Will do. Thank you, Matthew. I appreciate all the back-and-forth help. On Tue, Mar 14, 2017 at 7:44 PM, Glasser, Matthew <[email protected]> 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 <[email protected]> > Date: Tuesday, March 14, 2017 at 6:38 PM > > To: Matt Glasser <[email protected]> > Cc: "[email protected]" <[email protected]> > 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 <[email protected]> > wrote: > >> Dims of the gifti you read in. >> >> Peace, >> >> Matt. >> >> From: Rita Elena Loiotile <[email protected]> >> Date: Tuesday, March 14, 2017 at 6:07 PM >> >> To: Matt Glasser <[email protected]> >> Cc: "[email protected]" <[email protected]> >> 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 <[email protected]> >> wrote: >> >>> I was referring to the array you read into matlab. >>> >>> Peace, >>> >>> Matt. >>> >>> From: Rita Elena Loiotile <[email protected]> >>> Date: Tuesday, March 14, 2017 at 6:01 PM >>> >>> To: Matt Glasser <[email protected]> >>> Cc: "[email protected]" <[email protected]> >>> 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 <[email protected]> >>> wrote: >>> >>>> Is the input file only a single column? >>>> >>>> Peace, >>>> >>>> Matt. >>>> >>>> From: Rita Elena Loiotile <[email protected]> >>>> Date: Tuesday, March 14, 2017 at 3:34 PM >>>> >>>> To: Matt Glasser <[email protected]> >>>> Cc: "[email protected]" <[email protected]> >>>> 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 <[email protected]> >>>> wrote: >>>> >>>>> Do you have the latest version of the GIFTI matlab toolbox? >>>>> >>>>> Peace, >>>>> >>>>> Matt. >>>>> >>>>> From: Rita Elena Loiotile <[email protected]> >>>>> Date: Tuesday, March 14, 2017 at 1:27 AM >>>>> To: Matt Glasser <[email protected]> >>>>> Cc: "[email protected]" <[email protected]> >>>>> 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 <[email protected] >>>>> > 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: <[email protected]> on behalf of Rita >>>>>> Elena Loiotile <[email protected]> >>>>>> Date: Monday, March 13, 2017 at 8:00 PM >>>>>> To: "[email protected]" <[email protected]> >>>>>> 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] >>>>>> 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 >>>>>> [email protected] >>>>>> 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. 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