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 <gr...@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 <sharm...@tcd.ie > >> <mailto:sharm...@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 <fis...@nmr.mgh.harvard.edu > >> <mailto:fis...@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 > >> <fis...@nmr.mgh.harvard.edu > >> <mailto:fis...@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> > >>> 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 > >>> e-mail > >>> contains patient information, please contact the Partners > >> Compliance > >>> HelpLine at > >>> http://www.partners.org/complianceline . If the e-mail was > >> sent to you > >>> in error > >>> but does not contain patient information, please contact the > >> sender > >>> and properly > >>> dispose of the e-mail. > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > gr...@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 > > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
