Dear Stefanie,
The first error looks like you've mistyped the name of the file as it is constantly
complaining about "MNI152T_1_2mm_brain" rather than "MNI152_T1_2mm_brain"
(note that T_1 should be _T1). In your command line it looks correct, but maybe
that is because you retyped it into the email and inadvertently fixed it?!? It is hard
to be sure. However, your command line is still not good, as you need to specify
other options - specifically -applyxfm, -init and -out. Have a look at the example
usages in the documentation:
http://www.fmrib.ox.ac.uk/fsl/flirt/examples.html
I would also advise looking at the FSL Course material if you are this unfamiliar
with how things work.
The other error I suspect is to do with the that that you seem to have chosen
a filename of "1" which is very strange and may be misinterpretted as a number
rather than a name at some point. It is a very odd error though, so I would try
and get the command line working instead.
I'm assuming that you've run registration in your original FEAT analysis, in
which case you need to be using the example_func2standard transformations
in the *.feat/reg directory. Again, look at the FSL Course material and the FEAT
documentation for more help about this.
All the best,
Mark
On 22 Sep 2011, at 09:51, Stefanie Becker wrote:
> Hi,
>
> thanks for the response! And sorry for the confusion with FLOBS vs. canonical HRF; I've used FLOBS to analyse my data from separate runs, and I would like to average the results from the combined basis functions, or zfstats ('C1&C2&C3') across runs. Now, I've tried to register the corresponding zfstat1.nii.gz to standard space (only linear registration), but wasn't able to do it.
>
> First, I used flirt from the terminal window:
>
> flirt -in /mnt/hgfs/F/MRI/MRI_Jessie/Data/Converted/S1/DIM1_FLOBS.feat/thresh_zfstat1.nii.gz -ref /root/fsl/data/standard/MNI152_T1_2mm_brain
>
> ... but I got the following errors:
>
> ** ERROR (nifti_image_read): failed to find header file for '/root/fsl/data/standard/MNI152T_1_2mm_brain'
> ** ERROR: nifti_image_open(/root/fsl/data/standard/MNI152T_1_2mm_brain): bad header info
> ERROR: failed to open file /root/fsl/data/standard/MNI152T_1_2mm_brain
> ERROR: Could not open image /root/fsl/data/standard/MNI152T_1_2mm_brain
> Image Exception : #22 :: Failed to read volume /root/fsl/data/standard/MNI152T_1_2mm_brain
> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
> FE_bash.sh: line 11: 30613 Aborted
>
>
> Second, I tried using FLIRT from the FEAT GUI;
> [/root/fsl/bin/flirt -in /mnt/hgfs/F/MRI/MRI_Jessie/Data/Converted/S1/DIM1_FLOBS.feat/thresh_zfstat1.nii.gz -ref /root/fsl/data/standard/MNI152_T1_2mm_brain -out -omat 1.mat -bins 256 -cost corratio -searchrx -180 180 -searchry -180 180 -searchrz -180 180 -dof 12 -interp trilinear]
>
> but here the error message said:
> Unrecognised option 1
>
> I got the same error when I tried to register the zfstat to my T1-weighted, brain-extracted image:
> /root/fsl/bin/flirt -in /mnt/hgfs/F/MRI/MRI_Jessie/Data/Converted/S1/DIM1_FLOBS.feat/thresh_zfstat1.nii.gz -ref /mnt/hgfs/F/MRI/MRI_Jessie/Data/Converted/S1/T1_brain.nii.gz -out -omat 1.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear
> Unrecognised option 1
> Finished
>
> Any idea what's going wrong here?
> Also, in general, should I register the zfstat directly to standard space, or should I first register it to the T1-image?
>
> Thanks a lot in advance!
> Stef
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Stephen Smith [[log in to unmask]]
> Sent: Thursday, 22 September 2011 5:31 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Fixed effects with FLOBS?
>
> Hi - yes if you have done an F-test across the FLOBS basis functions you can resample the zstats or fstats into standard space and feed that into randomise.
> You can use the ApplyXFM GUI to resample the stats into standard space - though if you used nonlinear registration you would need to do this on the command line.
>
> However - the main question is that I'm confused that you're talking about both FLOBS and canonical HRFs - these are two distinct HRF options so I'm not sure quite what you've done...
>
> Cheers.
>
>
>
>
>
> On 20 Sep 2011, at 18:24, Stefanie Becker wrote:
>
>> Hi,
>>
>> I sent two messages to the list that don't appear in the September thread -- not sure what happened there.
>> I'll try again: I've got the problem that I need to combine data in a fixed effects analysis based on FLOBS, and I'd like to use the canonical HRF regression PEs. According to the posts, back in 2008, there was no simple solution to this problem, as the first-level analysis doesn't produce copes for the canonical HRF, only the single basis functions.
>>
>> Is there a simple solution now? If not, can I resample the zfstats into standard space and average across them using the function sum(z)/sqrt(n)?
>> This solution was suggested as an analogue to a fixed effects analysis in an earlier thread... but is it then possible to use the output for a third-level ME analysis comparing between different conditions?
>> And if yes, what function do I have to use for the resampling and averaging?
>>
>> THANKS!!!
>>
>> Stefanie
>>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
