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thanks Mark I am running Linux (redhat 9) so i'll have a go with the slower flirt. the registrations were fine for the other subject for which i completed a higher level analysis. the runs were quite variable though - i could see that from eye, looking at the locations of the activations (but each run was only made up of 30 volumes). i seem to have a problem looking at time series though - for most functional files that i load into fsl view, when i click time series nothing appears - even for stats images from the higher level analysis. the only time i am able to see time series is when i load an orignial series_2.*.hdr and overlay a stats image onto to it. is this correct? thanks again jane In message <[log in to unmask]> FSL - FMRIB's Software Library <[log in to unmask]> writes: > Hi Jane, > > I'm afraid you are experiencing the effects of an intermittent > bug in flirt which we think is caused by the compilers we use, > which was unexpected. What machine are you running it on? > If it is linux (redhat 8 or 9) then a non-optimised version of > flirt, which is slower but doesn't crash, can be installed. > See: > http://www.fmrib.ox.ac.uk/fslfaq/#flirt_crash > > You might need to get your sysadmin to do this for you. > > If you are not running on linux/redhat 8 or 9 then let us know. > > As for the group analysis, this can happen if there is a lot of > variation between the runs. Does the data from different runs > appear significantly different in fslview (look at the timeseries)? > Also, if your registrations aren't working then you won't get > any good higher level results. Do all the registrations in the > registrations reports look good? > > If you can't see anything obviously wrong in the above, then let > us know and we can try to have a look at your data/design. > > All the best, > Mark > > > > Jane Aspell wrote: > > >Hi > > > >I'm new to FSL and am having a few problems. When I run a first level > >analysis using FEAT for one of my subjects something seems to go wrong with > >the co-registration of the high res image to the standard brain. In Feat > >watcher i get the following error: > > > >/usr/local/fsl/bin/convert_xfm -matonly -inverse -omat standard2highres.mat > >highres2standard.mat > >Could not open matrix file highres2standard.mat > >Cannot read input-matrix > > > >/usr/local/fsl/bin/slicer highres2standard standard -s 1 -x 0.35 sla -x 0.45 > >slb -x 0.55 slc -x 0.65 sld -y 0.35 sle -y 0.45 slf -y 0.55 slg -y 0.65 slh > >-z 0.35 sli -z 0.45 slj -z 0.55 slk -z 0.65 sll ; /usr/local/fsl/bin/convert > >-colors 100 +append sla slb slc sld sle slf slg slh sli slj slk sll > >highres2standard.gif ; /bin/rm -f sla slb slc sld sle slf slg slh sli slj > >slk sll > >Cannot open volume highres2standard.hdr for reading! > >convertb: no delegate for this image format (sla). > >convertb: no delegate for this image format (slb). > >convertb: no delegate for this image format (slc). > >convertb: no delegate for this image format (sld). > >convertb: no delegate for this image format (sle). > >convertb: no delegate for this image format (slf). > >convertb: no delegate for this image format (slg). > >convertb: no delegate for this image format (slh). > >convertb: no delegate for this image format (sli). > >convertb: no delegate for this image format (slj). > >convertb: no delegate for this image format (slk). > >convertb: no delegate for this image format (sll). > >convertb: Missing an image file name. > > > >/bin/rm -f highres2standard.hdr highres2standard.img > > > >And I found that the highres2standard.mat transform is missing from the /reg > >directory in the relevant .feat directory. > >So i tried to create it with the command: > >flirt -in highres -ref standard -omat highres2standard.mat > >But that just returns 'Segmentation fault' > > > >I haven't had this problem with my other subject. Any ideas? > > > >My second problem is with higher level analysis. I ran successful first > >level analyses for the 5 series(runs) for a single subject and got good > >activations for my contrasts (z~6) but when i run the higher level analysis > >to put all the runs (which are simply repeats of the same conditions) > >together all the activation seems to disappear! I re-ran the higher level > >analysis with a lower z threshold (1.0) and was then able to see activations > >(z scores <3 could be seen). Is this the correct thing to do? I thought > >the activations would be more significant, not less, when I average all > >my runs together so I'm puzzled. > > > >Thanks very much for your help. > > > >Jane Aspell > > > > >