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
>> ----------------------------------------------------------------
>> --------
>> ---
>
>
> ----------------------------------------------------------------
> --------
> ---
> 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
------------------------------------------------------------------------
---
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