Re: [HCP-Users] GIFTI read and save in Matlab

2017-03-14 Thread Rita Elena Loiotile 
Will do.  Thank you, Matthew.  I appreciate all the back-and-forth help.

On Tue, Mar 14, 2017 at 7:44 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:

> In that case I am a bit surprised by this issue.  I would report it
> to Guillaume Flandin, the author of the GIFTI toolbox.
>
> Peace,
>
> Matt.
>
>
> From: Rita Elena Loiotile <rloiot...@gmail.com>
> Date: Tuesday, March 14, 2017 at 6:38 PM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>
> When imported to matlab, the gifti doesn't seem to have any data, other
> than the field "cdata" which is 32492 by 209. It's possible there are some
> private fields, but I don't have any experience with private fields in
> matlab so I'd have to look into this.
> I could also give you a header printout of the gifti file in the
> terminal.  Is this what you're referring to?
>
> On Tue, Mar 14, 2017 at 7:09 PM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> Dims of the gifti you read in.
>>
>> Peace,
>>
>> Matt.
>>
>> From: Rita Elena Loiotile <rloiot...@gmail.com>
>> Date: Tuesday, March 14, 2017 at 6:07 PM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>>
>> Sorry, I'm not sure what you mean.  I have a saved gifti file that I'm
>> reading into matlab and a matrix that I've made that I want to output as a
>> gifti. Can you specify the array?
>>
>> On Tue, Mar 14, 2017 at 7:04 PM, Glasser, Matthew <glass...@wustl.edu>
>> wrote:
>>
>>> I was referring to the array you read into matlab.
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Rita Elena Loiotile <rloiot...@gmail.com>
>>> Date: Tuesday, March 14, 2017 at 6:01 PM
>>>
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>>>
>>> both the gifti.cdata and the matrix have dimensions 32492 by 209.
>>>
>>> On Tue, Mar 14, 2017 at 5:29 PM, Glasser, Matthew <glass...@wustl.edu>
>>> wrote:
>>>
>>>> Is the input file only a single column?
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: Rita Elena Loiotile <rloiot...@gmail.com>
>>>> Date: Tuesday, March 14, 2017 at 3:34 PM
>>>>
>>>> To: Matt Glasser <glass...@wustl.edu>
>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>>>>
>>>> Hi Matthew,
>>>>
>>>> Thanks for the help.  I have 2 versions on my lab computer, both give
>>>> the same problem.  It seems like the newest version of GIFTI (according to
>>>> artefact) is 1.6.  Please let me know if there's a newer one that I'm
>>>> missing.
>>>>
>>>> I've attached screenshots of the info, in case there is really
>>>> something obvious that I'm doing incorrectly.
>>>>
>>>> Thanks again,
>>>> Rita
>>>>
>>>> On Tue, Mar 14, 2017 at 7:43 AM, Glasser, Matthew <glass...@wustl.edu>
>>>> wrote:
>>>>
>>>>> Do you have the latest version of the GIFTI matlab toolbox?
>>>>>
>>>>> Peace,
>>>>>
>>>>> Matt.
>>>>>
>>>>> From: Rita Elena Loiotile <rloiot...@gmail.com>
>>>>> Date: Tuesday, March 14, 2017 at 1:27 AM
>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>>>>>
>>>>> Hi Matthew and HCP,
>>>>>
>>>>> Thank you for the suggestion, Matthew.   I tried this a while back,
>>>>> and have since forgotten it.  I thought it might work (on account of
>>>>> preserving some internal info).  It is also the case that re-saving the
>>>>> original gifti under a new name produces a file that opens properly in
>>>>> other viewing softwa

Re: [HCP-Users] GIFTI read and save in Matlab

2017-03-14 Thread Glasser, Matthew 
In that case I am a bit surprised by this issue.  I would report it to 
Guillaume Flandin, the author of the GIFTI toolbox.

Peace,

Matt.


From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 6:38 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

When imported to matlab, the gifti doesn't seem to have any data, other than 
the field "cdata" which is 32492 by 209. It's possible there are some private 
fields, but I don't have any experience with private fields in matlab so I'd 
have to look into this.
I could also give you a header printout of the gifti file in the terminal.  Is 
this what you're referring to?

On Tue, Mar 14, 2017 at 7:09 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Dims of the gifti you read in.

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 6:07 PM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Sorry, I'm not sure what you mean.  I have a saved gifti file that I'm reading 
into matlab and a matrix that I've made that I want to output as a gifti. Can 
you specify the array?

