Sounds good, though it's probably better to use example_func to
register to the anatomical. If you've done registration inside FEAT
you should find all the transforms you need in the .feat/reg directory.
Cheers, Steve.
On 17 May 2006, at 20:17, Martin M. Monti wrote:
> Steve,
>
> my simple plan was the following:
>
> 1) Align filtered_func to the subject's anatomical via flirt
>
> 2) Register the mask (created in Standard space) to the individual
> subject by using the inverse of highres2standard.mat , and use the
> example_filtered_func as the reference. This way the mask is
> registered to the functional (i.e. they both are registered to the
> subject's anatomical) and the header of the mask is the same as the
> functional. (at this point I'll use avwmeants to pull out
> timecourses from that mask)
>
> [alternatively I could probably just apply to the 'standard' mask
> the inverse of the example_func2standard.mat, but I have several
> functionals and I'd like to concatenate them to then use once
> avwmeants]
>
> Makes good sense?
>
> Cheers & thanks for the continuous support,
>
> Martin
>
> ----- Original Message ----- From: "Steve Smith"
> <[log in to unmask]>
> To: <[log in to unmask]>
> Sent: Thursday, May 18, 2006 2:55 AM
> Subject: Re: [FSL] filtered_func & Peri-Stimulus plot
>
>
>> Hi,
>>
>> On 17 May 2006, at 18:13, Martin M. Monti wrote:
>>
>>> Mark,
>>>
>>> thank you, avwmeants works great!
>>> Only one question: does the mask used have to be in the FOV of
>>> the functional I'm pulling out the timecourses from?
>>>
>>> I.e. say I do: avwmeants -i filtered_func_data -o tseries.txt -m
>>> Mask --showall
>>>
>>> Does 'Mask' have to have same FOV and voxel resolution as
>>> filtered_func_data?
>>
>> Yes.
>>
>>> I presume I can use flirt on the mask with filtered_func_data as
>>> a reference image to have them have these same header properties?
>>
>> Indeed, as long as you have an appropriate FLIRT transform file
>> to tell it to apply to the mask.
>>
>> Cheers, Steve.
>>
>>
>>>
>>> Thank for the help,
>>>
>>> Martin
>>>
>>> ----- Original Message ----- From: "Mark Jenkinson"
>>> <[log in to unmask]>
>>> To: <[log in to unmask]>
>>> Sent: Tuesday, May 16, 2006 6:36 AM
>>> Subject: Re: [FSL] filtered_func & Peri-Stimulus plot
>>>
>>>
>>>> Hi Martin,
>>>>
>>>> You can get individual time courses or averages using avwmeants
>>>> (the output is in text form). This will let you process the
>>>> values later
>>>> in whatever way you want.
>>>>
>>>> You are correct about the filtered_func_data - it does not have
>>>> registration applied to it (but is motion corrected).
>>>>
>>>> I'm not quite sure what is wrong with your Featquery, but your
>>>> usage of avwroi is wrong, as you need to use voxel coordinates,
>>>> not mm coordinates. All the voxel coordinates should be integers
>>>> between 0 and N-1 (inclusive). Using -34 as a coordinate would be
>>>> well outside the volume and hence not give you anything except
>>>> zeros in the resulting output.
>>>>
>>>> All the best,
>>>> Mark
>>>>
>>>>
>>>> On 15 May 2006, at 19:42, Martin M. Monti wrote:
>>>>
>>>>> FSL masters,
>>>>>
>>>>> I have 2 ( somewhat unrelated questions)
>>>>>
>>>>> 1) the filtered_func_data: this is the data with all pre-
>>>>> processing steps I asked for, EXCEPT for registration with the
>>>>> High-res and MNI-Template? I'm trying a multi-voxel analysis
>>>>> of my data and need to pull out time-courses for various
>>>>> regions. Also, is there a way to pull out the time-courses
>>>>> associated to EACH voxel within a mask? I know avwroi will
>>>>> pull out one average from a given mask. Is there any pre-
>>>>> compiled utility to pull out each and all the voxels from a
>>>>> mask?
>>>>>
>>>>> 2) I tried featquery to get a peristimulus plot, but I get
>>>>> more event plots than I actually have (i.e. 8 instead of 5!).
>>>>> This is by selecting the filtered_func_data and clicking on
>>>>> the PE/% signal change and peri-stimulus plot options (I use a
>>>>> mask in MNI coordinated and use single-voxel coords). Indeed I
>>>>> think I remember someone mentioning that FSL is left to
>>>>> "guess" what an event is. Is there a way to instruct FSL as of
>>>>> the timepoints that make an event?
>>>>> Alternatively I was wondering whether I could just extract the
>>>>> raw timecourse from the filtered_func_data using avwroi and
>>>>> then manually create the plots (excel-style). Re this, one
>>>>> thing I'm unclear about is, when the syntax requires size: is
>>>>> that number of voxels or voxel size? I tried using 1 for all
>>>>> dimensions (e.g. avwroi filtered_func_data TC_out -34 1 60 1
>>>>> 4 1) but i then couldn't open the image. By changing the 1s
>>>>> to the voxel dimension I could successfully create a new
>>>>> image. Is this correct?
>>>>>
>>>>> cheers
>>>>>
>>>>> Martin
>>>>>
>>
>>
>> ---------------------------------------------------------------------
>> --- ---
>> 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
>> ---------------------------------------------------------------------
>> --- ---
------------------------------------------------------------------------
---
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
------------------------------------------------------------------------
---
|
