I craeted the average using make_average_surface. An average/mri/T1 directory gets created, but nothing is in there. There is no T1 volume at all. Is this because I'm using an older version of recon-all (v 1.104 2005/09/07)? Could this also explain my trouble creating scatterplots?
Alex Fornito M.Psych/PhD (clin. neuro.) candidate Melbourne Neuropsychiatry Centre and Department of Psychology National Neuroscience Facility The University of Melbourne Levels 2 & 3, Alan Gilbert Building 161 Barry St Carlton South Vic 3053 Australia Ph: +61 3 8344 1624 Fax: +61 3 9348 0469 email: [EMAIL PROTECTED] -----Original Message----- From: Doug Greve [mailto:[EMAIL PROTECTED] Sent: Wed 4/12/2006 2:42 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm How did you create the average subject? Is there a T1.mgz in the mri dir? If so, you might have an old version of tksurfer that is looking for COR files instead of mgz. Fornito, Alexander wrote: >That did the trick, but I'm having trouble displaying the results. >First issue is that I can't seem to load my average surface in tksurfer from >the command line.I get the following: > >tksurfer average rh inflated >surfer: current subjects dir: /data/nelson/work/alex/freesurfer/subjects_twins >surfer: not in "scripts" dir ==> using cwd for session root >surfer: session root data dir ($session) set to: >surfer: /data/nelson/work/alex/freesurfer/subjects_twins >ERROR: cound not stat >/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1/COR-.info. >Does it exist? >mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgh, >-1): could not open file >zcat: /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz.gz: >No such file or directory >mghRead(/data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz, >-1): read error >surfer: ### Could not find anatomical header information. > >What I do instead is load a subject's surface and then click load > Surface, >and select the average one. >When I load the sigt file as an overlay, what should I specify as the >registration matrix? >Clicking "calculate identity matrix" seems to work, so I'm assuming this is ok? > >After doing this, I can visualize the SPM ok, but have trouble when I try to >obtain scatterplots for a gven vertex. tksurfer closes and I get the error >below.(I've tried specifying markers and colors in the FSGD but it doesn't >seem to make a difference) >I'm using recon-all-nmr,v 1.104 2005/09/07. > > gdfReadHeader: reading > /data/nelson/work/alex/freesurfer/subjects_twins/stats/twin_qualcheck_fsgd.txt >WARNING: Marker for class class_subj1 was invalid. >WARNING: Color for class class_subj1 was invalid. >WARNING: Marker for class class_subj2 was invalid. >WARNING: Color for class class_subj2 was invalid. >WARNING: Marker for class class_subj3 was invalid. >WARNING: Color for class class_subj3 was invalid. >WARNING: Marker for class class_subj4 was invalid. >WARNING: Color for class class_subj4 was invalid. >WARNING: Marker for class class_subj5 was invalid. >WARNING: Color for class class_subj5 was invalid. >surfer: dmin=0.8701, vno=132952, x=14.6850, y=-30.1178, z=47.7694 >% surfer: curv=0.000000, fs=0.000000 >% surfer: val=2.132707, val2=0.000000 >% surfer: amp=2.132707, angle=0.000000 deg (0.000000) > >Thanks again, >A > > >Oh, I'm sorry. I see the problem now. When I said to create a class >for each subject, I meant for each person, not for each FreeSurfer >subject. So there should only be 5 classes, not 10. > >So do something like this: > >Class class_subj1 >Class class_subj2 >Class class_subj3 >Class class_subj4 >Class class_subj5 > >Variables Time >Input time1_subj1 class_subj1 -1 >Input time2_subj1 class_subj1 +1 >... > >doug > >On Tue, 11 Apr 2006, Fornito, Alexander wrote: > > > >>I still get the same error message. Maybe I've coded the variable wrong? >> >>gdfReadHeader: reading ./test_fsgd.txt >>INFO: gd2mtx_method is doss >>ERROR: Design Matrix: nrows (10) <= ncols (11) >> >> >> >>Alex Fornito >>M.Psych/PhD (clin. neuro.) candidate >>Melbourne Neuropsychiatry Centre and Department of Psychology >>National Neuroscience Facility >>The University of Melbourne >>Levels 2 & 3, Alan Gilbert Building >>161 Barry St >>Carlton South Vic 3053 Australia >>Ph: +61 3 8344 1624 >>Fax: +61 3 9348 0469 >>email: [EMAIL PROTECTED] >> >> >> >>-----Original Message----- >>From: Doug Greve [mailto:[EMAIL PROTECTED] >>Sent: Tue 4/11/2006 11:43 AM >>To: Fornito, Alexander >>Cc: freesurfer@nmr.mgh.harvard.edu >>Subject: RE: [Freesurfer] Repeated-measures in mris_glm >> >> >>Yes, mris_preproc is new with stable. In your FSGD file, try >>specifying the title as a single string without spaces. >> >>doug >> >> >> >>On Tue, 11 Apr 2006, Fornito, Alexander wrote: >> >> >> >>>Hi Doug, >>>Is mri_preproc a new addition to the stable version? I'm using >>>recon-all-nmr,v 1.104 2005/09/07 and can't seem to find it. >>>I tried running the analysis through mris_glm as per option 1 as you >>>described, but came across a problem. Command, error, and my FSGD are below. >>>Thanks, >>>Alex >>> >>>Command: >>> >>>mris_glm --surfmeas thickness --hemi lh --trgsubj ../average --fsgd >>>./test_fsgd.txt doss --beta ./beta_doss_thickness-100_lh bfloat --var >>>./var_doss_thickness-100_lh.w paint --y ./y_doss_thickness-100_lh_000.bfloat >>>--nsmooth 100 >>>gdfReadHeader: reading ./test_fsgd.txt >>>INFO: ignoring tag 1 >>>INFO: gd2mtx_method is doss >>>ERROR: Design Matrix: nrows (10) <= ncols (11) >>> >>>My FSGD: >>> >>>GroupDescriptorFile 1 >>>Title Time 1 vs Time 2 >>>Class class_time1_subj1 >>>Class class_time1_subj2 >>>Class class_time1_subj3 >>>Class class_time1_subj4 >>>Class class_time1_subj5 >>>Class class_time2_subj1 >>>Class class_time2_subj2 >>>Class class_time2_subj3 >>>Class class_time2_subj4 >>>Class class_time2_subj5 >>>Variables Time >>>Input time1_subj1 class_time1_subj1 -1 >>>Input time1_subj2 class_time1_subj2 -1 >>>Input time1_subj3 class_time1_subj3 -1 >>>Input time1_subj4 class_time1_subj4 -1 >>>Input time1_subj5 class_time1_subj5 -1 >>>Input time2_subj1 class_time2_subj1 1 >>>Input time2_subj2 class_time2_subj2 1 >>>Input time2_subj3 class_time2_subj3 1 >>>Input time2_subj4 class_time2_subj4 1 >>>Input time2_subj5 class_time2_subj5 1 >>>DefaultVariable Time >>> >>>Alex Fornito >>>M.Psych/PhD (clin. neuro.) candidate >>>Melbourne Neuropsychiatry Centre and Department of Psychology >>>National Neuroscience Facility >>>The University of Melbourne >>>Levels 2 & 3, Alan Gilbert Building >>>161 Barry St >>>Carlton South Vic 3053 Australia >>>Ph: +61 3 8344 1624 >>>Fax: +61 3 9348 0469 >>>email: [EMAIL PROTECTED] >>> >>> >>> >>>-----Original Message----- >>>From: Doug Greve [mailto:[EMAIL PROTECTED] >>>Sent: Tue 4/11/2006 9:31 AM >>>To: Fornito, Alexander >>>Cc: freesurfer@nmr.mgh.harvard.edu >>>Subject: Re: [Freesurfer] Repeated-measures in mris_glm >>> >>> >>>There are two ways to do it: >>> >>>1. You can use DOSS, making each subject it's own class. Then create one >>>"Variable". For a given input, set the variable to either +1 or -1 >>>depending upon whether it corresponds to the first or second time >>>point. Then create a contrast as [0 0 0 0 ... 0 0 0 1], where there are >>>as many 0s as subjects. The last "1" will correspond to the Time Point >>>variable. >>> >>>2. Alternatively, if you are using mris_preproc, you can specify >>>"--paired-diff", then just use a one-sample group mean test. See the >>>--help. This may be easier, and will also allow you to add a between >>>subject factor. >>> >>>doug >>> >>> >>>Fornito, Alexander wrote: >>> >>> >>> >>>>Hi, >>>>I'd like to run a simple repeated-measures analysis tetsing for change in >>>>thickness measures between 2 time points. There is no between-subjects >>>>factor, only the effect of time. Do I just set up a standard DOSS FSGD >>>>file, or do I use a different format? The tutorial only covers >>>>between-subjects designs. >>>>Thanks, >>>>Alex >>>> >>>> >>>> >>>>Alex Fornito >>>>M.Psych/PhD (clin. neuro.) candidate >>>>Melbourne Neuropsychiatry Centre and Department of Psychology >>>>National Neuroscience Facility >>>>The University of Melbourne >>>>Levels 2 & 3, Alan Gilbert Building >>>>161 Barry St >>>>Carlton South Vic 3053 Australia >>>>Ph: +61 3 8344 1624 >>>>Fax: +61 3 9348 0469 >>>>email: [EMAIL PROTECTED] >>>> >>>> >>>> >>>> >>>>_______________________________________________ >>>>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 [EMAIL PROTECTED] 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
