Dear Mark,
Thanks for the help, but I do have another question: I was using the MRI-Convert software that everyone raves about, and it only gives me 2 options for NIFTI: NIFTI and FSL NIFTI. Both result in the .hdr and .img file conversion. Also, I can open the individual file in FSL Viewer, but can't run anything on it, which tells me that mabye it isn't the file. Does this mean I am converting incorrectly?
Thanks,
Emily
----- Original Message -----
From: Mark Jenkinson <[log in to unmask]>
Date: Thursday, February 7, 2008 3:02 am
Subject: Re: [FSL] BET Error 'image file not valid'
> Dear Emily,
>
> It does sound like your files are corrupted or incorrect in some way.
> You were certainly right to remove spaces - that would definitely have
> caused problems.
>
> It shouldn't matter that you've transfered from a PC to a Mac as long
> as the PC software created a valid image file. I'm slightly surprised
> that you are using the two-file version of nifti (that is, with a .hdr
> and a .img) although that is perfectly valid, just less common that
> theone-file version (.nii). Note that zipping (.gz) can be done to
> any of
> the above.
>
> The best thing to do is probably to send us your files or try another
> converter (check the list for previous posts about converters).
> To send us your files use the upload site at:
> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi
> and send us the reference number.
>
> We should be able to tell you if your files are OK or not.
> All the best,
> Mark
>
>
>
> On 6 Feb 2008, at 18:22, Emily Stoneham wrote:
>
> > Hello!
> >
> > I am learning FSL and fMRI the hard way. I was given actual
> > data to try and use that is not as
> > easy as the feeds eval data. FEEDS works great, but when I try
> to
> > use actual data, I keep getting
> > errors. To give you some background:
> >
> > I am using a Mac power PC OSX 10.4.11, and going through the FSL
> GUI.> I converted the raw data from the scanner into FSL NIFTI
> format by
> > using the MRI Convert software
> > on a PC (I couldn't find one that worked for the Mac), and
> > transferred that the Mac.
> > It converted the files into .hdr and .img files (the latter
> doesn't
> > seem to be recognized by FSL)
> > At first, I was getting this error:
> >
> > wrong # args: should be "bet:select w ?dummy?"
> > wrong # args: should be "bet:select w ?dummy?"
> > while executing
> > "bet:select .rename /Users/MLE/Desktop/fMRI Data/36 Raw Converted
>
> > Data/KALBFLEISCH-5295-
> > 36/1_3_T1_FL_AX__(PhaseAP)_20080107/KALBFLEISCH-5295-36_1_3_T1_..."
> > ("eval" body line 1)
> > invoked from within
> > "eval "$command $outputfile1" "
> > (procedure "feat_file:invoke" line 29)
> > invoked from within
> > "feat_file:invoke .wdialog1 bet
> > (.rename,input) .rename.f.input.var_filhis
> .rename.f.input.var_selhis> ::FileEntry {bet:select .rename}"
> > (command bound to event)
> >
> > SO... I went to the archives and found something that indicated
> > that it might be because of gaps
> > (spaces) in the naming convention of each of the folders and
> files,
> > so I (think) I fixed it.
> >
> > Now I get this error:
> >
> > /Users/MLE/fsl/bin/bet
> > /Users/MLE/Desktop/fMRI_Data/36_Raw_Converted_Data/
> > KALBFLEISCH529536/1_3_T1_FL_AX_20
> > 080107/KALBFLEISCH529536_1_3_T1_FL_AX_20080107
> > /Users/MLE/Desktop/fMRI_Data/36_Raw_Converted_Data/
> > KALBFLEISCH529536/1_3_T1_FL_AX_20
> > 080107/KALBFLEISCH529536_1_3_T1_FL_AX_20080107_brain -f 0.5 -g 0
> >
> > Error: input image
> > /Users/MLE/Desktop/fMRI_Data/36_Raw_Converted_Data/
> > KALBFLEISCH529536/1_3_T1_FL_AX_20
> > 080107/KALBFLEISCH529536_1_3_T1_FL_AX_20080107 not valid
> >
> > child process exited abnormally
> > Finished
> > /Users/MLE/fsl/bin/bet /Users/MLE/Desktop/test
> /Users/MLE/Desktop/
> > test_brain -f 0.5 -g 0
> >
> > Error: input image /Users/MLE/Desktop/test not valid
> >
> > child process exited abnormally
> > Finished
> >
> > Do my file names need to be in .nii.gz format? If so, how do I
> get
> > them there?
> >
> > Regards,
> > Emily
> >
>
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