[HCP-Users] Merging a gifti file

[Rita Elena Loiotile]

Hi,

I'd like to merge two gifti files, each of format 32K x t timepoints.
I'd like the output to be 64K x t timepoints, so basically concatenating
the first dimension.
My understanding is that wb_command -metric-merge doesn't acomodate this.
Is there anything else I can try?
I tried converting to nifti format and using "fsl_merge -x" (which does do
what I'd like, but unfortunately caps the number of items in the each
dimension to well below 64K).

Thank you kindly in advance,
Rita

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

[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

[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

[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

[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 <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
>
>
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>
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[HCP-Users] GIFTI read and save in Matlab

[Rita Elena Loiotile]

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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