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cheba-nil / CNS

CHeBA NiL Software with UBO Detector to extract white matter hyperintensities
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Failure to output create #4

Open luanraguiar opened 3 years ago

luanraguiar commented 3 years ago

Dear all,

I'm trying to run UBO_detector for WMH extraction, and the following message appears below (from commandwindow). I will be very grateful if you can help me in this matter. My system is Windows (64bit), Matlab 2019a, FSL 6.0.4 (via the Windows Subsystem for Linux), and SPM12.

In step 5 of "Quick Start Guide - WMH extraction", I selected the option "Display on screen", and in step 6 "Extract without QC stops". However, no image appeared on the screen of "Web Browser - QC" , as well as in the output directory.(The directory's 'QC' options are empty, just with the Web Browser - QC link which has no image).

`UBO Detector: Starting WMH extraction pipeline (no QC stops) ... Starting parallel pool (parpool) using the 'local' profile ... Connected to the parallel pool (number of workers: 6). 'gunzip' não é reconhecido como um comando interno ou externo, um programa operável ou um arquivo em lotes. 'gunzip' não é reconhecido como um comando interno ou externo, um programa operável ou um arquivo em lotes. CNSP_webViewSlices_pair: 1 counterpart/s. CNSP_webViewSlices_pair: Slicing images ... CNSP_webViewSlices_pair: Generating webpage ... CNSP_webViewSlices_pair: Done. ! foi inesperado neste momento. CNSP_webViewSlices_overlay: 3 overlay image/s. CNSP_webViewSlices_overlay: Slicing images ... CNSP_webViewSlices_overlay: Generating webpage ... CNSP_webViewSlices_overlay: Done. ! foi inesperado neste momento. Warning: File: WMHextraction_preprocessing_Step4.m Line: 104 Column: 74 The temporary variable flowMap will be cleared at the beginning of each iteration of the parfor loop. Any value assigned to it before the loop will be lost. If flowMap is used before it is assigned in the parfor loop, a runtime error will occur. See Parallel for Loops in MATLAB, "Temporary Variables".

In UBO_Detector>WMHextraction_main_noQCstops (line 3360) In UBO_Detector>extractWithoutStops_Callback (line 666) In gui_mainfcn (line 95) In UBO_Detector (line 42) In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)UBO_Detector('extractWithoutStops_Callback',hObject,eventdata,guidata(hObject)) CNSP_webViewSlices_overlay: 1 overlay image/s. CNSP_webViewSlices_overlay: Slicing images ... CNSP_webViewSlices_overlay: Generating webpage ... CNSP_webViewSlices_overlay: Done. CNSP_webViewSlices_overlay: 1 overlay image/s. CNSP_webViewSlices_overlay: Slicing images ... CNSP_webViewSlices_overlay: Generating webpage ... CNSP_webViewSlices_overlay: Done. 0.01 hours elapsed to finish the whole extraction procedure.`

Could anyone tell where the error is? Could the reason be the FSL, or because it is running on the Windows system?

Thank you so much! Best, Luan .

luanraguiar commented 3 years ago

Hello @ForrestCKoch , could you help me with this problem? Please!

ForrestCKoch commented 3 years ago

Hi @luanraguiar, sorry for the delayed response -- I haven't worked on this project for a while, and when I did I wasn't very involved on the GUI side of things. @JiyangJiang is the current maintainer of this package I believe.

Could anyone tell where the error is? Could the reason be the FSL, or because it is running on the Windows system?

I see no error indicated by your output. I believe the warning is okay. If you are after the QC webpage, there should be a bunch of files in StudyFolder/subjects/QC. From memory, there is an "index.html" that you can open in your web-browser which should display the qc images.