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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