Re: [HCP-Users] cifti-resample of 32K dconn to 4K dconn

2016-07-17 Thread Timothy Coalson
To clarify, the ADAP_BARY_AREA method requires either the -*-area-surfs or
-*-area-metrics options of each spheres option.  While they would proceed
if you gave the spheres for the area surfs options, it is not recommended
(you should use midthickness surfaces for individuals, and midthickness
vertex areas averaged across a group for group data).

I will add this to the help info.

Tim


On Sat, Jul 16, 2016 at 10:03 AM, Glasser, Matthew 
wrote:

> Hi Georgios,
>
> Looks like you asked for adaptive barycentric resampling without providing
> areas to use (the algorithm does not accept spherical surfaces to be the
> source of anatomical vertex areas).  Resampling a dense connectome would
> only be appropriate for tractography data.  For fMRI data, you want to
> average the timeseries prior to running functional connectivity at the
> lower resolution.
>
> Peace,
>
> Matt.
>
> On 7/16/16, 9:59 AM, "Georgios Michalareas"
>  wrote:
>
> >Thanks for the tip Matt.
> >
> >I ll stick to parcellations for comparing fMRI and MEG connectivity in
> >the practicals.
> >
> >But in any case , if one would want to do such a deconn resampling , do
> >you know what is the mistake(s)  I am doing in the command below?
> >
> >Thanks again
> >
> >Giorgos
> >
> >
> >On 7/16/2016 4:49 PM, Glasser, Matthew wrote:
> >> Hi Georgios,
> >>
> >> I would not recommend downsampling a dense connectome.  Instead it would
> >> be better to downsample the dense timeseries and then recompute the
> >>dense
> >> connectome.
> >>
> >> Peace,
> >>
> >> Matt.
> >>
> >> On 7/16/16, 9:47 AM, "hcp-users-boun...@humanconnectome.org on behalf
> of
> >> Georgios Michalareas"  >>of
> >> giorgos.michalar...@esi-frankfurt.de> wrote:
> >>
> >>> Hi everyone,
> >>>
> >>> i am trying for the MEG practicals to downsample a 32K dconn fMRI group
> >>> functional connectivity cifti:
> >>>
> >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
> >>>
> >>> into a dconn cifti in the 4K space that we use in the MEG analysis in
> >>>OT4.
> >>>
> >>> I am trying to use cifti-resample to do so. I know i have to use it
> >>> twice, once along COLUMN and then along ROW directions.
> >>>
> >>> However I am not sure how to set the cifti-resample input arguments
> >>> correctly.
> >>>
> >>>
> >>> I have the following files :
> >>>
> >>> Input functional connectivity file from fMRI in 32K space:
> >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
> >>>
> >>> Input Sphere Left (32K space): S900.L.sphere.32k_fs_LR.surf.gii
> >>>
> >>> Input Sphere Right (32K space): S900.R.sphere.32k_fs_LR.surf.gii
> >>>
> >>> Output Sphere Left (4K space): Sphere.4k.L.surf.gii
> >>>
> >>> Output Sphere Right (4K space): Sphere.4k.R.surf.gii
> >>>
> >>> I have a "template" (not sure if it is actually suitable for a
> >>>template)
> >>> dconn file in the 4K space, called testtemplate4K.dconn.nii. This is a
> >>> just a dconn file of functional connectivity computed directly from MEG
> >>> data in the 4K space.
> >>>
> >>> The issue is that the 32K functional connectivity matrix contains
> >>> connectivity between all vertices , in both left and right hemispheres
> >>> and i am not sure if such a connectivity file can be divided into left
> >>> and right. So this file is defined over both hemispheres.
> >>>
> >>> Then I have the input and output spaces defined with sphere files,
> >>> different for left and right hemispheres.
> >>>
> >>> After reading the description of cifti-resample I tried running the
> >>> following (with wb_command 1.2):
> >>>
> >>> wb_command -cifti-resample
> >>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii COLUMN
> >>> testtemplate4K.dconn.nii COLUMN ADAP_BARY_AREA CUBIC
> >>> testdconnresamp1.dconn.gii -left-spheres
> >>> S900.L.sphere.32k_fs_LR.surf.gii Sphere.4k.L.surf.gii -right-spheres
> >>> S900.R.sphere.32k_fs_LR.surf.gii Sphere.4k.R.surf.gii
> >>>
> >>> and i got the error:
> >>>
> >>> ERROR: left area data is missing
> >>>
> >>> I thought that the left area data is in the input dconn 32K dconn
> >>>cifti.
> >>>
> >>> Could you please have a look in the above command and advice on what i
> >>> am doing wrong?
> >>>
> >>> Thank you very much
> >>>
> >>> Best
> >>>
> >>> Giorgos
> >>>
> >>>
> >>>
> >>>
> >>> ---
> >>> This email has been checked for viruses by Avast antivirus software.
> >>> https://www.avast.com/antivirus
> >>>
> >>> ___
> >>> 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 

Re: [HCP-Users] cifti-resample of 32K dconn to 4K dconn

2016-07-16 Thread Georgios Michalareas
Thanks


On 7/16/2016 5:03 PM, Glasser, Matthew wrote:
> Hi Georgios,
>
> Looks like you asked for adaptive barycentric resampling without providing
> areas to use (the algorithm does not accept spherical surfaces to be the
> source of anatomical vertex areas).  Resampling a dense connectome would
> only be appropriate for tractography data.  For fMRI data, you want to
> average the timeseries prior to running functional connectivity at the
> lower resolution.
>
> Peace,
>
> Matt.
>
> On 7/16/16, 9:59 AM, "Georgios Michalareas"
>  wrote:
>
>> Thanks for the tip Matt.
>>
>> I ll stick to parcellations for comparing fMRI and MEG connectivity in
>> the practicals.
>>
>> But in any case , if one would want to do such a deconn resampling , do
>> you know what is the mistake(s)  I am doing in the command below?
>>
>> Thanks again
>>
>> Giorgos
>>
>>
>> On 7/16/2016 4:49 PM, Glasser, Matthew wrote:
>>> Hi Georgios,
>>>
>>> I would not recommend downsampling a dense connectome.  Instead it would
>>> be better to downsample the dense timeseries and then recompute the
>>> dense
>>> connectome.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> On 7/16/16, 9:47 AM, "hcp-users-boun...@humanconnectome.org on behalf of
>>> Georgios Michalareas" >> of
>>> giorgos.michalar...@esi-frankfurt.de> wrote:
>>>
 Hi everyone,

 i am trying for the MEG practicals to downsample a 32K dconn fMRI group
 functional connectivity cifti:

 HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii

 into a dconn cifti in the 4K space that we use in the MEG analysis in
 OT4.

 I am trying to use cifti-resample to do so. I know i have to use it
 twice, once along COLUMN and then along ROW directions.

 However I am not sure how to set the cifti-resample input arguments
 correctly.


 I have the following files :

 Input functional connectivity file from fMRI in 32K space:
 HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii

 Input Sphere Left (32K space): S900.L.sphere.32k_fs_LR.surf.gii

 Input Sphere Right (32K space): S900.R.sphere.32k_fs_LR.surf.gii

 Output Sphere Left (4K space): Sphere.4k.L.surf.gii

 Output Sphere Right (4K space): Sphere.4k.R.surf.gii

 I have a "template" (not sure if it is actually suitable for a
 template)
 dconn file in the 4K space, called testtemplate4K.dconn.nii. This is a
 just a dconn file of functional connectivity computed directly from MEG
 data in the 4K space.

 The issue is that the 32K functional connectivity matrix contains
 connectivity between all vertices , in both left and right hemispheres
 and i am not sure if such a connectivity file can be divided into left
 and right. So this file is defined over both hemispheres.

 Then I have the input and output spaces defined with sphere files,
 different for left and right hemispheres.

 After reading the description of cifti-resample I tried running the
 following (with wb_command 1.2):

 wb_command -cifti-resample
 HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii COLUMN
 testtemplate4K.dconn.nii COLUMN ADAP_BARY_AREA CUBIC
 testdconnresamp1.dconn.gii -left-spheres
 S900.L.sphere.32k_fs_LR.surf.gii Sphere.4k.L.surf.gii -right-spheres
 S900.R.sphere.32k_fs_LR.surf.gii Sphere.4k.R.surf.gii

 and i got the error:

 ERROR: left area data is missing

 I thought that the left area data is in the input dconn 32K dconn
 cifti.

 Could you please have a look in the above command and advice on what i
 am doing wrong?

