what version of freesurfer is being used? type 'freesurfer --version' and its the last line.
On Mon, 2009-02-23 at 14:08 -0600, 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 > >> > > > >> > > > >> > > >> > _______________________________________________ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> ------------------------------------------------------------------------ > >> Windows Live™ Hotmail®:…more than just e-mail. Check it out. > >> <http://windowslive.com/explore?ocid=TXT_TAGLM_WL_t2_hm_justgotbetter_explore_022009> > >> > >> ------------------------------------------------------------------------ > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
