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 Wed, May 28, 2014 at 5:17 PM, Saloni Sharma <sharm...@tcd.ie> wrote: > Same error despite having run recon-qcache again. > > > On 28 May 2014 21:28, Saloni Sharma <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>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> >>> 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 >>> >> >> > > _______________________________________________ > Freesurfer mailing list > 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 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.
