New FSL FNIRT Normalisation Error

[PhilipM]

Hello again,

I’ve been getting good results with my data using the SPM12 Segment Nonlinear protocol but I thought I’d experiment with the new FSL FNIRT. Unfortunately I come up with the following error, is this a bug? I’ve processed my T1, FLAIR and post-op CT images and named them as usual. I use FSL FLIRT to co-register my images before running Lead-DBS, so I go straight in at the normalisation step. Thanks again!

fnirt::fnirt_clp: No file matching –refmask= found
Image Exception : #22 :: ERROR: Could not open image /Users/philipm/Desktop/Tractography/Lead_DBS_Analysis/Lead_DBS_056_Test2/glanatCompositeCoeffs
invwarp: Problem reading warp-file /Users/philipm/Desktop/Tractography/Lead_DBS_Analysis/Lead_DBS_056_Test2/glanatCompositeCoeffs.nii
Error using checkfilename>validateFilename (line 165)
Function GUNZIP was unable to find file
”/Users/philipm/Desktop/Tractography/Lead_DBS_Analysis/Lead_DBS_056_Test2/glanat.nii”.

Error in checkfilename (line 49)
[fullfilename, fid] = validateFilename( …

Error in gunzip>checkFilesURLInput (line 118)
[fullFileName, url] = checkfilename(inputFiles{1}, validExtensions,
fcnName, …

Error in gunzip (line 61)
[files, url, urlFilename] = checkFilesURLInput(files,
{‘gz’},’FILES’,mfilename);

Error in ea_fnirt (line 104)
gunzip(outputimage);

Error in ea_normalize_fsl (line 33)
ea_fnirt([options.earoot,’templates’,filesep,’mni_hires’,options.primarytemplate,’.nii’],…

Error in ea_autocoord (line 73)
eval([options.normalize.method,'(options)’]); % triggers the
normalization function and passes the options struct to it.

Error in ea_run (line 95)
ea_autocoord(options);

Error in lead_dbs>run_button_Callback (line 240)
ea_run(‘run’,options);

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in lead_dbs (line 43)
gui_mainfcn(gui_State, varargin{:});

Error in
matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)lead_dbs(‘run_button_Callback’,hObject,eventdata,guidata(hObject))
Error while evaluating UIControl Callback

[ningfei]

Hi Philip,

In the current release (v1.5.0.6), the FSL pipeline is not yet finished/stable enough. I had just fully incorporated the FSL FLIRT&FNIRT lately and tested on my side. It’s already there in github, but not released yet. Maybe you can wait for a few days? I guess we will have a new release soon.

Best,
Ningfei

[PhilipM]

Thank you, I will wait for later releases to test again. Best wishes.

[Author]

Posts