vectors across
> subjects.  If you specifically want only the cortex, you’d need to exclude
> the subcortical voxels from the grayordinates.
>
>
>
> There is no need to go back to voxels for what you are trying to do.
>
>
>
> Cheers,
>
> -MH
>
>
>
> --
>
> Michael Harms, Ph.D.
>
> ---
>
> Associate Professor of Psychiatry
>
> Washington University School of Medicine
>
> Department of Psychiatry, Box 8134
>
> 660 South Euclid Ave
> <https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.
> Tel: 314-747-6173 <(314)%20747-6173>
>
> St. Louis, MO  63110  Email: mha...@wustl.edu
>
>
>
> *From: *Yassine Benhajali <yanama...@gmail.com>
> *Date: *Tuesday, March 27, 2018 at 11:05 AM
> *To: *"Harms, Michael" <mha...@wustl.edu>
> *Cc: *NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users <
> hcp-users@humanconnectome.org>
>
>
> *Subject: *Re: [HCP-Users] Convert activation cifti data to volume nifti
>
>
>
> Ok, here te hole story behind what I try to achieve:
>
>
>
> - What I did?
>
> The surface maps you see on the figure is originally a volume based
> activation maps that I mapped on surface. This map is generated from
> unprocessed HCP data with our lab software NIAK
> <http://niak.simexp-lab.

Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-27 Thread Harms, Michael 

Certainly that can be done.  Take the beta (cope) maps from the CIFTI data, 
load them into (e.g., matlab), and correlate those vectors across subjects.  If 
you specifically want only the cortex, you’d need to exclude the subcortical 
voxels from the grayordinates.

There is no need to go back to voxels for what you are trying to do.

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
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: Yassine Benhajali <yanama...@gmail.com>
Date: Tuesday, March 27, 2018 at 11:05 AM
To: "Harms, Michael" <mha...@wustl.edu>
Cc: NEUROSCIENCE tim <tsc...@mst.edu>, hcp-users <hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] Convert activation cifti data to volume nifti

Ok, here te hole story behind what I try to achieve:

- What I did?
The surface maps you see on the figure is originally a volume based activation 
maps that I mapped on surface. This map is generated from unprocessed HCP data 
with our lab software NIAK<http://niak.simexp-lab.org/>. My analysis consist of 
stacking volume activation maps as vector of voxels, then correlate each 
subject vector with the rest of the dataset to have a subject by subject 
correlation matrix.

- What I'm trying to do?
My aim is to repeat the same process above but now with already computed 
activation map from HCP pipeline. So i need a way to transform activation 
surface map to a vector of voxels in order to correlate thse vector between 
subjects.

If you think that there is a way to correlate activation maps between subject 
directly from surface, I would be happy to know how.

Thanks
Yassine

Le mar. 27 mars 2018 à 10:04, Harms, Michael 
<mha...@wustl.edu<mailto:mha...@wustl.edu>> a écrit :

For the surfaces, why not quantify the activation via the surface area, rather 
than volume?

Cheers,
-MH

--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid 
Ave<https://maps.google.com/?q=660+South+Euclid+Ave=gmail=g>.  
  Tel: 314-747-6173<tel:(314)%20747-6173>
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 Yassine Benhajali 
<yanama...@gmail.com<mailto:yanama...@gmail.com>>
Date: Tuesday, March 27, 2018 at 8:58 AM
To: NEUROSCIENCE tim <tsc...@mst.edu<mailto:tsc...@mst.edu>>
Cc: hcp-users 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] Convert activation cifti data to volume nifti

Thank you for your reply.
I would like to extract the volume based activation maps from each subject and 
put it as vector and do the same for each subject then stack them all in one 
matrix like this figure. Then, I'll do some clustering on that  stack.
[age.png]

If you have any hint on how to accomplish that without loosing the benefit of 
surface based registration.

Best,
Yassine

Le lun. 26 mars 2018 à 17:20, Timothy Coalson 
<tsc...@mst.edu<mailto:tsc...@mst.edu>> a écrit :
For subcortical structures, it is as simple as wb_command -cifti-separate using 
-volume-all.

For surface data, you would need to map it back into volume, using that 
subject's surfaces, thereby losing the advantages of surface registration (for 
both analysis and display).  You would need to use -cifti-separate with 
-metric, and then use -metric-to-volume-mapping.

Why are you trying to do this?  We might have suggestions of other ways to 
accomplish your task.

Tim


On Mon, Mar 26, 2018 at 12:37 PM, Yassine Benhajali 
<yanama...@gmail.com<mailto:yanama...@gmail.com>> wrote:
Hi all,
Any one knows how to extract activation volume in nifti from cifti file like 
this one : 
'139435/FMRI/fMRI_EMOTION/tfMRI_EMOTION_hp200_s4_level2.feat/139435_tfMRI_EMOTION_level2_hp200_s4.dscalar.nii'

Best,
Yassine
--
Yassine Benhajali
Doctorant en Neuroanthropologie
au Laboratoire SIMEXP - http://www.simexp-lab.org/members/
Université de Montréal, Québec, Canada
514 839 0501<tel:(514)%20839-0501>

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--
Yassine Benhajali
Doctorant en Neuroanthropologie
au Laboratoire SIMEXP - http://www.simexp-lab.org/members/
Université de Montréal, Québec, Canada
514 839 0501<tel:(514)%20839-0501>

__

Re: [HCP-Users] Convert activation cifti data to volume nifti

2018-03-26 Thread Timothy Coalson 
For subcortical structures, it is as simple as wb_command -cifti-separate
using -volume-all.

For surface data, you would need to map it back into volume, using that
subject's surfaces, thereby losing the advantages of surface registration
(for both analysis and display).  You would need to use -cifti-separate
with -metric, and then use -metric-to-volume-mapping.

Why are you trying to do this?  We might have suggestions of other ways to
accomplish your task.

Tim


On Mon, Mar 26, 2018 at 12:37 PM, Yassine Benhajali 
wrote:

> Hi all,
> Any one knows how to extract activation volume in nifti from cifti file
> like this one : '139435/FMRI/fMRI_EMOTION/tfMRI_EMOTION_hp200_s4_level2.
> feat/139435_tfMRI_EMOTION_level2_hp200_s4.dscalar.nii'
>
> Best,
> Yassine
> --
> Yassine Benhajali
> Doctorant en Neuroanthropologie
> au Laboratoire SIMEXP - http://www.simexp-lab.org/members/
> Université de Montréal, Québec, Canada
> 514 839 0501 <(514)%20839-0501>
>
> ___
> HCP-Users mailing list
> HCP-Users@humanconnectome.org
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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[HCP-Users] Convert activation cifti data to volume nifti

2018-03-26 Thread Yassine Benhajali 
Hi all,
Any one knows how to extract activation volume in nifti from cifti file
like this one :
'139435/FMRI/fMRI_EMOTION/tfMRI_EMOTION_hp200_s4_level2.feat/139435_tfMRI_EMOTION_level2_hp200_s4.dscalar.nii'

Best,
Yassine
-- 
Yassine Benhajali
Doctorant en Neuroanthropologie
au Laboratoire SIMEXP - http://www.simexp-lab.org/members/
Université de Montréal, Québec, Canada
514 839 0501

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