Hi Hanna,
yes, this duplication problem would explain the mismatch between the number of timepoints in your 4D image and your statistical design.
You just need to delete the duplicated ones in struc/ and reconcatenate all the 56 subjects *_GM_mod.nii.gz using fslmerge to create your new, valid GM_mod_merg.nii.gz in stats/. Then just smooth it wih fslmaths -s 2 3 or 4.
Hope this helps,
Gwenaelle
> Hi Gwenaelle,
>
> see info below and design.mat attached. One thing I noticed
> is that (due to some nomenclature error) I had more files in
> the "struc" folder than in the higher order directory:
> Basically, I had run step one but single digit subject ids
> were wrong ("3" instead of "03", "4" instead of "04" and so
> on, for one of my two groups) which I had changed and rerun
> step one. It appears that it had simply added the new, then
> correctly named cases, so I basically had duplicates of the
> same file but with different filenames. I have now deleted
> those excessive cases from the struc folder and also some
> from the slicedir directory, but the problem still persists,
> I guess because there are probably some files whose names I
> cannot readily identify as referring to those excessive
> files. Does this mean I better rerun things alltogether?
>
> I appreciate your help! Thanks and best regards,
>
> hannah
>
>
>
> data_type FLOAT32
> dim1 91
> dim2 109
> dim3 91
> dim4 63
> datatype 16
> pixdim1 2.0000000000
> pixdim2 2.0000000000
> pixdim3 2.0000000000
> pixdim4 1.0000000000
> cal_max 2.1635
> cal_min 0.0000
> file_type NIFTI-1+
>
> Am 06.09.2010 um 18:58 schrieb Gwenaëlle DOUAUD:
>
> >
> >
> >
> > Hi Hannah,
> >
> > can you please attach your design.mat and also give us
> the result of an fslinfo on your 4D image?
> >
> > Cheers,
> > Gwenaelle
> >
> >> Hi,
> >>
> >> those numbers are equivalent, the subjects are
> also ordered
> >> as are in the template list (in case that matters
> at this
> >> point).
> >> Do you have any other suggestions what might have
> gone
> >> wrong?
> >>
> >> Thanks,
> >>
> >> Hannah
> >>
> >> On Sep 6, 2010, at 5:40 PM, JChurch wrote:
> >>
> >>> check your design matrix and make sure the
> amount of
> >> rows match the number of subjects in your
> directory
> >>>
> >>>
> >>> On Sep 6, 2010, at 10:56 AM, Hannah Bruehl
> wrote:
> >>>
> >>>> DearAll,
> >>>>
> >>>> I was just trying to run the randomize
> step of
> >> FSL-VBM and get the following error message:
> >>>>
> >>>> Loading Data:
> >>
> ***************************************************************
> >>>> Data loaded
> >>>> ERROR: Program failed
> >>>>
> >>>> An exception has been thrown
> >>>> Logic error:- detected by Newmat:
> incompatible
> >> dimensions
> >>>>
> >>>> MatrixType = Rect # Rows
> = 56; #
> >> Cols = 56
> >>>> MatrixType = Rect # Rows
> = 63; #
> >> Cols = 208920
> >>>> Trace: MatrixMult.
> >>>>
> >>>>
> >>>> Exiting
> >>>>
> >>>>
> >>>> Does anyone know what the cause could be.
> I have
> >> run the exact same command on a subgroup (and
> adapted design
> >> matrix file) and it appears to be doing fine.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Hannah
> >>
> >
> --------------------------------------------------------------------
> >
> > Gwenaëlle Douaud, PhD
> >
> > FMRIB Centre, University of Oxford
> > John Radcliffe Hospital, Headington OX3 9DU
> Oxford UK
> >
> > Tel: +44 (0) 1865 222 523 Fax: +44 (0) 1865 222
> 717
> >
> > www.fmrib.ox.ac.uk/~douaud
> >
> >
> --------------------------------------------------------------------
> >
> >
> >
>
> ......................................................................................................................................
> Dr. Hannah Brühl
> Freie Universität Berlin
> Institut für Psychologie
> Arbeitsbereich Emotionspsychologie und affektive
> Neurowissenschaft
> Habelschwerdter Allee 45 — Raum JK 25/222h
> 14195 Berlin
> Tel.: +49 (0)30 838 564 72
> ......................................................................................................................................
>
>
>
