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Thanks!...I am in the process of rerunning everything in the new version and hopefully that will solve the problem. Best, Marc On Mon, May 18, 2009 at 2:01 PM, Steve Smith <[log in to unmask]> wrote: > If you are mixing data up across the versions - yes that could be a problem > - in general there are other more serious reasons why you can't mix analyses > across the previous two TBSS versions (like completely different nonlinear > registration transformation formats). > > Cheers. > > > > On 18 May 2009, at 18:51, Marc Dubin wrote: > > Could it be that the previous version of tbss and the present one scale FA >> differently? When I ran the series of tbss scripts in the previous version, >> there was a step that rescaled everything from 0->10000 and that is no >> longer done in the current version of tbss. Could that somehow be leading to >> the sign error that I'm getting? >> Best, >> Marc >> >> On Thu, May 14, 2009 at 1:34 PM, Marc Dubin < >> [log in to unmask]> wrote: >> Hi Steve, >> >> You might think so, but I have also tried changing the FSL design, not >> de-meaning EV2 and getting rid of the constant EV1 (and making the cog >> non-demeaned score the only EV). This is the same as the ROQS analysis and I >> get almost the same exact confusing reults. >> >> Best, >> Marc >> >> >> On Thu, May 14, 2009 at 10:26 AM, Steve Smith <[log in to unmask]> >> wrote: >> Hi, >> >> >> On 14 May 2009, at 17:54, Marc Dubin wrote: >> >> Hi Steve, >> >> Thanks so much for getting back to me... >> >> The randomise command that I used is: >> >> randomise -i all_FA -o tbssFA_Elision_PN -m mean_FA_mask3000 -d >> designElision_PN.mat -t designElision_PN.con -n 5000 -V -x -D >> >> I have used this with and without the -1 option and with and without the >> -D option and get the same results. >> >> Because the design matrix includes a mean EV you shouldn't demean the data >> (so don't use -D option) and the -1 option also doesn't make sense in this >> scenario. The rest looks fine. I take it you are comparing the second >> contrast [0 -1] with the 'hand' approach below. >> >> >> I have also attached the design files. >> >> By manual, I mean the ROQS automatic segmentation technique developed by >> Niogi and McCandliss (Neuroimage, 2007, 35:166:174). I am using this to >> automatically isolate the left SCR by finding its boundary and then taking >> the average FA inside this boundary. This single number average correlates >> positively with my cognitive score. >> >> I assume you are doing equivalent modelling - i.e. either demeaning the >> data extracted in this way, or including a mean EV in your regression? >> >> >> However, when I run the above FSL analysis, I get no positive correlation >> with any of the voxels in the left (or right) SCR. However, when I modify >> the FSL/TBSS analysis so the Elision contrast is (0 -1) instead of (0 1), I >> get voxels of significance throughout the entire left SCR , as expected, >> however these voxels are negatively correlated with the cognitive score >> (Elision). There seems to be a sign error somewhere. >> >> Seems like there must be a dodgy step in this "hand" analysis.... >> >> Cheers. >> >> >> >> Any thoughts you have on what I'm doing wrong would be most appreciated! >> >> Best, >> Marc >> >> On Thu, May 14, 2009 at 9:18 AM, Steve Smith <[log in to unmask]> >> wrote: >> Hi, back from Hawaii now....catching up.... >> >> No - this sounds straightforward so there shouldn't be this inversion. The >> randomise-based modelling looks simple and correct - maybe you should tell >> us exactly what syntax you used for the randomise command - and also explain >> in more detail what you mean by "more direct, manual, FA analysis"? >> >> Cheers. >> >> >> >> >> On 8 May 2009, at 14:58, Marc Dubin wrote: >> >> Dear All, >> >> I have a TBSS & linear regression question. >> >> I have run a simple linear regression with one independent (cognitive test >> score) and one dependent variable (fractional anisotropy) that I set up in >> GLM_gui. >> >> EV1 = constant >> EV2 = cognitive test score (which is demeaned by GLM_gui) >> >> contrast of interest (contrast 2) is (0, -1) >> >> The problem is I get almost the same exact region of significance as I get >> in a different, more direct, manual FA analysis. However, with the manual >> approach, the correlation is positive, not negative. Does anyone have ideas >> about what might be giving rise to this sign error? >> >> Thanks in advance! >> >> Best, >> Marc >> >> On Wed, Jan 21, 2009 at 8:44 AM, Steve Smith <[log in to unmask]> >> wrote: >> Ah, good point. I was thinking more of the options where other programs >> were run _before_ bet2 as opposed to _after_. >> >> It _might_ be good enough to run bet2 with the mesh output option turned >> on, using as input the brain-extracted output from the first run of bet with >> the -S option. ?? >> >> Cheers. >> >> >> >> On 20 Jan 2009, at 18:11, Marc Lalancette wrote: >> >> Thanks for your prompt reply. >> >> I suspect that for you the easiest thing >> would be to amend the -S option so that it gave the surface outputs >> you need, and then run the betsurf second-stage stuff separately >> afterwards." >> >> I looked at the script, but I don't know how to do that. The -S option >> first runs bet2, then applies corrections to the masks with fslmaths >> calls. >> If I add the option to output the surface meshes in the bet2 call, I would >> get the same mesh as without the -S option. >> >> Is there a tool I can use to convert a mask to a mesh directly? Or is >> that >> code only in bet2? >> >> Cheers, >> Marc Lalancette >> >> >> >> >> --------------------------------------------------------------------------- >> 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<http://www.fmrib.ox.ac.uk/%7Esteve> >> >> --------------------------------------------------------------------------- >> >> >> >> >> -- >> Marc Dubin, MD PhD >> Clinical Research Fellow >> Brain Imaging Laboratory >> NYSPI & Columbia University >> >> Office: 212-543-6702 >> Mobile: 646-831-8886 >> >> >> >> --------------------------------------------------------------------------- >> 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<http://www.fmrib.ox.ac.uk/%7Esteve> >> >> --------------------------------------------------------------------------- >> >> >> >> -- >> Marc Dubin, MD PhD >> Clinical Research Fellow >> Brain Imaging Laboratory >> NYSPI & Columbia University >> >> Office: 212-543-6702 >> Mobile: 646-831-8886 >> <Archive.zip> >> >> >> >> --------------------------------------------------------------------------- >> 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<http://www.fmrib.ox.ac.uk/%7Esteve> >> >> --------------------------------------------------------------------------- >> >> >> >> -- >> Marc Dubin, MD PhD >> Clinical Research Fellow >> Brain Imaging Laboratory >> NYSPI & Columbia University >> >> Office: 212-543-6702 >> Mobile: 646-831-8886 >> >> >> >> -- >> Marc Dubin, MD PhD >> Clinical Research Fellow >> Brain Imaging Laboratory >> NYSPI & Columbia University >> >> Office: 212-543-6702 >> Mobile: 646-831-8886 >> > > > --------------------------------------------------------------------------- > 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<http://www.fmrib.ox.ac.uk/%7Esteve> > --------------------------------------------------------------------------- > -- Marc Dubin, MD PhD Clinical Research Fellow Brain Imaging Laboratory NYSPI & Columbia University Office: 212-543-6702 Mobile: 646-831-8886