Hi Catherine, this usually means that something funny is going on with the contrast matrix. Eg, you made the contrast under windows? If so, then make it again under linux. If not , then send the contrast file doug
On 06/24/2013 09:52 AM, Catherine Bois wrote: > Dear Freesurfer experts, I am currently trying to do a cortical > thickness group analysis with one factor, three levels . I have run > mri_preproc and mri_surf2surf, and am now trying to run > > mri_glmfit --y lh.group.thickness.10B.mgh --fsgd easy2.file --C > contrast1.mtx --surf fsaverage lh --cortex --glmdir lh.group > > However, I keep getting this error; > > INFO: gd2mtx_method is doss > Saving design matrix to lh.group/Xg.dat > Normalized matrix condition is 1 > Matrix condition is 7 > Found 149955 points in label. > Pruning voxels by thr: 0.000000 > Found 149953 voxels in mask > Saving mask to lh.group/mask.mgh > Reshaping mriglm->mask... > search space = 74612.446501 > MatrixReadTxT: could not scan value [2][1] > > > The format of both the fsgd file and the contrast file is ASCII text > > My fsgd file is formatted as follows: > > GroupDescriptorFile 1 > Title Group analysis > Class HR > Class Con > Class ILL > Input EHRS_XXXX_2 HR > Input EHRS_XXXX_2 HR > Input EHRS_XXXX_2 HR > Input EHRS_XXXX_2 Con > Input EHRS_XXXX_2 Con > Input EHRS_XXXX_2 ILL > > and my contrast file is; > > 1 -1 0 > > I do not understand why I keep getting this error. When I include the > flag -no-contrasts-is-ok, the mri_glmfit does work. There are no > commas in either file. > This leads me to believe something is wrong with my contrast file? > However I am not certain what this could be. Help would be greatly > appreciated. > > Thank you very much, > > Cathy > -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
