Re: [Freesurfer] URGENT: Error in analyse

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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