Sorry, this is a bug. The work-around requires that you: 1. Re-run mkbrainmask-sess without the "-nero 1" 2. cd into the mask directory in each run and run mri_binarize, like this cd /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/masks mri_binarize --i brain.nii.gz --o brain.e3.nii.gz --min 0.5 --erode 1 3. Then re-run selxavg3-sess
doug Meryem Ayse Yucel wrote: > I tried this. It is still giving the same error. Should I check my mask > files? > > Thanks. > > >> The mask used to compute the global mean does not have any voxels in it >> because the field of view is so small. Try running >> mkbrainmask-sess -s session -nero 1 -fsd bold >> Then run selxavg again. The above mkbrainmask command tells it to only >> erode the mask by one voxel (the default in preproc-sess is 3 which is >> removing all of them). >> >> doug >> >> >> >> Meryem Ayse Yucel wrote: >> >>> Hi, >>> >>> Now it seems to be working with the par file but I am getting this >>> error. >>> Any help will be appreciated. Thanks, >>> >>> Meryem >>> >>> >>> Computing compensation for resdual AR1 bias >>> 1 -0.5 -0.473129 (t=0.192235) >>> 2 -0.25 -0.238292 (t=1.09283) >>> 3 0 -0.00411884 (t=1.27811) >>> 4 0.25 0.228971 (t=2.16243) >>> 5 0.5 0.459511 (t=2.33787) >>> AR1 Correction M: 0.00580007 1.07178 >>> Computing contrast matrices >>> OLS Beta Pass >>> run 1 t= 0.0 >>> Global Mean Global In-Mask Mean = ??? Error using ==> mrdivide >>> Matrix dimensions must agree. >>> >>> Error in ==> fast_selxavg3 at 399 >>> RescaleFactor = flac0.inorm/gmean; >>> >>> >>> >>> >>> >>> >>>> Hi, >>>> >>>> >>>> I am trying to use selxavg3-sess function and getting this error. Below >>>> is >>>> the error I get. I actually have this fingertap.par file but freesurfer >>>> somehow does not see it. Any help would be >>>> appreciated. >>>> >>>> Thanks! >>>> >>>> Meryem Yucel >>>> PMI Lab >>>> >>>> >>>> >>>> Extension format = nii.gz >>>> ERROR: opening >>>> /autofs/space/moe_002/users/mayucel/PROJECT/Subject20/bold/001/fingertap >>>> No such file or directory >>>> ??? Output argument "partype" (and maybe others) not assigned during >>>> call >>>> to "/usr/local/freesurfer/stable5_1_0/fsfast/toolbox/fast_ldpar4.m >>>> (fast_ldpar4)". >>>> >>>> Error in ==> fast_ldpar4 at 45 >>>> par4 = []; >>>> >>>> Error in ==> flac_customize at 121 >>>> [par partype] = fast_ldpar4(parpath); >>>> >>>> Error in ==> fast_selxavg3 at 65 >>>> flac0 = flac_customize(flac0); >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> >> >> > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