 Thank you very much

 Best

 Giorgos




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>>> 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
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>
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> 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 

Re: [HCP-Users] cifti-resample of 32K dconn to 4K dconn

2016-07-16 Thread Glasser, Matthew
Hi Georgios,

Looks like you asked for adaptive barycentric resampling without providing
areas to use (the algorithm does not accept spherical surfaces to be the
source of anatomical vertex areas).  Resampling a dense connectome would
only be appropriate for tractography data.  For fMRI data, you want to
average the timeseries prior to running functional connectivity at the
lower resolution.

Peace,

Matt.

On 7/16/16, 9:59 AM, "Georgios Michalareas"
 wrote:

>Thanks for the tip Matt.
>
>I ll stick to parcellations for comparing fMRI and MEG connectivity in
>the practicals.
>
>But in any case , if one would want to do such a deconn resampling , do
>you know what is the mistake(s)  I am doing in the command below?
>
>Thanks again
>
>Giorgos
>
>
>On 7/16/2016 4:49 PM, Glasser, Matthew wrote:
>> Hi Georgios,
>>
>> I would not recommend downsampling a dense connectome.  Instead it would
>> be better to downsample the dense timeseries and then recompute the
>>dense
>> connectome.
>>
>> Peace,
>>
>> Matt.
>>
>> On 7/16/16, 9:47 AM, "hcp-users-boun...@humanconnectome.org on behalf of
>> Georgios Michalareas" >of
>> giorgos.michalar...@esi-frankfurt.de> wrote:
>>
>>> Hi everyone,
>>>
>>> i am trying for the MEG practicals to downsample a 32K dconn fMRI group
>>> functional connectivity cifti:
>>>
>>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
>>>
>>> into a dconn cifti in the 4K space that we use in the MEG analysis in
>>>OT4.
>>>
>>> I am trying to use cifti-resample to do so. I know i have to use it
>>> twice, once along COLUMN and then along ROW directions.
>>>
>>> However I am not sure how to set the cifti-resample input arguments
>>> correctly.
>>>
>>>
>>> I have the following files :
>>>
>>> Input functional connectivity file from fMRI in 32K space:
>>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
>>>
>>> Input Sphere Left (32K space): S900.L.sphere.32k_fs_LR.surf.gii
>>>
>>> Input Sphere Right (32K space): S900.R.sphere.32k_fs_LR.surf.gii
>>>
>>> Output Sphere Left (4K space): Sphere.4k.L.surf.gii
>>>
>>> Output Sphere Right (4K space): Sphere.4k.R.surf.gii
>>>
>>> I have a "template" (not sure if it is actually suitable for a
>>>template)
>>> dconn file in the 4K space, called testtemplate4K.dconn.nii. This is a
>>> just a dconn file of functional connectivity computed directly from MEG
>>> data in the 4K space.
>>>
>>> The issue is that the 32K functional connectivity matrix contains
>>> connectivity between all vertices , in both left and right hemispheres
>>> and i am not sure if such a connectivity file can be divided into left
>>> and right. So this file is defined over both hemispheres.
>>>
>>> Then I have the input and output spaces defined with sphere files,
>>> different for left and right hemispheres.
>>>
>>> After reading the description of cifti-resample I tried running the
>>> following (with wb_command 1.2):
>>>
>>> wb_command -cifti-resample
>>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii COLUMN
>>> testtemplate4K.dconn.nii COLUMN ADAP_BARY_AREA CUBIC
>>> testdconnresamp1.dconn.gii -left-spheres
>>> S900.L.sphere.32k_fs_LR.surf.gii Sphere.4k.L.surf.gii -right-spheres
>>> S900.R.sphere.32k_fs_LR.surf.gii Sphere.4k.R.surf.gii
>>>
>>> and i got the error:
>>>
>>> ERROR: left area data is missing
>>>
>>> I thought that the left area data is in the input dconn 32K dconn
>>>cifti.
>>>
>>> Could you please have a look in the above command and advice on what i
>>> am doing wrong?
>>>
>>> Thank you very much
>>>
>>> Best
>>>
>>> Giorgos
>>>
>>>
>>>
>>>
>>> ---
>>> This email has been checked for viruses by Avast antivirus software.
>>> https://www.avast.com/antivirus
>>>
>>> ___
>>> 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.
>
>
>---
>This email has been checked for viruses by Avast antivirus software.
>https://www.avast.com/antivirus
>



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 

Re: [HCP-Users] cifti-resample of 32K dconn to 4K dconn

2016-07-16 Thread Georgios Michalareas
Thanks for the tip Matt.

