NITRC CIFTI Connectivity File Format Forum: open-discussion

RE: converting nifit to cifit post minimal preprocessing in fmriprep

Natasza Orlov — Sun, 19 Jun 2022 14:10:30 GMT

thank you :)
N

RE: converting nifit to cifit post minimal preprocessing in fmriprep

Tim Coalson — Wed, 15 Jun 2022 19:57:19 GMT

fmriprep was developed by someone else, you could ask them for help.

The HCP pipelines are our preprocessing pipelines, which now have options for operating on "legacy-style" datasets, for instance not having a T2w image. We still consider fieldmaps to be very important, as "fieldmap-less" distortion correction of EPI has not been convincingly helpful in our testing.

As another option, you could look at ciftify:

https://github.com/edickie/ciftify

Tim

converting nifit to cifit post minimal preprocessing in fmriprep

Natasza Orlov — Wed, 15 Jun 2022 12:43:34 GMT

Dear Community,

I have data minimally preprocessed with the fmriprep pipeline, without the cifit output option. Is there a way to introduce to converstion after the preprocessing and if so can you please point me to code that I would be able to use.
thank you very much
Natasza

RE: Error using ciftiopen in Matlab

Tim Schaefer — Tue, 04 Aug 2020 20:40:56 GMT

I do not have Windows, but the error looks like you specified only the path to wb_command, without the wb_command executable/binary, and it wants the path including the executable.

Try 'C:\Users\magda\Documents\Matlab\workbench\bin_windows64\wb_command.exe', or whatever the executable is called under Windows (and ensure the path is correct).

Error using ciftiopen in Matlab

mdelrio — Wed, 22 Jul 2020 14:23:20 GMT

Hi experts,

I'm trying to access the functional connectivity matrix in the HCP_S900_820_rfMRI_MSMAll_groupPCA_d4500ROW_zcorr.dconn.nii file using the ciftiopen command for Matlab - I installed the connectome workbench and downloaded the GIFTI toolbox (http://www.artefact.tk/software/matlab/gifti/) as per the instructions here (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?), but I am getting the following error

'C:\Users\magda\Documents\Matlab\workbench\bin_windows64' is not recognized as an internal or external command,
operable program or batch file.
Error using xml_parser
Cannot read XML document

Error in gifti_read (line 14)
t = xml_parser(filename);
Error in gifti (line 105)
this = gifti_read(varargin{1},giftistruct);
Error in ciftiopen (line 34)
cifti = gifti([tmpfile '.gii']);

I'm hoping someone might have some idea about how to resolve this!

RE: cannot use the CIFTI-2 toolbox in matlab with MacOS system

Jiajia Zhao — Mon, 23 Mar 2020 11:52:36 GMT

thank you, after I removed .mexmaci64 files, it works.
Looking forward your new toolbox.

RE: cannot use the CIFTI-2 toolbox in matlab with MacOS system

Tim Coalson — Wed, 04 Mar 2020 19:32:07 GMT

I would guess that the mex files were compiled for a version of OS X that is too old for your current system to use. Deleting the .mexmaci64 file should allow it to function, the .mexmaci64 file is only there to increase the speed. If I am correct, you may need to delete any other .mexmaci64 files as well.

However, note that the ft_ functions are not what the HCP recommends for loading MRI-based cifti files, see FAQ 2 here:

https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?

If you need access to more than just the data matrix (which is basically all ciftiopen exposes), we are working on a new toolbox, but it is still being tested.

If you are working with MEG data, you may have better luck simply installing the full FieldTrip suite, as it should be more up to date.

cannot use the CIFTI-2 toolbox in matlab with MacOS system

Jiajia Zhao — Wed, 04 Mar 2020 10:36:14 GMT

I have encountered a problem when adding CIFTI-2 code into my matlab with MacOS system. when I read a .dtseries.nii data using ft_read_cifti, error appeared "Invalid MEX-file '/Users/jia/Desktop/UPAN/rscode/cifti-matlab-master/private/ft_getopt.mexmaci64':
dlopen(/Users/jia/Desktop/UPAN/rscode/cifti-matlab-master/private/ft_getopt.mexmaci64, 6): Symbol not found:_mxErrMsgTxt."

my computer system is macOS Mojave Version10.14.2 and the version of matlab is matlab R2018a. I don't know how to solve this problem.

CiftiLib released

Tim Coalson — Wed, 07 May 2014 19:44:54 GMT

To software developers interested in the CIFTI data format:

CiftiLib, a C++ library for CIFTI-2 file reading/writing, is now available on github, at [url=https://github.com/Washington-University/CiftiLib]https://github.com/Washington-University/CiftiLib[/url]. It additionally supports CIFTI-1 files, and supports both on-disk and in-memory access. It also provides C++ code for reading and writing generic NIfTI-1 and NIfTI-2 files. As noted in the README, QT is required.

This code is released under the BSD 2-clause license.

Sincerely,
The Connectome Workbench software development team.

RE: Final CIFTI-2 file formats

Tim Coalson — Fri, 07 Mar 2014 22:02:45 GMT

The initial release of the CIFTI-2 XML parsing/manipulating/writing code is available on the NITRC download page, [url=http://www.nitrc.org/frs/?group_id=454]http://www.nitrc.org/frs/?group_id=454[/url]. It additionally supports CIFTI-1 XML, but note that supporting CIFTI-1 requires dealing with reversed dimensions in the NIfTI-2 header (CIFTI-2 does not have this problem). It also does not include code for reading or writing NIfTI-2 files.

This code is released under the BSD 2-clause license.