Oh, I need to give you an updated mri_binarize. Here is one for centos6. If that does not work for you, let me know what your platform is. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize
On 11/25/2013 03:38 PM, cel...@nmr.mgh.harvard.edu wrote: > Hi Doug and freesurfer team > > We just realized that the output framemask created by mri_binarize does > not have the same dimension than the input file y.mgh, which is a > concatenated file created through mris_preproc. > > so the dimension of our y.mgh is: 163842 x 1 x 1 x 33 > and by running this command (see below): mri_binarize --i y.mgh --abs > --min .0000000000001 --o framemask.mgh > > the dimension of output file framemask.mgh is: 163842 x 1 x 1 > > Would there be a way to get a 4D binary mask of zero-voxels that I could > use subsequently with the --frame-mask flag of mri_glmfit? > > Thanks for your help > Celine > > >> Yes thanks so much, it worked very fine >> Celine >> >>> In that case, I think you will want to change the design at each voxel >>> based on which subjects are present. I have not tried to do this with >>> pvr, but there is no reason it should not work. To do this, create a >>> binary volume from your data that has the 0s in it, something like >>> >>> mri_binarize --i y.mgh --abs --min .0000000000001 --o framemask.mgh >>> >>> The run mri_glmfit with --frame-mask framemask.mgh >>> >>> doug >>> >>> >>> On 11/08/2013 01:11 PM, cel...@nmr.mgh.harvard.edu wrote: >>>> Thanks Doug, >>>> Actually it is still the --pvr analysis, so I am regressing vertex by >>>> vertex two different modalities in one group of subjects, but for one >>>> of >>>> them, we apply a threshold to remove regions that have bad quality >>>> data. >>>> Let me know if I am not clear! >>>> Celine >>>> >>>>> you will want to use the -no-prune flag.If thisis a group analysis, >>>>> you >>>>> should be very, very careful that you know what you are doing. In >>>>> general, setting values to 0 prior to group analysis will create >>>>> biased >>>>> results. What you really need to do is have adifferent model for each >>>>> voxel that includes/excludes certain subjects at certain voxels. If >>>>> this >>>>> is what you want, let me know and I'll give you instructions on how to >>>>> do it. >>>>> >>>>> doug >>>>> >>>>> >>>>> On 11/08/2013 12:46 PM, cel...@nmr.mgh.harvard.edu wrote: >>>>>> Hi, >>>>>> When using glm_fit with an input volume that has many voxels with a 0 >>>>>> value (due to a previous thresholding for quality reasons), and the >>>>>> voxel >>>>>> removes might be distributed randomly across our population, is there >>>>>> a >>>>>> way not to take into account those voxels in the glm_fit model? I saw >>>>>> the >>>>>> --pune flag, but I am not sure if it is the one to use. >>>>>> Thanks >>>>>> Celine >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer@nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> gr...@nmr.mgh.harvard.edu >>>>> 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 >>>>> Freesurfer@nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>>>> >>>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> 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 >> 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 > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu 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 Freesurfer@nmr.mgh.harvard.edu 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.