I ll stick to parcellations for comparing fMRI and MEG connectivity in 
the practicals.

But in any case , if one would want to do such a deconn resampling , do 
you know what is the mistake(s)  I am doing in the command below?

Thanks again

Giorgos


On 7/16/2016 4:49 PM, Glasser, Matthew wrote:
> Hi Georgios,
>
> I would not recommend downsampling a dense connectome.  Instead it would
> be better to downsample the dense timeseries and then recompute the dense
> connectome.
>
> Peace,
>
> Matt.
>
> On 7/16/16, 9:47 AM, "hcp-users-boun...@humanconnectome.org on behalf of
> Georgios Michalareas"  giorgos.michalar...@esi-frankfurt.de> wrote:
>
>> Hi everyone,
>>
>> i am trying for the MEG practicals to downsample a 32K dconn fMRI group
>> functional connectivity cifti:
>>
>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
>>
>> into a dconn cifti in the 4K space that we use in the MEG analysis in OT4.
>>
>> I am trying to use cifti-resample to do so. I know i have to use it
>> twice, once along COLUMN and then along ROW directions.
>>
>> However I am not sure how to set the cifti-resample input arguments
>> correctly.
>>
>>
>> I have the following files :
>>
>> Input functional connectivity file from fMRI in 32K space:
>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
>>
>> Input Sphere Left (32K space): S900.L.sphere.32k_fs_LR.surf.gii
>>
>> Input Sphere Right (32K space): S900.R.sphere.32k_fs_LR.surf.gii
>>
>> Output Sphere Left (4K space): Sphere.4k.L.surf.gii
>>
>> Output Sphere Right (4K space): Sphere.4k.R.surf.gii
>>
>> I have a "template" (not sure if it is actually suitable for a template)
>> dconn file in the 4K space, called testtemplate4K.dconn.nii. This is a
>> just a dconn file of functional connectivity computed directly from MEG
>> data in the 4K space.
>>
>> The issue is that the 32K functional connectivity matrix contains
>> connectivity between all vertices , in both left and right hemispheres
>> and i am not sure if such a connectivity file can be divided into left
>> and right. So this file is defined over both hemispheres.
>>
>> Then I have the input and output spaces defined with sphere files,
>> different for left and right hemispheres.
>>
>> After reading the description of cifti-resample I tried running the
>> following (with wb_command 1.2):
>>
>> wb_command -cifti-resample
>> HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii COLUMN
>> testtemplate4K.dconn.nii COLUMN ADAP_BARY_AREA CUBIC
>> testdconnresamp1.dconn.gii -left-spheres
>> S900.L.sphere.32k_fs_LR.surf.gii Sphere.4k.L.surf.gii -right-spheres
>> S900.R.sphere.32k_fs_LR.surf.gii Sphere.4k.R.surf.gii
>>
>> and i got the error:
>>
>> ERROR: left area data is missing
>>
>> I thought that the left area data is in the input dconn 32K dconn cifti.
>>
>> Could you please have a look in the above command and advice on what i
>> am doing wrong?
>>
>> Thank you very much
>>
>> Best
>>
>> Giorgos
>>
>>
>>
>>
>> ---
>> This email has been checked for viruses by Avast antivirus software.
>> https://www.avast.com/antivirus
>>
>> ___
>> 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.


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Re: [HCP-Users] cifti-resample of 32K dconn to 4K dconn

2016-07-16 Thread Glasser, Matthew
Hi Georgios,

I would not recommend downsampling a dense connectome.  Instead it would
be better to downsample the dense timeseries and then recompute the dense
connectome.

Peace,

Matt.