On Tue, Mar 14, 2017 at 7:04 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I was referring to the array you read into matlab.

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 6:01 PM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

both the gifti.cdata and the matrix have dimensions 32492 by 209.

On Tue, Mar 14, 2017 at 5:29 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Is the input file only a single column?

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 3:34 PM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Hi Matthew,

Thanks for the help.  I have 2 versions on my lab computer, both give the same 
problem.  It seems like the newest version of GIFTI (according to artefact) is 
1.6.  Please let me know if there's a newer one that I'm missing.

I've attached screenshots of the info, in case there is really something 
obvious that I'm doing incorrectly.

Thanks again,
Rita

On Tue, Mar 14, 2017 at 7:43 AM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Do you have the latest version of the GIFTI matlab toolbox?

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 1:27 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Hi Matthew and HCP,

Thank you for the suggestion, Matthew.   I tried this a while back, and have 
since forgotten it.  I thought it might work (on account of preserving some 
internal info).  It is also the case that re-saving the original gifti under a 
new name produces a file that opens properly in other viewing software.  That 
suggested that this was the right approach.

Unfortunately, I can't seem to assign new values to the original gifti.cdata.

The command "gnew.cdata=M" yields the following: Error using gifti/subsasgn 
(line 95) Syntax not implemented.

Perhaps this has been updated if it works for you?  A very dumb workaround for 
this would be to loop through every possible index of the matrix M and assign 
each value separately.  However, I'd very much like to avoid this if possible, 
since it's quite slow.

Please let me know if this works for you, and/or if I am missing something 
obvious.

Thank you again,
Rit

Re: [HCP-Users] GIFTI read and save in Matlab

2017-03-14 Thread Rita Elena Loiotile 
Sorry, I'm not sure what you mean.  I have a saved gifti file that I'm
reading into matlab and a matrix that I've made that I want to output as a
gifti. Can you specify the array?

On Tue, Mar 14, 2017 at 7:04 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:

> I was referring to the array you read into matlab.
>
> Peace,
>
> Matt.
>
> From: Rita Elena Loiotile <rloiot...@gmail.com>
> Date: Tuesday, March 14, 2017 at 6:01 PM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>
> both the gifti.cdata and the matrix have dimensions 32492 by 209.
>
> On Tue, Mar 14, 2017 at 5:29 PM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> Is the input file only a single column?
>>
>> Peace,
>>
>> Matt.
>>
>> From: Rita Elena Loiotile <rloiot...@gmail.com>
>> Date: Tuesday, March 14, 2017 at 3:34 PM
>>
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>>
>> Hi Matthew,
>>
>> Thanks for the help.  I have 2 versions on my lab computer, both give the
>> same problem.  It seems like the newest version of GIFTI (according to
>> artefact) is 1.6.  Please let me know if there's a newer one that I'm
>> missing.
>>
>> I've attached screenshots of the info, in case there is really something
>> obvious that I'm doing incorrectly.
>>
>> Thanks again,
>> Rita
>>
>> On Tue, Mar 14, 2017 at 7:43 AM, Glasser, Matthew <glass...@wustl.edu>
>> wrote:
>>
>>> Do you have the latest version of the GIFTI matlab toolbox?
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: Rita Elena Loiotile <rloiot...@gmail.com>
>>> Date: Tuesday, March 14, 2017 at 1:27 AM
>>> To: Matt Glasser <glass...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>>>
>>> Hi Matthew and HCP,
>>>
>>> Thank you for the suggestion, Matthew.   I tried this a while back, and
>>> have since forgotten it.  I thought it might work (on account of preserving
>>> some internal info).  It is also the case that re-saving the original gifti
>>> under a new name produces a file that opens properly in other viewing
>>> software.  That suggested that this was the right approach.
>>>
>>> Unfortunately, I can't seem to assign new values to the original
>>> gifti.cdata.
>>>
>>> The command "gnew.cdata=M" yields the following: Error using
>>> gifti/subsasgn (line 95) Syntax not implemented.
>>>
>>> Perhaps this has been updated if it works for you?  A very dumb
>>> workaround for this would be to loop through every possible index of the
>>> matrix M and assign each value separately.  However, I'd very much like to
>>> avoid this if possible, since it's quite slow.
>>>
>>> Please let me know if this works for you, and/or if I am missing
>>> something obvious.
>>>
>>> Thank you again,
>>> Rita
>>>
>>> On Mon, Mar 13, 2017 at 11:04 PM, Glasser, Matthew <glass...@wustl.edu>
>>> wrote:
>>>
>>>> I find it better to reuse the GIFTI object one read into matlab in the
>>>> first place:
>>>>
>>>> gnew=g;
>>>> gnew.cdata=M;
>>>> save(gnew,’saveName.gii’);
>>>>
>>>> Peace,
>>>>
>>>> Matt.
>>>>
>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Rita Elena
>>>> Loiotile <rloiot...@gmail.com>
>>>> Date: Monday, March 13, 2017 at 8:00 PM
>>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>>> Subject: [HCP-Users] GIFTI read and save in Matlab
>>>>
>>>> Hi,
>>>>
>>>> I’m hoping someone can recommend a fix for a problem I’m having.  I
>>>> have been using GIFTI library (http://www.artefact.tk/softwa
>>>> re/matlab/gifti/) to read GIFTIs into Matlab and perform
>>>> computations.  I would like to save as a gifti.  Using the software, I have
>>>> tried the following:
>>>>
>>>> M;  % matrix of values [vertices by timepoints]
>

