Hi Steve,
I'll try what you suggest tomorrow.
I have only used one computer for the analysis, but we did put more
RAM in half way through the analysis (specifically after tbss_2
failed) to try and speed things up. Would that have had an effect?
Best wishes
Suzanna
On 23 Jun 2007, at 07:45, Steve Smith wrote:
> Hi - if you look at all_FA, or alternatively the *_nonlinear_hr.hdr
> images in FAi, you can check which nonlinear-registered images
> failed. If they are empty the most likely cause is that you mixed
> the analysis across different computer types?
>
> Cheers.
>
>
> On 22 Jun 2007, at 13:49, Suzanna Laycock wrote:
>
>
>> Hi Steve,
>>
>> Sorry for the delay in replying - only just got around to doing
>> what you suggested.
>>
>> I'm afraid I've had difficulty doing what you suggested. I ran
>> tbss3_postreg, and found out which brain it considered
>> representative. Looking at the .msf files, all 18 files contains
>> data. However, running avwinfo all_FA_skeletonised file shows that
>> the file only contains 15 of the 18 datasets/time points. This
>> meant I got errors when running randmoise.
>>
>> Ughhh!!!
>>
>> What can I try next?
>>
>> Best wishes
>> Suzanna
>>
>> -------------------------------------
>> Date: Fri, 18 May 2007 06:47:16 +0100
>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
>> Sender: FSL - FMRIB's Software Library <[log in to unmask]>
>> From: Steve Smith <[log in to unmask]>
>> Subject: Re: randomise - tbss
>> In-Reply-To: <000801c79898$cd1820f0$9949a78f@suzanna>
>> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>>
>> urrrgh - I'm pretty sure this is a bug in the IRTK software
>> - but hopefully if this has not happened too many times you can get
>> around it.
>>
>> If you just try running tbss_3_postreg, hopefully it will choose a
>> target subject for whom all the subjectN_to_chosentarget.msf files
>> exist....note which target it chooses and then test that all the
>> relevant .msf files are complete.
>>
>> Cheers, Steve.
>>
>> On 17 May 2007, at 16:34, Suzanna Laycock wrote:
>>
>> > Hi Steve,
>> >
>> > I did what you suggested, and got a number of error warnings. I've
>> > copied
>> > the whole list from the start as this will, undoubtedly, mean a lot
>> > more to
>> > you.
>> >
>> > Can you suggest anything?
>> >
>> > Best wishes
>> > Suzanna
>> >
>> > Suzanna@suzanna ~/FSL_DATA/tbss
>> > $
>> >
>> > -----Original Message-----
>> > From: FSL - FMRIB's Software Library
>> > [mailto:[log in to unmask]] On Behalf Of Steve Smith
>> > Sent: 16 May 2007 16:24
>> > To: [log in to unmask]
>> > Subject: Re: [FSL] randomise
>> >
>> >
>> > Hi - sounds like some of them failed - I suggest that you find the
>> > empty .msf files
>> > ls -l *.msf
>> > and delete the empty ones, then just run tbss_2_reg again and it
>> will
>> > only do the missing registrations.
>> >
>> > Cheers.
>> >
>> >
>> >
>> > On 16 May 2007, at 15:50, Suzanna Laycock wrote:
>> >
>> >> Thanks Steve...should have noticed that.
>> >>
>> >> I've gone back and looked at the files I have, and I was wondering
>> >> if I
>> >> could check the following with you.
>> >>
>> >> I have two groups of 9, so tbss_2_reg should generate 324 files.
>> >>
>> >> But it hasn't, 24 of the files seem to be missing, even though the
>> >> script
>> >> ended.
>> >>
>> >> I take it this isn't normal? Do you have any suggestions why this
>> >> happened?
>> >> I don't want to start re-running the script as it took 10 days to
>> >> complete,
>> >> if we're going to get the same problem.
