Hi Keyma,
I'll leave this for Doug (or Brian).
Bruce
On Fri, 28 Jan 2005, Keyma Prince wrote:
Thanks,
I also ran mris_glm for thickness differences based on age of the subjects with the following command and got the following output. Can you tell me how to I can read the results in tksurfer?
mris_glm --design ons_glm.mtx --hemi lh --surfmeas thickness --trgsubj average_ons -nsmooth 50 --beta beta bfloat --var var bfloat
mris_glm --design ons_glm.mtx --hemi lh --trgsubj average_ons --beta_in beta bfloat --var_in var bfloat --gcv 0 0 1 --sigt ./age-sigt-lh.w paint
INFO: loading surface /space/engram/6/users/emoaging//average_ons/surf/lh.sphere.reg corRead(): can't open file /space/engram/6/users/emoaging//average_ons/surf/../mri/orig/COR-.info INFO: cannot find mri/orig volume to get c_(ras) information. INFO: transform src volume information cannot be found. assume c_(ras_ = 0 INFO: destination surface points may be shifted in the volume. INFO: you should put the src info in the transform. INFO: transform dst volume information cannot be found. INFO: if the target is MNI average_305, then you can do 'setenv USE_AVERAGE305 true' INFO: otherwise c_(ras) is set to 0. destination surface points may be shifted. nvertices = 163842 surface nvertices 163842 surface area 125674.750000 INFO: loading beta_in beta Reading /autofs/space/engram_006/users/emoaging/beta_000.bfloat ... INFO: bvolumeRead: min = 0.406867, max = 5.76361 INFO: loading var_in var Loading surface source data var as bfloat Reading /autofs/space/engram_006/users/emoaging/var_000.bfloat ... INFO: bvolumeRead: min = 0.00363081, max = 0.725406 Done Loading var writing surface values to ./age-sigt-lh.w. avg = -1.378, stdev = 2.493, min = -14.280, max = 9.789 done
Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139
On Fri, 28 Jan 2005, Bruce Fischl wrote:
Hi Keyma,
mris_twoclass is for making maps of thickness differences, not for the output of parcellate_subject, which you can just import into excel (using mris_anatomical_stats -a $annot_file -b $subject $hemi. In any case, mris_twoclass has been deprecated since Doug wrote mris_glm
cheers, Bruce
On Fri, 28 Jan 2005, Keyma Prince wrote:
Hello,
I am trying to use mri_twoclass for the first time to do a simple comparision of means for the output from parcellate_subject(i.e. cortical thickness and cortical volume) between 2 groups. This the command line i'm using but I keep getting the following output:
mris_twoclass -o average7 lh thickness c1_emot_104 c1_emot_106:c2_emot_101 c2_emot_103 -t .01
output: using average7 as output subject mris_twoclass: must spectify ':' between class lists
location: /space/engram/6/users/emoaging/
Also is mri_twoclass better than mris_glm to use for comparing the parcellation results between 2 groups?
thanks,
-Keyma
Keyma Prince Massachusetts Institute of Technology Department of Brain and Cognitive Sciences NE20-392 Cambridge, MA 02139 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer