error when run RunFile.m

[Zhenya97]

Undefined function or variable 'MRIread'.
Error in RunFile (line 14)
DataVol = MRIread([DataPath,FileName]);

[abhi4ssj]

Hi,

MRIread is a function within FreeSurfer matlab library which reads the MRI file. Make sure you download FreeSurfer and add it to the path before executing the RunFile.

[Zhenya97]

Thank you very much.

[Zhenya97]

Sorry for bothering you again. Do you have Win10 OS version? Or could you please give some advise about running this method on Win10 OS? Since we most use Win10 OS here, I appreciate it if you can give me some advise.

Thanks

[abhi4ssj]

Hi,

I think MRIread.m can be used in Windows 10 for reading. Or you can some other MRI Volume readers. Just make sure the orientation after reading matches, i.e. coronal slices should go in coronal net and vice-versa. You might need to play around this.

There is an important pre-processing step for any random MRI scans. You need to execute a FreeSurfer command from the terminal:

mri_convert (input_volume.mgz) (out_volume.mgz) --conform

Unfortunately, FreeSurfer only runs in MAC and Linux. In this case, I suggest installing a virtual machine in your Win 10 machine with Linux, pre-process all the volume and use the tool.

Best
Abhijit

[Zhenya97]

Thank you very much. I have met another error when I ran the codes.

Error in SegmentVol_EstimateUncertainty (line 10)
fnet = dagnn.DagNN.loadobj(net);

Error in RunFile (line 18)
[Predictions, cv_s, iou_s, SegTime] =
SegmentVol_EstimateUncertainty(DataVol,NumFrames,
NumMCsamples, out_dir);

I appreciate it if you could give me some help with this.

Thanks

[abhi4ssj]

It seems you did not add MatConvNet to the path. Please follow the instructions in

https://github.com/ai-med/QuickNATv2

for the installation of the tool and then use my code.