I actually abandoned this for a while so that I could get some real
work done... but now I'm coming back to it.
If I do the registration step I can't get an identity matrix... it
always wants to nudge my data a little one way or another. Not a huge
deal, but noise is noise. I tried initializing with an identity
matrix, and also specified no search and 3 dof. I tried dof=0, and
that seems to do a dof=12!
Is there a way to lie to feat? E.g. just populate the reg directory
with appropriate .mat files or similar. I'm actually writing some
python scripts to do all this stuff, so if I can set it up in a way
that's reliable, it's OK if it's brittle... as the scripts will take
care of any necessary precision.
Cheers,
Dav
On Jan 12, 2009, at 1:45 PM, wolf zinke wrote:
> Hi Dav,
>
> Apparently there was no reply yet, so I give it a try, especially
> because I think that your point of the group analysis without
> coregistration to a standard template might be an interesting point.
>
> Dav Clark wrote:
>> Currently, FSL is not doing a very good job coregistering my
>> various images using FLIRT. (And also, I can't figure out how to
>> tell FLIRT to motion correct an EPI BOLD sequence to a frame from
>> another EPI!).
> There have been several discussions about improving flirt results.
> Overall I have to say that flirt is doing quiet a good job. However,
> some of the useful options are available via the command line call.
> It is important to use an appropriate cost function. Depending on
> the data type and quality you might get better results by changing
> the degrees of freedom or by applying a fieldmap undistortion prior
> coregistration if this data is available. It also might help to get
> the images roughly aligned before doing Flirt (check out the Nudge
> tool) in case the data is not already in the same orientation. If
> you reorient the data several times I would recommend to combine
> transformation matrices and apply only one final image
> transformation in order to avoid multiple interpolations (check out
> the convert_xfm tool for this).
> Usually you could use mcflirt for motion correction, since flirt is
> coregistering only 3d volumes. However, it is possible to split your
> 4D epi timeseries (fslsplit) and run flirt on each volume
> separately. If you search earlier discussions about this topic you
> might find some suggestions how to implement such a loop in BASH.
>>
>> So specifically - is there a way I can give FEAT some already
>> motion corrected EPI, do low-level analyses on these, and then do a
>> higher-level analysis without doing any registration (i.e. - tell
>> FEAT that they are already registered).
> It should be quiet simple to use motion corrected EPI data for a
> feat analysis, you just select it as input data and uncheck the
> mcflirt option for he preprocessing. If you still want to include
> motion correction parameter for the glm analysis you could create
> extra regressors for each parameter or use the new nice option of a
> confound matrix. If you did use flirt on a splitted timeseries you
> could derive the motion parameter easily from the resulting
> transformation matrix with the avscale function (using the --
> allparams option). Again you will find quiet a bit more information
> about these issues in earlier discussions.
>
> For the higher level analysis it is important that your data is in a
> kind of common space, so it would not make much sense to run higher-
> level analysis without any coregistration to a standard space.
> However, if you collect data from some kind of single subject where
> you could assume that after alignment to a reference scan all data
> is in a common space you might consider to skip the coregistration
> within feat. I do not know if something like this is possible, but
> it might help in some cases (for example mine). Anyway, if the data
> is already aligned, you could run a 'fake' coregistration, where you
> specify the reference scan again, but you do a 3 dof transformation
> (translation only) and use the no search option. additionally you
> can specify an identity matrix ($FSLDIR/etc/flirtsch/ident.mat) as
> initialisation transform. This is one of the nice hidden features
> you find when looking behind the GUIs. You can specify such a matrix
> at the end of the design.fsf file (following the comment # Now
> options that don't appear in the GUI) and run feat after editing the
> file.
>
>>
>> More generally - the HTML documentation is incredibly sparse... is
>> there a meatier source of documentation somewhere?
> I guess you can find far more information in this mailing list,
> especially if you are able to ask specific question where your
> problems are described in a well understandable manner. I think
> there are many people out there happy to help and share their
> knowledge and experience. You also could check the slides from
> previous FSL courses and the technical reports to find some more
> details. Attend the next FSL course. I also find it very helpful to
> check al the log files to see what actually is done in each step.
> Many command line tools provide some information (ok, sparse again)
> about there meaning and usage if you just type them in. You can use
> for example ls $FSLDIR/bin/ to get a list of available tools. You
> also could open bash scripts in the $FSLDIR/bin directory to see
> what's going on there or check the source code.
>
> I hope I was able to give you some hints,
> wolf
>>
>> Thanks!
>> Dav Clark
>> --
>> CognAc (aka Ivry) Lab
>> UC Berkeley
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