I think Doug meant the 1.3. Therefore the line should be something like: mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache 1.3 --sim-sign neg
What exactly did you type? (try separating it with lines instead of quotes) HTH, D On Mar 13, 2014, at 6:22 PM, Dusan Hirjak wrote: > Dear Doug, > > no, I did not put it in quotes. I just typed the mentioned command, but it is > still not working. > I can not find the file comprising the thickness, area or folding values at > peak maxima after Monte Carlo simulation. > Sorry for asking so many questions, but it is still not working. > What should I do next? > > Best regards, > > DH > > > Date: Thu, 13 Mar 2014 15:15:23 -0400 > > From: gr...@nmr.mgh.harvard.edu > > To: dusanhir...@hotmail.com; freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] Extracting thickness, area and folding values > > from Qdec > > > > are you puttting it in quotes? If so, don't > > doug > > > > On 03/13/2014 01:46 PM, Dusan Hirjak wrote: > > > Dear Doug, > > > > > > I typed 1.3 but it is still not working. > > > > > > Any other ideas??? > > > > > > Thanks for your help. > > > > > > DH > > > > > > > Date: Thu, 13 Mar 2014 12:20:57 -0400 > > > > From: gr...@nmr.mgh.harvard.edu > > > > To: freesurfer@nmr.mgh.harvard.edu > > > > Subject: Re: [Freesurfer] Extracting thickness, area and folding > > > values from Qdec > > > > > > > > Use 1.3 not 1,3 > > > > > > > > doug > > > > On 03/13/2014 10:12 AM, Dusan Hirjak wrote: > > > > > Dear Freesurfer Experts, > > > > > > > > > > I did a correlational analysis in qdec and found several significant > > > > > clusters after Monte-Carlo simulation (0.05). > > > > > Now, I would like to extract the mean cortical thickness, area and > > > > > folding values (peak maximum) of each study subject above the > > > > > significant cluster. > > > > > > > > > > I tried to run "mri_glmfit-sim --glmdir mc-z.neg.th13.pdf.dat --cache > > > > > "1,3" --sim-sign neg" > > > > > > > > > > However, I got the ERROR: thresh = 1.3 not completely converted > > > > > > > > > > What am I doing wrong? Any other ideas? > > > > > > > > > > Is the pdf.dat file the right one to use??? > > > > > > > > > > Thanks! > > > > > > > > > > DH > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > > > > > > > > > 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. > > > > > > > > -- > > 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 > > > 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
