On 28 May 2014 23:31, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Daniel found your problem as he mentioned in his previous email (see
below). Change the qdec table to have the name of the subject be
000054987500_output.

Also, I noticed that you have gender as a continuous variable. It should
be discrete

-------- Original Message --------
Subject: Re: [Freesurfer] URGENT: Error in analyse
Date: Wed, 28 May 2014 17:30:11 -0400
From: dgw <dgwakeman@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
CC: nicks@nmr.mgh.harvard.edu

Your subject name is wrong.

You are saying the subject name is: 000054987500

While it is actually: 000054987500_output

You should either change the name of the SUBJECT directory or change the
subject id you are giving to mri_glmfit.

HTH
D

On 05/28/2014 05:17 PM, Saloni Sharma wrote:
> Same error despite having run recon-qcache again.
>
>
> On 28 May 2014 21:28, Saloni Sharma <sharmasa@tcd.ie

> <mailto:sharmasa@tcd.ie>> wrote:
>
> Dear Nick,
>
> I am certain of it because the analysis runs fine when I analyze
> it with just a discrete variable group.levels...the moment I add
> factor.levels as another variable along with groups it gives me
> the error. And if I remove this particular subject from the data
> table(this subject is the first on the data list) and try running
> it again it shows the same error for the next subject on the list.
>
> I am attaching a screen shot of the said file existing as well.
>
> However, I am also running the command you gave again as we speak,
> just to see if it works.
>
>
>
> On 28 May 2014 20:48, Nick Schmansky, MGH

> <nicks@nmr.mgh.harvard.edu <mailto:nicks@nmr.mgh.harvard.edu>> wrote:
>
> 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 <mailto: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>

> > >> <mailto: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>

> > >> <mailto: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>

> > >> <mailto: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
> > >>> _______________________________________________
> > >>> Freesurfer mailing list
> > >>> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>

> > >> <mailto:Freesurfer@nmr.mgh.harvard.edu

> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
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> > >>
> > >>
> > >>
> > >>
> > >>
> > >> _______________________________________________
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>

> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > > --
> > > Douglas N. Greve, Ph.D.
> > > MGH-NMR Center

> > > greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> > > Phone Number: 617-724-2358 <tel:617-724-2358>
> > > Fax: 617-726-7422 <tel:617-726-7422>
> > >
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> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

> > > Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> > >
> > > _______________________________________________
> > > Freesurfer mailing list
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> <mailto:Freesurfer@nmr.mgh.harvard.edu>
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> >
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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
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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