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 BruceOn Mon, 26 May 2014, Saloni Sharma wrote:Dear Freesurfers,
So I have followed all the instructions given on
your websitein order touse qdec. When i analyse the images only using a file
group.levels thatdefines the two groups I'm comparing the analysis
runs fineand gives meresults, but when I add gender, for instance, as a
discretefactor, it loadsthe 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.thickness.fwhm10.fsaverage.mgh
Please guide me as to what is going wrong and what I
can do tofix it. Iwould appreciate a quick response as my thesis
submission isdue in twoweeks and I cannot proceed until this problem is sorted.
Thanks and regards, Saloni
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