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 <dgwake...@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> CC: ni...@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 <sharm...@tcd.ie > <mailto:sharm...@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 > <ni...@nmr.mgh.harvard.edu <mailto:ni...@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 > <gr...@nmr.mgh.harvard.edu <mailto: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> > > >> <mailto: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> > > >> <mailto: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> > > >> <mailto: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> > > >> <mailto: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> > > >> <mailto: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 > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > > > Phone Number: 617-724-2358 <tel:617-724-2358> > > > Fax: 617-726-7422 <tel:617-726-7422> > > > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > > > 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 > > > 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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > 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