Re: [HCP-Users] GIFTI read and save in Matlab

2017-03-14 Thread Glasser, Matthew 
I was referring to the array you read into matlab.

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 6:01 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

both the gifti.cdata and the matrix have dimensions 32492 by 209.

On Tue, Mar 14, 2017 at 5:29 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Is the input file only a single column?

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 3:34 PM

To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Hi Matthew,

Thanks for the help.  I have 2 versions on my lab computer, both give the same 
problem.  It seems like the newest version of GIFTI (according to artefact) is 
1.6.  Please let me know if there's a newer one that I'm missing.

I've attached screenshots of the info, in case there is really something 
obvious that I'm doing incorrectly.

Thanks again,
Rita

On Tue, Mar 14, 2017 at 7:43 AM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Do you have the latest version of the GIFTI matlab toolbox?

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 1:27 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Hi Matthew and HCP,

Thank you for the suggestion, Matthew.   I tried this a while back, and have 
since forgotten it.  I thought it might work (on account of preserving some 
internal info).  It is also the case that re-saving the original gifti under a 
new name produces a file that opens properly in other viewing software.  That 
suggested that this was the right approach.

Unfortunately, I can't seem to assign new values to the original gifti.cdata.

The command "gnew.cdata=M" yields the following: Error using gifti/subsasgn 
(line 95) Syntax not implemented.

Perhaps this has been updated if it works for you?  A very dumb workaround for 
this would be to loop through every possible index of the matrix M and assign 
each value separately.  However, I'd very much like to avoid this if possible, 
since it's quite slow.

Please let me know if this works for you, and/or if I am missing something 
obvious.

Thank you again,
Rita

On Mon, Mar 13, 2017 at 11:04 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I find it better to reuse the GIFTI object one read into matlab in the first 
place:

gnew=g;
gnew.cdata=M;
save(gnew,’saveName.gii’);

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Rita Elena Loiotile 
<rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Monday, March 13, 2017 at 8:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] GIFTI read and save in Matlab

Hi,

I’m hoping someone can recommend a fix for a problem I’m having.  I have been 
using GIFTI library (http://www.artefact.tk/software/matlab/gifti/) to read 
GIFTIs into Matlab and perform computations.  I would like to save as a gifti.  
Using the software, I have tried the following:

M;  % matrix of values [vertices by timepoints]
g=gifti(M);  % converts my matrix to a gifti object with M stored under g.cdata;
save(g, ’saveName.gii’);

This seems to work fine.  I can re-load the saved gift into Matlab— 
newGifti=gifti(’saveName.gii’);— and it looks correct.  However, when I try to 
open saveName.gii using a non-Matlab visualization software— e.g. tksurfer, 
wb_view, freeview— I either encounter errors or load what looks like a gift 
containing all 0’s.

Has anyone had success using GIFTI library to save or is there an alternative 
technique?

Thank you very much in advance,
Rita

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

_

Re: [HCP-Users] GIFTI read and save in Matlab

2017-03-14 Thread Rita Elena Loiotile 
both the gifti.cdata and the matrix have dimensions 32492 by 209.

