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> 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 > >>>>