make_average_subject did the trick. However, although I can load the lh results as an overlay in tksurfer, if I try to adjust the display settings through View> Configure > Overlay, tksurfer crashes and I get the message below. I don't have this problem when overlaying the rh results.
tksurfer average lh smoothwm 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 surfer: Reading header info from /data/nelson/work/alex/freesurfer/subjects_twins/average/mri/T1.mgz surfer: vertices=163842, faces=327680 corRead(): can't open file /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/../mri/orig/COR-.info MRISreadVertexPosition(/data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.orig): could not open file /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.orig No such file or directory surfer: single buffered window Xlib: extension "XFree86-DRI" missing on display ":0.0". surfer: using interface /usr/local/freesurfer-dev20050905/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer-dev20050905/lib/tcl/tkUtils.tcl Read /usr/local/freesurfer-dev20050905/surface_labels.txt, found 95 structures Successfully parsed tksurfer.tcl % offset is 0.25 surfer: reading canonical coordinates from surfer: /data/nelson/work/alex/freesurfer/subjects_twins/average/surf/lh.sphere.reg too big, x major ticks can't be 80000002 Abort 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: Thu 4/13/2006 1:45 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Repeated-measures in mris_glm Try using make_average_subject. That will create a T1 volume. Alternatively, you can run make_average_volume, which will just do the volume (make_average_subject will re-do the volume). Or even faster would be to copy the T1 volume from average7 or talairach into your average subject mri dir. You can do this and see if the problem goes away. doug Fornito, Alexander wrote: >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
