Saloni,
are you certain that you ran recon-qcache on subject 000054987500? the
error message says that the file lh.thickness.fwhm10.fsaverage.mgh is
missing, and this file is created by -qcache. i'd suggest running:
recon-all -s 000054987500 -qcache
then confirm that this file exists.
Nick
On Wed, 2014-05-28 at 01:21 +0100, Saloni wrote:
> It prints out fine and gives results if I only use it to analyse two groups(differentiated on stress levels) but if I add gender as a discrete variable or even as a continuous one along with the groups it shows this error.
>
> Sent from my iPhone
>
> > On 27 May 2014, at 23:40, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
> >
> >
> > Does it print out anything else? An alternative is to use the command
> > line stream (create your own fsgd file, run mris_preproc, smooth,
> > mri_glmfit, mri_glmfit-sim)
> > doug
> >
> >
> >
> >
> >> On 05/27/2014 06:38 AM, Saloni Sharma wrote:
> >> I am attaching a screen shot of the error, if it helps!
> >>
> >>
> >> On 26 May 2014 17:14, Saloni Sharma <sharmasa@tcd.ie
> >> <mailto:sharmasa@tcd.ie>> wrote:
> >>
> >> yes exactly, if I click analyze without the gender it works fine.
> >> No thats okay, what do you need from me again?
> >>
> >>
> >> On 26 May 2014 17:11, Bruce Fischl <fischl@nmr.mgh.harvard.edu
> >> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
> >>
> >> so if you click "analyze" without gender it works fine? Sorry,
> >> I missed
> >> that. I think you'll need to wait for Doug or Nick to reply,
> >> but you might
> >> send your qdec file and the group.levels files
> >>
> >> sorry
> >> Bruce
> >>
> >>> On Mon, 26 May 2014, Saloni Sharma wrote:
> >>>
> >>> Hey Bruce,
> >>>
> >>> Yes, that directory exists, as I said if I only choose
> >> groups(high stress
> >>> and low stress) as the discrete variables its runs fine and
> >> analyses, it
> >>> only shows the error if I add more factors (like gender)
> >> into the software.
> >>>
> >>> My subjects directory is set to
> >>> export
> >> SUBJECTS_DIR=/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/
> >>>
> >>> and yes I have run recon-all-qcache on all my subjects.
> >>>
> >>> Saloni
> >>>
> >>>
> >>> On 26 May 2014 16:58, Bruce Fischl
> >> <fischl@nmr.mgh.harvard.edu
> >> <mailto:fischl@nmr.mgh.harvard.edu>> wrote:
> >>> Hi Saloni
> >>>
> >>> Does that directory exist? What is your SUBJECTS_DIR
> >> set to? And
> >>> have you
> >>> run recon-all -qcache on all your subjects?
> >>>
> >>> cheers
> >>> Bruce
> >>>> On Mon, 26 May 2014, Saloni Sharma wrote:
> >>>>
> >>>> Dear Freesurfers,
> >>>>
> >>>> So I have followed all the instructions given on
> >> your website
> >>> in order to
> >>>> use qdec. When i analyse the images only using a file
> >>> group.levels that
> >>>> defines the two groups I'm comparing the analysis
> >> runs fine
> >>> and gives me
> >>>> results, but when I add gender, for instance, as a
> >> discrete
> >>> factor, it loads
> >>>> the data successfully but when I click analyse it
> >> shows the
> >>> following error:
> >>>>
> >>>> Error in Analyze: Couldn't
> >> openfile/tallaght-disk4/IMAGEN/Saloni_data/freesurfer_output/000072882642/surf/
> >>> lh.t
> >>>> hickness.fwhm10.fsaverage.mgh
> >>>>
> >>>> Please guide me as to what is going wrong and what I
> >> can do to
> >>> fix it. I
> >>>> would appreciate a quick response as my thesis
> >> submission is
> >>> due in two
> >>>> weeks and I cannot proceed until this problem is sorted.
> >>>>
> >>>> Thanks and regards,
> >>>> Saloni
> >>> _______________________________________________
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> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>> The information in this e-mail is intended only for the
> >> person to whom
> >>> it is
> >>> addressed. If you believe this e-mail was sent to you in
> >> error and the
> >>> contains patient information, please contact the Partners
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> >>> HelpLine at
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> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >
> > --
> > Douglas N. Greve, Ph.D.
> > MGH-NMR Center
> > greve@nmr.mgh.harvard.edu
> > Phone Number: 617-724-2358
> > Fax: 617-726-7422
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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> >
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