Error with batch_fitting

[Blake Neyland]

Hi Gary,

I am new to the NODDI Toolbox and have been running into some issues when trying to process the example dataset you provide in your tutorial. I have downloaded Matlab 2019b, niftimatlib 1.2, noddi toolbox 1.01, and the matlab optimization toolbox. Create_ROI is running fine, but then I get halted at batch_fitting. The error is posted below:

>> cd /Users/bneyland/Documents/Tools/noddi/practice/

>> CreateROI('NODDI_DWI.hdr', 'roi_mask.hdr', 'NODDI_roi.mat');

loading the DWI volume : NODDI_DWI.hdr

loading the brain mask : roi_mask.hdr

creating the output ROI ...

saving the output ROI as NODDI_roi.mat

done

>> protocol = FSL2Protocol('NODDI_protocol.bval', 'NODDI_protocol.bvec');

>> noddi = MakeModel('WatsonSHStickTortIsoV_B0');

>> batch_fitting('NODDI_roi.mat', protocol, noddi, 'FittedParams.mat', 8);

Error: File: batch_fitting.m Line: 92 Column: 17

Invalid syntax for calling function 'roi' on the path. Use a valid syntax or explicitly initialize 'roi' to make it

a variable.

Have you or anyone else run into this issue? If so, is there a way for me to fix this? I apologize if this is a simple question.

This is line 92 from the batch_fitting.m script:  voxel = roi(i,:)';

As far as I can tell, the 'roi' variable should just pull from my already defined NODDI_roi.mat so I am not sure why there is an error.

Thank you ahead of time and please let me know if you need more information.

Thank you,

Blake

[Hui Zhang]

Hi Blake,

Your error seems to suggest that you have a function also called 'roi' in your matlab environment.

Gary

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[Jan Valošek]

Hi Blake and Gary,

I have encountered same problem as reported by Blake. Problem is not in the another function named 'roi'. Cause of this problem is, that parfor loop command requires initialization of all used variables inside this parallel loop. However, 'roi' variable is not initialized in the batch_fitting.m function and is only loaded which is not assumed as initialization. I solved it by adding roi=[]; before load(roifile) command.

I use matlab R2019b, maybe previous version of parallel loop have different requirements. 

Cheers,

Jan 

Dne sobota 28. září 2019 10:40:18 UTC+2 Gary napsal(a):

Hi Blake,

Your error seems to suggest that you have a function also called 'roi' in your matlab environment.

Gary

On Sat, Sep 28, 2019 at 9:34 AM Blake Neyland <bl.n...@hotmail.com> wrote:

Hi Gary,

I am new to the NODDI Toolbox and have been running into some issues when trying to process the example dataset you provide in your tutorial. I have downloaded Matlab 2019b, niftimatlib 1.2, noddi toolbox 1.01, and the matlab optimization toolbox. Create_ROI is running fine, but then I get halted at batch_fitting. The error is posted below:

>> cd /Users/bneyland/Documents/Tools/noddi/practice/

>> CreateROI('NODDI_DWI.hdr', 'roi_mask.hdr', 'NODDI_roi.mat');

loading the DWI volume : NODDI_DWI.hdr

loading the brain mask : roi_mask.hdr

creating the output ROI ...

saving the output ROI as NODDI_roi.mat

done

>> protocol = FSL2Protocol('NODDI_protocol.bval', 'NODDI_protocol.bvec');

>> noddi = MakeModel('WatsonSHStickTortIsoV_B0');

>> batch_fitting('NODDI_roi.mat', protocol, noddi, 'FittedParams.mat', 8);

Error: File: batch_fitting.m Line: 92 Column: 17

Invalid syntax for calling function 'roi' on the path. Use a valid syntax or explicitly initialize 'roi' to make it

a variable.

Have you or anyone else run into this issue? If so, is there a way for me to fix this? I apologize if this is a simple question.

This is line 92 from the batch_fitting.m script:  voxel = roi(i,:)';

As far as I can tell, the 'roi' variable should just pull from my already defined NODDI_roi.mat so I am not sure why there is an error.

Thank you ahead of time and please let me know if you need more information.

Thank you,

Blake

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[Blake Neyland]

Thanks Jan, I tried this as well and it worked fine!

[Hui Zhang]

Hi all,

Jan’s diagnosis was spot on.  This was never an issue for the earlier Matlab versions I have developed and tested the toolbox in, but has become an issue now.  A permanent fix is now available as version 1.02.

Gary

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