On Tue, Mar 14, 2017 at 5:29 PM, Glasser, Matthew <glass...@wustl.edu>
wrote:

> Is the input file only a single column?
>
> Peace,
>
> Matt.
>
> From: Rita Elena Loiotile <rloiot...@gmail.com>
> Date: Tuesday, March 14, 2017 at 3:34 PM
>
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>
> Hi Matthew,
>
> Thanks for the help.  I have 2 versions on my lab computer, both give the
> same problem.  It seems like the newest version of GIFTI (according to
> artefact) is 1.6.  Please let me know if there's a newer one that I'm
> missing.
>
> I've attached screenshots of the info, in case there is really something
> obvious that I'm doing incorrectly.
>
> Thanks again,
> Rita
>
> On Tue, Mar 14, 2017 at 7:43 AM, Glasser, Matthew <glass...@wustl.edu>
> wrote:
>
>> Do you have the latest version of the GIFTI matlab toolbox?
>>
>> Peace,
>>
>> Matt.
>>
>> From: Rita Elena Loiotile <rloiot...@gmail.com>
>> Date: Tuesday, March 14, 2017 at 1:27 AM
>> To: Matt Glasser <glass...@wustl.edu>
>> Cc: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>> Subject: Re: [HCP-Users] GIFTI read and save in Matlab
>>
>> Hi Matthew and HCP,
>>
>> Thank you for the suggestion, Matthew.   I tried this a while back, and
>> have since forgotten it.  I thought it might work (on account of preserving
>> some internal info).  It is also the case that re-saving the original gifti
>> under a new name produces a file that opens properly in other viewing
>> software.  That suggested that this was the right approach.
>>
>> Unfortunately, I can't seem to assign new values to the original
>> gifti.cdata.
>>
>> The command "gnew.cdata=M" yields the following: Error using
>> gifti/subsasgn (line 95) Syntax not implemented.
>>
>> Perhaps this has been updated if it works for you?  A very dumb
>> workaround for this would be to loop through every possible index of the
>> matrix M and assign each value separately.  However, I'd very much like to
>> avoid this if possible, since it's quite slow.
>>
>> Please let me know if this works for you, and/or if I am missing
>> something obvious.
>>
>> Thank you again,
>> Rita
>>
>> On Mon, Mar 13, 2017 at 11:04 PM, Glasser, Matthew <glass...@wustl.edu>
>> wrote:
>>
>>> I find it better to reuse the GIFTI object one read into matlab in the
>>> first place:
>>>
>>> gnew=g;
>>> gnew.cdata=M;
>>> save(gnew,’saveName.gii’);
>>>
>>> Peace,
>>>
>>> Matt.
>>>
>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Rita Elena
>>> Loiotile <rloiot...@gmail.com>
>>> Date: Monday, March 13, 2017 at 8:00 PM
>>> To: "hcp-users@humanconnectome.org" <hcp-users@humanconnectome.org>
>>> Subject: [HCP-Users] GIFTI read and save in Matlab
>>>
>>> Hi,
>>>
>>> I’m hoping someone can recommend a fix for a problem I’m having.  I have
>>> been using GIFTI library (http://www.artefact.tk/software/matlab/gifti/)
>>> to read GIFTIs into Matlab and perform computations.  I would like to save
>>> as a gifti.  Using the software, I have tried the following:
>>>
>>> M;  % matrix of values [vertices by timepoints]
>>> g=gifti(M);  % converts my matrix to a gifti object with M stored under
>>> g.cdata;
>>> save(g, ’saveName.gii’);
>>>
>>> This seems to work fine.  I can re-load the saved gift into Matlab—
>>> newGifti=gifti(’saveName.gii’);— and it looks correct.  However, when I
>>> try to open saveName.gii using a non-Matlab visualization software— e.g.
>>> tksurfer, wb_view, freeview— I either encounter errors or load what looks
>>> like a gift containing all 0’s.
>>>
>>> Has anyone had success using GIFTI library to save or is there an
>>> alternative technique?
>>>
>>> Thank you very much in advance,
>>> Rita
>>>
>>> ___
>>> HCP-Users mailing list
>>> HCP-Users@humanconnectome.org
>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>
>>>
>>> --
>>>
>>> The materials in

Re: [HCP-Users] GIFTI read and save in Matlab

2017-03-14 Thread Glasser, Matthew 
Is the input file only a single column?

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 3:34 PM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Hi Matthew,

Thanks for the help.  I have 2 versions on my lab computer, both give the same 
problem.  It seems like the newest version of GIFTI (according to artefact) is 
1.6.  Please let me know if there's a newer one that I'm missing.

