The .gfeat directory (and its subdirectories) structure is required as input to fmripower (http://www.fmripower.org/). I'd like to know what my power is for a particular type of analysis stream, which doesn't use the FEAT registration. So, I guess I'll choose the latter that you've listed below; mimic the structure. Ouch. Oh well, off I go!
Thank you again for your help
-Daniel
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Steve Smith [[log in to unmask]]
Sent: Tuesday, September 08, 2009 11:48 PM
To: [log in to unmask]
Subject: Re: [FSL] FLAME without feat registration...
Hi, I don't understand why you want to create the .gfeat directory
structure if you already have all the data in standard space. Anyway,
On 8 Sep 2009, at 16:21, Daniel Schwartz wrote:
> So, if I need the .gfeat directory structure, I have two choices, I
> think:
>
> 1) I need to manually create the .gfeat/.cope1 directory structure
> with the output of flameo (change ./stats in the exmaple you
> mentioned below)
>
> -or-
>
> 2) I have to do single subject registrations in FSL. It seems
> strange that this needs to happen to get the standard directory
> structure. Is there a way to run the FEAT scripts WITHOUT doing
> within subject registrations?
Sure - you can turn off registration in the GUI - but I can't see why
you would want to do this.
As far as I can see, your two choices that make the most sense are
either to run FEAT fully from scratch using the GUI, or make flameo
run from the command line without running the full FEAT analyses or
generating the FEAT output directory structure. Anything in between
will be complicated as you will need to know exactly how to mimic the
FEAT output structure, which will be more work than just running FEAT.
Cheers.
>
> Thanks
> -Daniel
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
> Of Steve Smith [[log in to unmask]]
> Sent: Friday, September 04, 2009 10:41 PM
> To: [log in to unmask]
> Subject: Re: [FSL] FLAME without feat registration...
>
> Hi - no, the FEAT scripts generate the .gfeat output directory -
> flameo outputs into a directory determined by the --ld option. An
> example call is:
>
> flameo --cope=cope4D --vc=varcope4D --mask=mask3D --ld=stats --
> dm=design.mat --cs=design.grp \
> --tc=design.con --runmode=flame12 --nj=10000 --
> bi=500 --se=1 --fm --zlt=2.25 --zut=2.65
>
> Cheers
>
>
> On 4 Sep 2009, at 21:28, Daniel Schwartz wrote:
>
>> Well, I tried this, using:
>>
>>> fslmerge -t COPE1 *.feat/cope1.nii.gz
>>
>> to concatenate the cope1 files for each subject into one file,
>>
>> then
>>
>>> flameo --cope="COPE1.nii.gz" --mask="mask.nii.gz" --dm=GRP.mat --
>>> tc=GRP.con --cs=GRP.grp --runmode=flame1
>>
>> and I get a logfile, with results, but no .gfeat directory.
>> Shouldn't this be the output of 'flameo' along with a .gfeat/.cope1
>> directory?
>>
>>
>> Thankyou for your prompt replies!
>> -Daniel
>>
>>
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>> Of Daniel Schwartz [[log in to unmask]]
>> Sent: Friday, September 04, 2009 10:05 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] FLAME without feat registration...
>>
>> More specifically, I guess, ( I think I understand the usage of all
>> the rest of the flameo options), what is the "--cope" cope regressor
>> datafile? A 4D file of all the regression coefficients for that
>> particular condition concatenated over all runs/subjects?
>>
>> -Daniel
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>> Of Daniel Schwartz [[log in to unmask]]
>> Sent: Friday, September 04, 2009 9:18 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] FLAME without feat registration...
>>
>> Hahahaha... I apologize, I had thought that the 'flame' command line
>> program had vanished... but didn't think it might've been renamed.
>> Why isn't in on the feat tools page? Anyway, I was trying to run
>> FLAME from the GUI, and got the error message that "it seems some
>> reg's hadn't been done". But since I have you on the line, I might
>> as well ask how to do my ridiculously easy analysis in 'flameo'...
>>
>> I have 24 subjects, 12 in one group, 12 in another, 2 runs for each
>> subject (separate .feat directories), two conditions (copes?) for
>> each run, and I just want to know the group contrast for the
>> regression coefficient of each condition (again, for input to
>> fmripower, which requires a .gfeat type of setup). So how should I
>> run it from $>?
>>
>> Thankyou SO MUCH for your help...
>> ________________________________________
>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>> Of Steve Smith [[log in to unmask]]
>> Sent: Friday, September 04, 2009 9:09 AM
>> To: [log in to unmask]
>> Subject: Re: [FSL] FLAME without feat registration...
>>
>> Ah - ok, so you don't need the FEAT scripts at all - just the correct
>> call to 'flameo' on the command line. What command are you trying
>> and what's the error message?
>> Cheers.
>>
>>
>> On 4 Sep 2009, at 17:02, Daniel Schwartz wrote:
>>
>>> I've done ALL my preprocessing with AFNI, then just converted to
>>> NIFTI and ran the single subject GLM for each subject with all
>>> preprocessing turned off (including reg) in feat. There ARE
>>> no .feat/
>>> reg* directories...
>>>
>>> How can I fake them? Do I need to, or is there a way to run the
>>> second level without registration info?
>>> -Daniel
>>> ________________________________________
>>> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf
>>> Of Steve Smith [[log in to unmask]]
>>> Sent: Friday, September 04, 2009 9:00 AM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] FLAME without feat registration...
>>>
>>> Hi - if you've overwritten the lower-level FEAT registration
>>> information correctly (or udpated the .feat/reg_standard directories
>>> correctly) using your custom registrations, then the higher-level
>>> FEAT
>>> (using FLAME etc) should run fine.....at what stage are you
>>> inserting
>>> your custom registrations?
>>>
>>> Cheers.
>>>
>>>
>>> On 4 Sep 2009, at 16:57, Daniel Schwartz wrote:
>>>
>>>> How do I do it? I'm trying to use fmripower for a power analysis,
>>>> I've run
>>>> feat (after my own registration script, and with all registration
>>>> turned
>>>> off) and now want to run FLAME. I get the error message,
>>>> though... I
>>>> noticed
>>>> that there is a solution from 2002, about using the flame command
>>>> line
>>>> program... but it isn't in more recent distros? (Maybe I'm wrong
>>>> about
>>>> this.) Help!
>>>>
>>>> -Daniel
>>>>
>>>
>>>
>>> ---------------------------------------------------------------------------
>>> 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
>> ---------------------------------------------------------------------------
>>
>
>
> ---------------------------------------------------------------------------
> 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
---------------------------------------------------------------------------
|