On 7/16/16, 9:47 AM, "hcp-users-boun...@humanconnectome.org on behalf of
Georgios Michalareas"  wrote:

>Hi everyone,
>
>i am trying for the MEG practicals to downsample a 32K dconn fMRI group
>functional connectivity cifti:
>
>HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
>
>into a dconn cifti in the 4K space that we use in the MEG analysis in OT4.
>
>I am trying to use cifti-resample to do so. I know i have to use it
>twice, once along COLUMN and then along ROW directions.
>
>However I am not sure how to set the cifti-resample input arguments
>correctly.
>
>
>I have the following files :
>
>Input functional connectivity file from fMRI in 32K space:
>HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii
>
>Input Sphere Left (32K space): S900.L.sphere.32k_fs_LR.surf.gii
>
>Input Sphere Right (32K space): S900.R.sphere.32k_fs_LR.surf.gii
>
>Output Sphere Left (4K space): Sphere.4k.L.surf.gii
>
>Output Sphere Right (4K space): Sphere.4k.R.surf.gii
>
>I have a "template" (not sure if it is actually suitable for a template)
>dconn file in the 4K space, called testtemplate4K.dconn.nii. This is a
>just a dconn file of functional connectivity computed directly from MEG
>data in the 4K space.
>
>The issue is that the 32K functional connectivity matrix contains
>connectivity between all vertices , in both left and right hemispheres
>and i am not sure if such a connectivity file can be divided into left
>and right. So this file is defined over both hemispheres.
>
>Then I have the input and output spaces defined with sphere files,
>different for left and right hemispheres.
>
>After reading the description of cifti-resample I tried running the
>following (with wb_command 1.2):
>
>wb_command -cifti-resample
>HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii COLUMN
>testtemplate4K.dconn.nii COLUMN ADAP_BARY_AREA CUBIC
>testdconnresamp1.dconn.gii -left-spheres
>S900.L.sphere.32k_fs_LR.surf.gii Sphere.4k.L.surf.gii -right-spheres
>S900.R.sphere.32k_fs_LR.surf.gii Sphere.4k.R.surf.gii
>
>and i got the error:
>
>ERROR: left area data is missing
>
>I thought that the left area data is in the input dconn 32K dconn cifti.
>
>Could you please have a look in the above command and advice on what i
>am doing wrong?
>
>Thank you very much
>
>Best
>
>Giorgos
>
>
>
>
>---
>This email has been checked for viruses by Avast antivirus software.
>https://www.avast.com/antivirus
>
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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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[HCP-Users] cifti-resample of 32K dconn to 4K dconn

2016-07-16 Thread Georgios Michalareas
Hi everyone,

i am trying for the MEG practicals to downsample a 32K dconn fMRI group 
functional connectivity cifti:

HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii

into a dconn cifti in the 4K space that we use in the MEG analysis in OT4.

I am trying to use cifti-resample to do so. I know i have to use it 
twice, once along COLUMN and then along ROW directions.

However I am not sure how to set the cifti-resample input arguments 
correctly.


I have the following files :

Input functional connectivity file from fMRI in 32K space: 
HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii

Input Sphere Left (32K space): S900.L.sphere.32k_fs_LR.surf.gii

Input Sphere Right (32K space): S900.R.sphere.32k_fs_LR.surf.gii

Output Sphere Left (4K space): Sphere.4k.L.surf.gii

Output Sphere Right (4K space): Sphere.4k.R.surf.gii

I have a "template" (not sure if it is actually suitable for a template) 
dconn file in the 4K space, called testtemplate4K.dconn.nii. This is a 
just a dconn file of functional connectivity computed directly from MEG 
data in the 4K space.

The issue is that the 32K functional connectivity matrix contains 
connectivity between all vertices , in both left and right hemispheres 
and i am not sure if such a connectivity file can be divided into left 
and right. So this file is defined over both hemispheres.

Then I have the input and output spaces defined with sphere files, 
different for left and right hemispheres.

After reading the description of cifti-resample I tried running the 
following (with wb_command 1.2):

wb_command -cifti-resample 
HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii COLUMN 
testtemplate4K.dconn.nii COLUMN ADAP_BARY_AREA CUBIC 
testdconnresamp1.dconn.gii -left-spheres 
S900.L.sphere.32k_fs_LR.surf.gii Sphere.4k.L.surf.gii -right-spheres 
S900.R.sphere.32k_fs_LR.surf.gii Sphere.4k.R.surf.gii

and i got the error:

ERROR: left area data is missing

I thought that the left area data is in the input dconn 32K dconn cifti.

Could you please have a look in the above command and advice on what i 
am doing wrong?

Thank you very much

Best

Giorgos




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