Same error despite having run recon-qcache again.
On 28 May 2014 21:28, Saloni Sharma 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.eduwrote:
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 BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Hey Bruce,
Yes, that directory exists, as I said if I only choose
groups(high stressand low stress) as the discrete variables its runs fine and
analyses, itonly 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_DIRset to? Andhave 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 websitein 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 fineand gives me> results, but when I add gender, for instance, as a
discretefactor, it loads> the data successfully but when I click analyse it
shows thefollowing 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 tofix it. I> would appreciate a quick response as my thesis
submission isdue in two> weeks and I cannot proceed until this problem is sorted. > > Thanks and regards, > Saloni _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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