I've attached screenshots of the info, in case there is really something 
obvious that I'm doing incorrectly.

Thanks again,
Rita

On Tue, Mar 14, 2017 at 7:43 AM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
Do you have the latest version of the GIFTI matlab toolbox?

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 1:27 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Hi Matthew and HCP,

Thank you for the suggestion, Matthew.   I tried this a while back, and have 
since forgotten it.  I thought it might work (on account of preserving some 
internal info).  It is also the case that re-saving the original gifti under a 
new name produces a file that opens properly in other viewing software.  That 
suggested that this was the right approach.

Unfortunately, I can't seem to assign new values to the original gifti.cdata.

The command "gnew.cdata=M" yields the following: Error using gifti/subsasgn 
(line 95) Syntax not implemented.

Perhaps this has been updated if it works for you?  A very dumb workaround for 
this would be to loop through every possible index of the matrix M and assign 
each value separately.  However, I'd very much like to avoid this if possible, 
since it's quite slow.

Please let me know if this works for you, and/or if I am missing something 
obvious.

Thank you again,
Rita

On Mon, Mar 13, 2017 at 11:04 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I find it better to reuse the GIFTI object one read into matlab in the first 
place:

gnew=g;
gnew.cdata=M;
save(gnew,’saveName.gii’);

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Rita Elena Loiotile 
<rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Monday, March 13, 2017 at 8:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] GIFTI read and save in Matlab

Hi,

I’m hoping someone can recommend a fix for a problem I’m having.  I have been 
using GIFTI library (http://www.artefact.tk/software/matlab/gifti/) to read 
GIFTIs into Matlab and perform computations.  I would like to save as a gifti.  
Using the software, I have tried the following:

M;  % matrix of values [vertices by timepoints]
g=gifti(M);  % converts my matrix to a gifti object with M stored under g.cdata;
save(g, ’saveName.gii’);

This seems to work fine.  I can re-load the saved gift into Matlab— 
newGifti=gifti(’saveName.gii’);— and it looks correct.  However, when I try to 
open saveName.gii using a non-Matlab visualization software— e.g. tksurfer, 
wb_view, freeview— I either encounter errors or load what looks like a gift 
containing all 0’s.

Has anyone had success using GIFTI library to save or is there an alternative 
technique?

Thank you very much in advance,
Rita

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Re: [HCP-Users] GIFTI read and save in Matlab

2017-03-14 Thread Glasser, Matthew 
Do you have the latest version of the GIFTI matlab toolbox?

Peace,

Matt.

From: Rita Elena Loiotile <rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Tuesday, March 14, 2017 at 1:27 AM
To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] GIFTI read and save in Matlab

Hi Matthew and HCP,

Thank you for the suggestion, Matthew.   I tried this a while back, and have 
since forgotten it.  I thought it might work (on account of preserving some 
internal info).  It is also the case that re-saving the original gifti under a 
new name produces a file that opens properly in other viewing software.  That 
suggested that this was the right approach.

Unfortunately, I can't seem to assign new values to the original gifti.cdata.

The command "gnew.cdata=M" yields the following: Error using gifti/subsasgn 
(line 95) Syntax not implemented.

Perhaps this has been updated if it works for you?  A very dumb workaround for 
this would be to loop through every possible index of the matrix M and assign 
each value separately.  However, I'd very much like to avoid this if possible, 
since it's quite slow.

Please let me know if this works for you, and/or if I am missing something 
obvious.

Thank you again,
Rita

On Mon, Mar 13, 2017 at 11:04 PM, Glasser, Matthew 
<glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote:
I find it better to reuse the GIFTI object one read into matlab in the first 
place:

gnew=g;
gnew.cdata=M;
save(gnew,’saveName.gii’);

Peace,

Matt.

From: 
<hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>>
 on behalf of Rita Elena Loiotile 
<rloiot...@gmail.com<mailto:rloiot...@gmail.com>>
Date: Monday, March 13, 2017 at 8:00 PM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" 
<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] GIFTI read and save in Matlab

Hi,

I’m hoping someone can recommend a fix for a problem I’m having.  I have been 
using GIFTI library (http://www.artefact.tk/software/matlab/gifti/) to read 
GIFTIs into Matlab and perform computations.  I would like to save as a gifti.  
Using the software, I have tried the following:

M;  % matrix of values [vertices by timepoints]
g=gifti(M);  % converts my matrix to a gifti object with M stored under g.cdata;
save(g, ’saveName.gii’);

This seems to work fine.  I can re-load the saved gift into Matlab— 
newGifti=gifti(’saveName.gii’);— and it looks correct.  However, when I try to 
open saveName.gii using a non-Matlab visualization software— e.g. tksurfer, 
wb_view, freeview— I either encounter errors or load what looks like a gift 
containing all 0’s.

