Ta
I have problems with running Gui from my processor
Any command line input that do it?
DC
>-----Original Message-----
>From: FSL - FMRIB's Software Library
>[mailto:[log in to unmask]] On Behalf Of Andreas Bartsch
>Sent: 04 October 2006 10:56
>To: [log in to unmask]
>Subject: [FSL] AW: [FSL] melodic high pass filter cutoff
>
>Hi,
>no - it doesn't. You will need mcflirt for it, preferably
>prior to smoothing. Also: --Ostats in melodic will output the
>stats maps for you.
>Hope this helps,
>Cheers-
>Andreas
>
>________________________________
>
>Von: FSL - FMRIB's Software Library im Auftrag von D A Cousins
>Gesendet: Mi 04.10.2006 11:18
>An: [log in to unmask]
>Betreff: Re: [FSL] melodic high pass filter cutoff
>
>
>
>Hi Steve
>I have managed to get the pre-processing sorted out and
>melodic runs quite happily from the command line. The commands
>used as follows
>
>bet <input> <output> -m
>ip_16SI <file from bet> <pre-processing output> 0.2 -s 5 -I
>1000 -t 80 1 melodic --nobet --mask=<file from bet> --tr=3
>--report -v -I <file from
>pre-processing>
>
>Does that look ok? (TR3000ms TE40 slice thickness 6 voxel 80
>high pass as DeLuca paper 250s)
>
>The main question I have is........ Does the above command
>perform motion correction, and if not, how do I request it?
>Ta
>
>DC
>>-----Original Message-----
>>From: FSL - FMRIB's Software Library
>>[mailto:[log in to unmask]] On Behalf Of Steve Smith
>>Sent: 26 September 2006 12:48
>>To: [log in to unmask]
>>Subject: Re: [FSL] melodic high pass filter cutoff
>>
>>Hi - a general comment is that we really don't recommend
>using Windows
>>for larger analyses - for one thing, Windows just doesn't
>handle large
>>RAM jobs well - I don't know if this is relevant to your problem or
>>not. Another general thing to check is that you have the
>exact version
>>of Cygwin described on the FSL installation page (as the
>latest version
>>of Cygwin is broken wrt TC/TK/TIX).
>>
>>So - to answer your command-line queries:
>>
>>1. If you are doing command-line processing then all stages of the
>>pre-stats need doing, does the FEAT GUI work for you? In which case I
>>would use that maybe. You can do intensity normalisation using "ip" -
>>though we generally recommend NOT doing intensity normalisation.
>>
>>2. Same as above - and again this is an option to "ip".
>>
>>3. Ditto!
>>
>>Cheers, Steve.
>>
>>
>>
>>On 26 Sep 2006, at 10:56, David Cousins wrote:
>>
>>> Hi there
>>> I am running Melodic on resting state fMRI, in effect trying to
>>> replicate the DeLuca 2006 analysis
>>>
>>> Windows XP PC with Cygwin
>>> Melodic runs well from the command line but not from the GUI - it
>>> fails to make new folders etc (lots of disc space and numerous file
>>> locations tried)
>>>
>>> I was wondering how to set preferences in the command line
>so that i
>>> can run melodic from there. In particular
>>>
>>> 1. How do i request mean-based intensity normalisation in
>>the prestats
>>> 2. How do i change the spatial smoothing of FWHM to 5mm 3. How do i
>>> set a high-pass filter cutoff of 250s
>>>
>>> Many thanks
>>> DC
>>
>>
>>---------------------------------------------------------------
>>---------
>>---
>>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
>>---------------------------------------------------------------
>>---------
>>---
>>
>
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