what do you get if you run mri_info on the sval file?
bell0...@umn.edu wrote:
Thanks for the info. I am getting an error on the mri_surf2surf step
of the thickdiffmap.sh script. It occurs whether I use subj1, subj2,
fsaverage, or a different person (subj3) in the command below. There
was one comment from Bruce in the archives that says this error will
occur if the registration is poor. The inter-subject, i.e.
subj1_to_subj2, registration is fine, as shown with tkregister2. I am
not sure how to quality/error check the registration to the sphere. On
a more general note, this step is supposed to resample the cortical
difference map to the template subject (--trgsubject), I guess I am a
bit unclear as to why sphere.reg is needed, considering that my
--trgsubject could be anything, not necessary the standard sphere.
Does mri_surf2surf first align the subj1 standard sphere vertices to
the --trgsubject and then align the difference map using the same
transform? Thanks for any help.
thickdiffmap.sh 1633_20170_1271 1633_20240_1280 fsaverage lh 1 2 3 |
tee > output5.log
mri_surf2surf --srcsubject 1633_20170_1271 --sval
/home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271
/surf/lh.thickness_diff_1633_20170_1271_to_1633_20240_1280.mgh
--trgsubject fsaverage --tval /home/bfs-raid3/chris/18
2_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20170_1271_to_1633_20240_1280_resampled
_to_fsaverage.mgh --hemi lh --surfreg sphere.reg Registration surface
changed to sphere.reg srcsubject = 1633_20170_1271 srcval =
/home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.thickness_diff_1633_20170_12
71_to_1633_20240_1280.mgh srctype = trgsubject = fsaverage trgval =
/home/bfs-raid3/chris/182_REPRO_free/new_proc_names/groupstudy/1633_20170_1271_lh_thickness_diff_1633_20
170_1271_to_1633_20240_1280_resampled_to_fsaverage.mgh trgtype =
surfreg = sphere.reg srchemi = lh trghemi = lh frame = 0 fwhm-in = 0
fwhm-out = 0 Reading source surface reg
/home/bfs-raid3/chris/182_REPRO_free/new_proc_names/1633_20170_1271/surf/lh.sphere.reg
Loading source data Segmentation fault (above is in my log file)
(below is error printed to the screen) INFO:try to get src info from
transform. MRIalloc(1879048192, -1125858646, 317): bad parm Cannot
allocate memory
On Feb 23 2009, Douglas N Greve wrote:
Info on doing the paired t is here:
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Don Hagler wrote:
You could extend the analysis described on that wiki page by
calculating tstats and pvalues (in addition to mean and stdev). Then
you have a paired t-test, whereas mri_glmfit with qdec would be
doing an unpaired t-test. I think preproc has an option to calculate
within subject differences for a paired t-test with mri_glmfit as
well. As you may know, paired t-tests are more sensitive than
unpaired t-tests, and are generally more appropriate when you make
within subject comparisons. On the other hand, if you intend your
exercise to be a test for the likelihood of false positive
differences between groups, the unpaired t-test may be more
appropriate.
> Subject: Re: [Freesurfer] qdec thickness and repeatability
> From: ni...@nmr.mgh.harvard.edu
> To: bell0...@umn.edu
> Date: Fri, 20 Feb 2009 15:15:10 -0500
> CC: freesurfer@nmr.mgh.harvard.edu
>
> The two methods are very different. In the method described on the
> thickness repeatability page, its computing a mean and stddev of the
> thickness for your group. This a direct and easily interpretable
> measure, but doesn't give you a statistical measure (but you could do
> that on your own with some external package).
>
> In qdec (mri_glmfit), it would be conducting a GLM-based analysis
> looking for statistical significance, expressed as a p-value at each
> vertex, in thickness between groups. Here, raw thickness differences
> are hidden in the analysis.
>
> However, you can of course do both analysis, and compare them,
which I
> would suggest you do. You would hope the areas of change are the
same.
> Note that you can load external surface maps, such as a thickness-
> diff.mgh map, onto the fsaverage surface in qdec, so that you can
view
> both analysis (or just load the thickness-diff.mgh map in tksurfer).
>
> Its on the list of things to add to qdec to create two-group
thickness
> difference maps, as well as just viewing the mean group thickness, to
> save some work for this sort of thing.
>
> Nick
>
>
> On Fri, 2009-02-20 at 12:53 -0600, bell0...@umn.edu wrote:
> > All,
> >
> > I am going to run an analysis of cortical thickness
reproducibility; there
> > are at least two methods that seem obvious. I could run qdec
analysis with
> > time1 and time2 as different groups or I could run the methods
below. Are
> > the commands below the same ones used in the qdec GUI? As far as
I can
> > tell, they will both give me cortical thickness differences on a
vertex by
> > vertex basis. There are probably some subtle differences in the
way they
> > are coded, but any major changes? Thanks.
> >
> > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
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