Has anyone had success using GIFTI library to save or is there an alternative 
technique?

Thank you very much in advance,
Rita

___
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HCP-Users@humanconnectome.org<mailto: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.



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] GIFTI read and save in Matlab

2017-03-14 Thread Rita Elena Loiotile 
Hi Matthew and HCP,

Thank you for the suggestion, Matthew.   I tried this a while back, and
have since forgotten it.  I thought it might work (on account of preserving
some internal info).  It is also the case that re-saving the original gifti
under a new name produces a file that opens properly in other viewing
software.  That suggested that this was the right approach.

Unfortunately, I can't seem to assign new values to the original
gifti.cdata.

The command "gnew.cdata=M" yields the following: Error using gifti/subsasgn
(line 95) Syntax not implemented.

Perhaps this has been updated if it works for you?  A very dumb workaround
for this would be to loop through every possible index of the matrix M and
assign each value separately.  However, I'd very much like to avoid this if
possible, since it's quite slow.

Please let me know if this works for you, and/or if I am missing something
obvious.

Thank you again,
Rita

On Mon, Mar 13, 2017 at 11:04 PM, Glasser, Matthew 
wrote:

> I find it better to reuse the GIFTI object one read into matlab in the
> first place:
>
> gnew=g;
> gnew.cdata=M;
> save(gnew,’saveName.gii’);
>
> Peace,
>
> Matt.
>
> From:  on behalf of Rita Elena
> Loiotile 
> Date: Monday, March 13, 2017 at 8:00 PM
> To: "hcp-users@humanconnectome.org" 
> Subject: [HCP-Users] GIFTI read and save in Matlab
>
> Hi,
>
> I’m hoping someone can recommend a fix for a problem I’m having.  I have
> been using GIFTI library (http://www.artefact.tk/software/matlab/gifti/)
> to read GIFTIs into Matlab and perform computations.  I would like to save
> as a gifti.  Using the software, I have tried the following:
>
> M;  % matrix of values [vertices by timepoints]
> g=gifti(M);  % converts my matrix to a gifti object with M stored under
> g.cdata;
> save(g, ’saveName.gii’);
>
> This seems to work fine.  I can re-load the saved gift into Matlab—
> newGifti=gifti(’saveName.gii’);— and it looks correct.  However, when I
> try to open saveName.gii using a non-Matlab visualization software— e.g.
> tksurfer, wb_view, freeview— I either encounter errors or load what looks
> like a gift containing all 0’s.
>
> Has anyone had success using GIFTI library to save or is there an
> alternative technique?
>
> Thank you very much in advance,
> Rita
>
> ___
> 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] GIFTI read and save in Matlab

2017-03-13 Thread Glasser, Matthew 
I find it better to reuse the GIFTI object one read into matlab in the first 
place:

gnew=g;
gnew.cdata=M;
save(gnew,’saveName.gii’);

Peace,

Matt.

From: 
>
 on behalf of Rita Elena Loiotile 
>
Date: Monday, March 13, 2017 at 8:00 PM
To: "hcp-users@humanconnectome.org" 
>
Subject: [HCP-Users] GIFTI read and save in Matlab

Hi,

I’m hoping someone can recommend a fix for a problem I’m having.  I have been 
using GIFTI library (http://www.artefact.tk/software/matlab/gifti/) to read 
GIFTIs into Matlab and perform computations.  I would like to save as a gifti.  
Using the software, I have tried the following:

M;  % matrix of values [vertices by timepoints]
g=gifti(M);  % converts my matrix to a gifti object with M stored under g.cdata;
save(g, ’saveName.gii’);

This seems to work fine.  I can re-load the saved gift into Matlab— 
newGifti=gifti(’saveName.gii’);— and it looks correct.  However, when I try to 
open saveName.gii using a non-Matlab visualization software— e.g. tksurfer, 
wb_view, freeview— I either encounter errors or load what looks like a gift 
containing all 0’s.

Has anyone had success using GIFTI library to save or is there an alternative 
technique?

Thank you very much in advance,
Rita

___
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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