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:
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: alexander.fornito@wh.org.au
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer