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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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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