Hi Lucia
On 14 Apr 2015, at 12:51, Li, Lucia M <[log in to unmask]> wrote:
> Dear Ludovica,
>
> Thank you so much for your answers!
>
> Can I just check a quick follow-on point?
>
>
>> c) this cleaned data will go into FEAT analyses - is it appropriate to remove the motion confounds using fix OR should we do MCFLIRT Motion Correction in the FEAT GUI?
> Motion correction with MCFLIRT re-aligns the volumes and produces the motion parameters that are then removed by FIX (together with the components listed in the txt file). So you still need to do MCFLIRT motion correction as part of the preprocessing.
>
> What you can avoid after using FIX is to include the motion parameters as confounds in a first-level GLM design matrix (as their contribution has been already regressed out by FIX).
>
> --> I assume that this latter sentence only applies if you use the "-m" option when doing "fix -a …"?
Yes, exactly. This is if you use the -m option. You can also use the -m option when you use the “full” FIX call:
fix <single-session.ica> <train>.RData <thresh> -m
>
> Kind regards,
> Lucia
>
>
Best,
Ludovica
—
Ludovica Griffanti, PhD
Analysis Postdoctoral Research Assistant
Oxford Centre for Functional MRI of the Brain (FMRIB)
Nuffield Department of Clinical Neurosciences, University of Oxford
John Radcliffe Hospital
Oxford, OX3 9DU, UK
email: [log in to unmask]
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Ludovica Griffanti [[log in to unmask]]
> Sent: Tuesday, April 14, 2015 12:44 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FIX - motion parameter correction
>
> Hi Lucia,
> On 13 Apr 2015, at 16:53, Lucia M Li <[log in to unmask]> wrote:
>
>> Dear FSL users & experts,
>>
>> I have a quick query regarding using FIX.
>>
>> We have run fix on some single session ICA data, using a set of training data we made previously. We used the command:
>>
>> fix <single-session.ica> <train>.RData <thresh>
>>
>> We then altered some of the labels created in the fix4melview_<train>_<thresh>.txt file, and now wish to apply these labels to our original data again, and we would like to correct for the motion as well. So we will run:
>>
>> fix -a <single-session.ica/new_fix4melview_file.txt> -m
>>
>> Our question is:
>> a) is this the appropriate command to use to apply the new .txt file labels to the original data?
> yes
>
>> b) does running the first command (fix <single-session.ica> <train>.RData <thresh>) remove motion confounds?
> no
>
>> c) this cleaned data will go into FEAT analyses - is it appropriate to remove the motion confounds using fix OR should we do MCFLIRT Motion Correction in the FEAT GUI?
> Motion correction with MCFLIRT re-aligns the volumes and produces the motion parameters that are then removed by FIX (together with the components listed in the txt file). So you still need to do MCFLIRT motion correction as part of the preprocessing.
> What you can avoid after using FIX is to include the motion parameters as confounds in a first-level GLM design matrix (as their contribution has been already regressed out by FIX).
>
>> d) because this cleaned data has already had the standard preprocessing through the single-subject ICA (pre-stats menu: BET, MCFLIRT MOTION correction, smoothing, highpass filtering, B0 unwarping), should we untick these options in the FEAT GUI to prevent running these steps twice?
> Yes, you don’t need to do any pre-stats anymore.
>>
>> Many thanks in advance for your help.
>>
>> Kind regards,
>> Lucia
>
>
> Hope that helps.
> Best,
> Ludovica
>
> —
> Ludovica Griffanti, PhD
> Analysis Postdoctoral Research Assistant
> Oxford Centre for Functional MRI of the Brain (FMRIB)
> Nuffield Department of Clinical Neurosciences, University of Oxford
> John Radcliffe Hospital
> Oxford, OX3 9DU, UK
> email: [log in to unmask]
|