Hi!
In my case, MRIConvert FSL NIFTI gives a .nii file. Maybe your
MRIConvert is not working properly?
Cheers,
Markus
Quoting Emily T Stoneham <[log in to unmask]>:
> 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
>> >
>>
>
--
Dr. med. Markus Gschwind, M.D.
Laboratory for Neurology and Imaging of Cognition
Dept of Neurosciences
University Medical Center (CMU)
1 Michel-Servet - 1211 GENEVA - CH
Tel 0041 (0) 22 379 5324
Fax 0041 (0) 22 379 5402
email: [log in to unmask]
http://labnic.unige.ch
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