NITRC GIFTI Forum: open-discussion

convert gifti to nifti files with CAT12

ali pauline — Tue, 05 Mar 2019 14:54:36 GMT

Dear all,

I'm using CAT12 to do gyrification and surfaces comparaison: as results i have gifti files (.gii) but i don't know how to convert them in to nifti files: is anyone has a Matlab script or find how to do that on CAT12 directly?

Thank you so much,
Pauline,

Error reading func.gii giles into MATLAB

Lauren Nelson — Wed, 08 Feb 2017 18:32:01 GMT

Hi all,

I'm working with HCP data. Starting with some of their cifti dscalar.nii files of individual subject myelin and task-based contrasts, I pulled out specific columns from their task-based contrasts using -cifti-merge. Then, I combined these individual one-column dscalar files into one cifti file with 500 columns again using cifti-merge. Finally, I converted this to a metric gifti using cifti-separate. The gifti looks great in wb_view. However, I'm getting an error reading it into matlab with Guillaume Flandin's gifti library at http://www.artefact.tk/software/matlab/gifti/.

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file
AllWM14CLeft.func.gii failed.

Error in gifti (line 71)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Any help would be greatly appreciated! I'm using the 1.6 version of the gifti library so I think it's up to date.

Thanks,
Lauren

Error reading gifti into Matlab

Lauren Nelson — Tue, 07 Feb 2017 19:02:12 GMT

Hi all,

I'm working with HCP data. Starting with some of their cifti dscalar.nii files of individual subject myelin and task-based contrasts, I pulled out specific columns from their task-based contrasts using -cifti-merge. Then, I combined these individual one-column dscalar files into one cifti file with 500 columns again using cifti-merge. Finally, I converted this to a metric gifti using cifti-separate. The gifti looks great in wb_view. However, I'm getting an error reading it into matlab with Guillaume Flandin's gifti library:

Error using read_gifti_file_standalone (line 20)
[GIFTI] Loading of XML file
AllWM14CLeft.func.gii failed.
Error in gifti (line 71)
this = read_gifti_file_standalone(varargin{1},giftistruct);

Any help would be greatly appreciated! I'm using the 1.6 version of the gifti library so I think it's up to date.
Thanks,
Lauren

RE: freesurfer_annot_to_gifti files DataType

Richard Reynolds — Tue, 08 Nov 2016 14:20:37 GMT

Byte-wise RGBA datasets might be stored as UINT8,
with INTENT_CODE NIFTI_INTENT_RGBA_VECTOR.

Each element would essentially be a 4-byte vector,
which would sit in memory the exact same way as with
the UINT32 datum.

Does that seem reasonable?

- rick

RE: freesurfer_annot_to_gifti files DataType

Nick Schmansky — Mon, 07 Nov 2016 23:30:27 GMT

Hi, in the case of the annotation file lh.aparc.a2009s.gii, the data is RGBA values, which are unsigned, so technically i suppose UINT32 is the accurate data type. however, it appears the fact that UINT32 is not one of the required gifiti datatypes means that it probably should be defined as INT32. i'm not sure what to do at this point, as an argument could be made either which should change: either UINT32 is added as a valid datatype (thus making the freesurfer_annot valid), or freesurfer should change the datatype for annot labels to INT32. maybe you have thoughts on this. in any case, it gets interpreted as an RGBA value, so it doesnt really matter.

Nick

freesurfer_annot_to_gifti files DataType

John Muschelli — Mon, 07 Nov 2016 22:32:54 GMT

From the GIFTI DTD I have:

DataType (NIFTI_TYPE_UINT8 |
NIFTI_TYPE_INT32 |
NIFTI_TYPE_FLOAT32) #REQUIRED

But in the lh.aparc.a2009s.gii file from freesurfer_annot_to_gifti.tgz, the format is NIFTI_TYPE_UINT32. Is the DTD not complete with data types or is this a misspecification?

RE: Create gifti surfaces for matlab

Nick Schmansky — Tue, 25 Oct 2016 14:50:05 GMT

Hi,

You will need to download the 'development' version of the entire freesurfer package in order to get the binary mris_convert. Note that is version is pre-version 6 release, which we hope to release within a month.

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev

Nick

RE: Create gifti surfaces for matlab

Rogier Mars — Tue, 25 Oct 2016 12:13:01 GMT

Dear Nick,

Is this version available for Mac (Yosemite) as well?

Thanks very much,

Rogier

RE: Write gifti to file

Mac Shine — Thu, 04 Dec 2014 22:01:47 GMT

Sorry, just wanted to add that I want to export a 'shape' file, not a surface file.

Write gifti to file

Mac Shine — Thu, 04 Dec 2014 21:53:00 GMT

Hi there

I've created some experimental data that I'd like to map back onto the surface. I first used the 'gifti' command to read a '.gii' file (with each vertex labelled according to a parcellation scheme) into matlab, after which time I replaced each parcellation label with a statistical value. Is there a way to use gifti to export this data into a gifti file that I could then open in a program like connectome workbench?

Thanks in advance for the help.

Mac