error with SaveParamsAsNIfTI

[Karin Kantarovich]

Hi Gary and NODDI Team,

I'm currently practicing using NODDI with the example dataset and when I try to convert the estimated NODDI parameters into volumetric parameter maps using the SaveParamsAsNIfTI command,  I get the following error msg:

>> SaveParamsAsNIfTI('FittedParams.mat', 'NODDI_roi.mat', 'brain_mask.hdr', 'example')

loading the fitted parameters from : FittedParams.mat

loading the roi from : NODDI_roi.mat

loading the target volume : brain_mask.hdr

Undefined function or variable 'model'.

Error in SaveParamsAsNIfTI (line 31)

idxOfFitted = find(model.GD.fixed(1:end-2)==0);

I went into line 31 of the script but I'm not sure what needs to be changed or if there is something I did wrong on my end?

Any help is appreciated, thanks in advance!

Karin

[Hui Zhang]

Hi Karin,

Are you using the existing FittedParams.mat file in the example dataset?  That file is outdated I am afraid.  You need to run through the steps before that to create a new version of that file first.

Gary

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[Karin Kantarovich]

Hi Gary,

Yes I was, thanks for the tip. I deleted that file and created a FittedParams.mat file using the batch_fitting_single command, but now when I run the SaveParamsAsNIfTI command the following error comes up:

>> SaveParamsAsNIfTI('FittedParams.mat', 'NODDI_roi.mat', 'brain_mask.hdr', 'example')

loading the fitted parameters from : FittedParams.mat

loading the roi from : NODDI_roi.mat

loading the target volume : brain_mask.hdr

converting the fitted parameters into volumetric maps ...

Saving the volumetric maps of the fitted parameters ...

Undefined function or variable 'spm_type'.

Error in nifti/subsasgn>assigndat (line 354)

    if any(sz > spm_type('int16','maxval')) && ~use_nifti2

Error in nifti/subsasgn>fun (line 76)

            obj      = assigndat(obj,val);

Error in nifti/subsasgn (line 20)

        obji    = fun(obji,subs,val);

Error in SaveAsNIfTI (line 27)

N.dat = dat;

Error in SaveParamsAsNIfTI (line 117)

    SaveAsNIfTI(reshape(squeeze(vols(:,i)), [xsize ysize zsize]), niftiSpecs, output);

On Wednesday, May 6, 2020 at 1:37:41 PM UTC-4, Gary wrote:

Hi Karin,

Are you using the existing FittedParams.mat file in the example dataset?  That file is outdated I am afraid.  You need to run through the steps before that to create a new version of that file first.

Gary

On Tue, May 5, 2020 at 2:13 PM Karin Kantarovich <kar.kan...@gmail.com> wrote:

Hi Gary and NODDI Team,

I'm currently practicing using NODDI with the example dataset and when I try to convert the estimated NODDI parameters into volumetric parameter maps using the SaveParamsAsNIfTI command,  I get the following error msg:

>> SaveParamsAsNIfTI('FittedParams.mat', 'NODDI_roi.mat', 'brain_mask.hdr', 'example')

loading the fitted parameters from : FittedParams.mat

loading the roi from : NODDI_roi.mat

loading the target volume : brain_mask.hdr

Undefined function or variable 'model'.

Error in SaveParamsAsNIfTI (line 31)

idxOfFitted = find(model.GD.fixed(1:end-2)==0);

I went into line 31 of the script but I'm not sure what needs to be changed or if there is something I did wrong on my end?

Any help is appreciated, thanks in advance!

Karin

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[Hui Zhang]

Hi Karin,

You must have a version of SPM installed that is clashing with niftimatlib-1.2.  You need to first remove it from your PATH fist.  The command should like like this for SPM8: rmpath(genpath('/usr/local/pkg/spm8'))

Gary

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[Hui Zhang]

Hi Karin,

Thanks to your tip, I have now updated the NODDI example dataset with an up-to-date version of FittedParams.mat included in the output folder.

(No need for you to download it again)

Gary

[Karin Kantarovich]

Hi Gary,

Amazing, thanks! Your advice worked (to remove the path containing a version of SPM that was clashing with niftimatlib-1.2). I did have issues with nifti after that (similar to some of the mex-file issues that previous people reported), I ended up having to re-compile the files through MATLAB as one user in the google group suggested and downloading the full X-Code (not just command line tools) through Apple for Developers. After that everything has been working smoothly.

I'm wondering, is there a google group like this one for AMICO? 

Karin

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[Hui Zhang]

Thanks Karin for the update and reminding me of the issue with niftimatlib.  In fact, there is a more recent version of that library now which would have saved your trouble.  I have updated the NODDI toolbox homepage to reflect that.

For AMICO help, I think you can report issues through its GitHub portal.  Copying Alex, here.

But you are welcome to ask AMICO-NODDI related questions here.  I will try to answer any that I can but Alex will likely be happy to chime in.

Gary

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[Alessandro Daducci]

Hi Karin and Gary,

yes, the best place to ask for help on AMICO is through github’s “issues” feature: https://github.com/daducci/AMICO/issues

Best,

Ale

[Karin Kantarovich]

Great, thank you both!

Karin