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New FSL FNIRT Normalisation Error

You are here: Home1 / Forums2 / Support forum ARCHIVED – Please use Slack Channel instead3 / New FSL FNIRT Normalisation Error4
Viewing 3 posts - 1 through 3 (of 3 total)
  • Author
    Posts
  • 11/16/2016 at 8:49 AM #1637
    PhilipM
    Participant

    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

    11/16/2016 at 10:54 AM #1639
    ningfei
    Keymaster

    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

    11/16/2016 at 2:19 PM #1641
    PhilipM
    Participant

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

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