>> >>
>> >> Best wishes
>> >> Suzanna
>> >>
>> >>
>> >>
>> >> -----Original Message-----
>> >> From: FSL - FMRIB's Software Library [mailto:[log in to
>> unmask]] On
>> >> Behalf Of Steve Smith
>> >> Sent: 14 May 2007 16:24
>> >> To: [log in to unmask]
>> >> Subject: Re: [FSL] randomise
>> >>
>> >>
>> >> Your model has 18 timepoints but your data only has 15! Steve.
>> >>
>> >>
>> >> On 14 May 2007, at 16:21, Suzanna Laycock wrote:
>> >>
>> >>> Hi Steve,
>> >>>
>> >>> It says the following:
>> >>>
>> >>> Suzanna@suzanna ~/FSL_DATA/tbss/stats
>> >>> $ avwinfo all_FA_skeletonised
>> >>> data_type
>> >>> dim1 182
>> >>> dim2 218
>> >>> dim3 182
>> >>> dim4 15
>> >>> datatype 16
>> >>> pixdim1 -1.0000000000
>> >>> pixdim2 1.0000000000
>> >>> pixdim3 1.0000000000
>> >>> pixdim4 1.0000000000
>> >>> cal_max 0.0000
>> >>> cal_min 0.0000
>> >>> glmax 0
>> >>> glmin 0
>> >>> origin1 91
>> >>> origin2 127
>> >>> origin3 73
>> >>> file_type ANALYZE-7.5
>> >>>
>> >>>
>> >>> -----Original Message-----
>> >>> From: FSL - FMRIB's Software Library [mailto:[log in to
>> unmask]] On
>> >>> Behalf Of Steve Smith
>> >>> Sent: 11 May 2007 15:19
>> >>> To: [log in to unmask]
>> >>> Subject: Re: [FSL] randomise
>> >>>
>> >>>
>> >>> What does
>> >>> avwinfo all_FA_skeletonised
>> >>> say?
>> >>>
>> >>>
>> >>>
>> >>> On 11 May 2007, at 14:35, Suzanna Laycock wrote:
>> >>>
>> >>>> Hi,
>> >>>>
>> >>>> I'm trying to run the last part of tbss - randomise, and I
>> get the
>> >>>> following error message. Any suggestions why? I have 9 control
>> >>>> and
>> >>>> 9 patient subjects. Below is the design.mat and design.con
>> >>>> files.
>> >>>>
>> >>>> Suzanna@suzanna ~/FSL_DATA/tbss/stats
>> >>>> $ design_ttest2 design 9 9
>> >>>>
>> >>>> Suzanna@suzanna ~/FSL_DATA/tbss/stats
>> >>>> $ randomise -i all_FA_skeletonised -o tbss -m mea
>> >>>> n_FA_skeleton_mask
>> >>>> -d design.mat -t design.con -n 5000 -c 3 -V 48620 permutations
>> >>>> required for exhaustive test number of rows in design matrix
>> >>>> doesn't
>> >>>> match numb er of "time points" in input data!
>> >>>>
>> >>>>
>> >>>> My design.mat is:
>> >>>>
>> >>>> /NumWaves 2
>> >>>> /NumPoints 18
>> >>>> /PPheights 1 1
>> >>>> /Matrix
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 1 0
>> >>>> 0 1
>> >>>> 0 1
>> >>>> 0 1
>> >>>> 0 1
>> >>>> 0 1
>> >>>> 0 1
>> >>>> 0 1
>> >>>> 0 1
>> >>>> 0 1
>> >>>>
>> >>>> And my design.con is:
>> >>>>
>> >>>> /NumWaves 2
>> >>>> /NumContrasts 2
>> >>>> /PPheights 1 1
>> >>>> /Matrix
>> >>>> 1 -1
>> >>>> -1 1
>> >>>>
>>
>>
>
>
> ----------------------------------------------------------------------
> -----
> 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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