Hi, Thank you for your response! I solve this problem of mris_preproc. The next step is to do mri_glmfit. And, when I type the following command: mri_glmfit --y lh.noise_0.5-1-5.thickness.10.mgh --fsgd noise_0.5-1-5.fsgd dods --C noise_0.5-1.mtx --surf fsaverage lh --cortex --glmdir lh.noise_0.5- 1.glmdir
The terminal shows: ERROR: Option --cortex unknown Would you tell me what’s wrong? And how do I do to solve this error? Thank you in advance! Feng-Xian On Tue, 07 Jul 2009 11:49:32 -0400, Douglas N Greve wrote > Is there a space between "--" and "hemi"? > > caching is just a way to speed some analyses by pre-smoothing and > sampling to the standard space. > > doug > > Feng-Xian wrote: > > Hi, > > > > I copied the default average subject from $FREESURFER_HOME/subjects dir > > to my analysis dir. > > > > Then, I make a FSGD file and some contrast matrices and put them into my > > analysis dir. > > > > After that, I start to run group analysis. > > > > But, when I type the following commands: > > > > mris_preproc --fsgd noise_0.5-1-5.fsgd --target fsaverage -- hemi lh -- meas > > thickness --out lh.noise_0.5-1-5.thickness.00.mgh > > > > The terminal shows: > > > > ERROR: flag -- not recognized > > > > > > Now, I have two problems want to ask. > > > > 1) What's wrong about the commands that I type? And, how to solve the > > problem? > > > > 2) I found this commands from the FreeSurfer web. And, I'm confused about > > that two ways to do analysis. > > One is cached (qcached) data, and the other is uncached data. What's > > way is suitable to my subjects? (My subjects is one factor and three > > levels, had run QDEC before, but QDEC is not good job to analysis, and, I > > want to change the analysis method from QDEC to DODS) > > So, which way do I choose to analysis my subjects?? Idon't understand > > the differences from them. > > > > > > Thank you in advance! > > > > Feng-Xian > > > > > > > > On Fri, 26 Jun 2009 15:25:12 -0400, Nick Schmansky wrote > > > >> in general, it is not necessary to run make_average_subject prior to > >> performing an analysis. using the default average subject that > >> freesurfer provides, named 'fsaverage', is sufficient for most cases, > >> because it doesnt affect the analysis, its only used as a target upon > >> which to project results. the 'fsaverage' subject is in the > >> $FREESURFER_HOME/subjects dir, and you should copy it to your own > >> SUBJECTS_DIR prior to performing any group analysis. > >> > >> Nick > >> > >> On Fri, 2009-06-26 at 10:48 +0800, Feng-Xian wrote: > >> > >>> Hi, > >>> > >>> I know I wont to do QDEC now, so I want to change the method of group > >>> analysis from QDEC to the web you tell me. But, I did QDEC before. > >>> > >>> Before I do DODS, should I do make_average_subject to view the result of > >>> > > my > > > >>> subjects? Or, I have another method to view the results?? > >>> > >>> Thank you in advance! > >>> > >>> Feng-Xian > >>> > >>> > >>> > >>> > >>> On Thu, 25 Jun 2009 12:01:21 -0400, Nick Schmansky wrote > >>> > >>>> Feng-xian, > >>>> > >>>> I should also mention that i dont think creating your own average > >>>> subject will solve the problem you describe, where you need to work > >>>> > > with > > > >>>> three levels in your group. for that, you wont be able to use qdec, > >>>> but will need to run things manually. these pages give examples: > >>>> > >>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > >>>> > >>>> and note one of them is 1 Factor, 3 Levels. > >>>> > >>>> Nick > >>>> > >>>> On Thu, 2009-06-25 at 11:55 -0400, Nick Schmansky wrote: > >>>> > >>>>> Feng-Xian, > >>>>> > >>>>> It appears that you do not have permission on your system to change > >>>>> > > the > > > >>>>> limits. So you will have to edit the scripts make_average_volume, > >>>>> make_average_surface and make_average_subject to comment out > >>>>> > > the 'limit' > > > >>>>> line, so that it looks like this: > >>>>> > >>>>> #limit descriptors unlimited > >>>>> > >>>>> > >>>>> Nick > >>>>> > >>>>> On Thu, 2009-06-25 at 15:51 +0800, Feng-Xian wrote: > >>>>> > >>>>>> Hi, > >>>>>> > >>>>>> I have a problem with make_average_subject. > >>>>>> > >>>>>> After running all commands (including ln -s > >>>>>> $FREESURFER_HOME/subjects/fsaverage > >>>>>> and recon-all -s <subjid> -qcache for all my subjects) about > >>>>>> > > running > > > >>> QDEC, I > >>> > >>>>>> found that QDEC could not analysis my group. > >>>>>> > >>>>>> Because the group have 1 factor and three levels, QDEC can't run. > >>>>>> > >>>>>> So, I want to change the method of analysis from QDEC to DODS. > >>>>>> > >>>>>> > >>>>>> I had a fsaverage file when I running QDEC, but the fsaverage did > >>>>>> > > not > > > >>> use my > >>> > >>>>>> subjects to make. > >>>>>> > >>>>>> So, can I use the fsaverage file to run DODS? > >>>>>> > >>>>>> If not, I should make a new fsaverage with my subjects. > >>>>>> > >>>>>> But, I encounter the problem about make_average_subject. > >>>>>> > >>>>>> > >>>>>> When I type: > >>>>>> > >>>>>> make_average_subject --subects <subjid1> <subjid2> ... > >>>>>> > >>>>>> the terminal show that: > >>>>>> > >>>>>> limit: descriptors: Can't remove limit > >>>>>> > >>>>>> > >>>>>> What's wrong about the command I type? And, how to solve the > >>>>>> > > problem? > > > >>>>>> > >>>>>> > >>>>>> Thank you in advance! > >>>>>> > >>>>>> Feng-Xian > >>>>>> > >>>>>> > >>>>>> ------------------------------------------------- > >>>>>> Chang Gung University Mail Server Web Mail system > >>>>>> By Chang-Gung University Information Center > >>>>>> (http://www.cgu.edu.tw/ic/) > >>>>>> > >>>>>> _______________________________________________ > >>>>>> Freesurfer mailing list > >>>>>> Freesurfer@nmr.mgh.harvard.edu > >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>>> > >>>>>> > >>>>>> > >>> ------------------------------------------------- > >>> Chang Gung University Mail Server Web Mail system > >>> By Chang-Gung University Information Center > >>> (http://www.cgu.edu.tw/ic/) > >>> > >>> > >>> > > > > > > ------------------------------------------------- > > Chang Gung University Mail Server Web Mail system > > By Chang-Gung University Information Center > > (http://www.cgu.edu.tw/ic/) > > > > _______________________________________________ > > 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 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/) _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
