I don't think so - so find the images which are empty and maybe  
remove their .msf files and rerun tbss_2_reg which should just run on  
them.
Cheers.


On 24 Jun 2007, at 17:53, Suzanna Laycock wrote:

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


------------------------------------------------------------------------ 
---
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
------------------------------------------------------------------------ 
---