Yes! It worked! Thank you so much for all your help! Best Regards, Saloni
On 28 May 2014 23:31, Douglas N Greve <gr...@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 <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 >
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