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 the
one-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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