Hi,
In addition to what Mark said, you also appear to have a couple of
errors in your command.
Your ref is:
-ref /Applications/fsl-5.0.4/data/standard/MNI152_T1_2mm brain
(Notice the space between mm and brain - this is why you're getting
the 'Unrecognised option b' error. ) It should be 2mm_brain
You're also missing a dash before searchrx in your command.
On Sat, Jun 28, 2014 at 7:21 PM, Mark Jenkinson
<[log in to unmask]> wrote:
> Hi,
>
> It looks like you are running FLIRT rather than MCFLIRT, which is probably why you are getting the error. I'm not sure what the "mcflirt tab" is, so I'm not sure what this is running. The -plots option in mcflirt (not flirt) should generate a *.par output file that contains the information you want.
>
> All the best,
> Mark
>
>
>
>
>
>
> On 27 Jun 2014, at 18:52, Damji Heo <[log in to unmask]> wrote:
>
>> Hello,
>>
>> I keep getting a problem whenever I try to run motion parameters using fsl.
>>
>> The motpars I got is 4x4 volumes, but I need to get more volumes so that I could plot 4:6.
>>
>> I kept running this command line mcflirt -in filename -out bold_mcf -plots -report
>>
>> but its still same.
>>
>> So, I tried this time to use mcflirt tab, and modified the command lines as
>>
>> /Applications/fsl-5.0.4/bin/flirt -in /filename -ref /Applications/fsl-5.0.4/data/standard/MNI152_T1_2mm brain -out bold_mcf -plots -bins 256 -cost corratio searchrx -90 90 searchry -90 90 -searchrz -90 90 -dof 6 -interp trilinear
>>
>> and I keep getting 'Unrecognised option b'
>>
>> What is the way to get more volumes for motpars?
>>
>>
>> Thanks in advance,
>>
>> Damji
>>
--
Niels Bergsland
Integration Director
Buffalo Neuroimaging Analysis Center
100 High St. Buffalo NY 14203
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