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: alexander.fornito@wh.org.au
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] 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: alexander.fornito@wh.org.au
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] 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: alexander.fornito@wh.org.au
-----Original Message----- From: Doug Greve [mailto:greve@nmr.mgh.harvard.edu] 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:
- 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.
- 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: alexander.fornito@wh.org.au
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