I can't tell from that message. Can you copy mask.nii.gz and rho1mn.nii.gz somewhere I can access?
On 04/01/2015 12:14 PM, SHAHIN NASR wrote: > Hi Doug, > Selxavg3-sess started without any problem but then I faced the > below error. Do you know what is the problem? > > Global In-Mask Mean = 1316.7 (8.68411) > Rescale Target = 100 > RescaleFactor = 0.0759477 > OLS Residual Pass > run 1 t= 0.0 > Saving rho1 > run 2 t=144.1 > Saving rho1 > run 3 t=289.9 > Saving rho1 > run 4 t=432.6 > Saving rho1 > run 5 t=580.0 > Saving rho1 > run 6 t=731.8 > Saving rho1 > run 7 t=884.9 > Saving rho1 > run 8 t=1042.3 > Saving rho1 > run 9 t=1194.9 > Saving rho1 > run 10 t=1341.4 > Saving rho1 > > Smoothing ACF > /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz > > --i > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz > > --o > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz > > --fwhm 20.000000 --smooth-only > /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz > > --i > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz > > --o > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz > > --fwhm 20.000000 --smooth-only: Segmentation fault > voxelvolume 1 mm3 > Loading mask > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz > Search region is 708874 voxels = 708874.000000 mm3 > Smoothing input by fwhm=20.000000, gstd=8.493218 > Segmentation fault (core dumped) > > ERROR: /usr/local/freesurfer/stable5_3_0/bin/mri_fwhm --mask > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/mask.nii.gz > > --i > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.nii.gz > > --o > /autofs/cluster/tootell/pitcairn/1/shahin/Face_Scene_HighRes/Subjects/myla1/bold/Multi_Localizer_native/rho1mn.sm.nii.gz > > --fwhm 20.000000 --smooth-only > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > > On Fri, Mar 27, 2015 at 3:34 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > Yes. Note that that will produce huge files (float images 256^3 by > number of time points). > doug > > > On 03/27/2015 01:50 PM, SHAHIN NASR wrote: > > Hi Surfers, > I want to find a way to analyze subcortical activities in > native space and still take advantage of per-run > registration. As far as I understand, this is not possible in > current preproc-sess. We need one extra step in which we have > to map all fmcpr.nii.gz files to subject's orig.mgz. I am trying: > > mri_vol2vol --mov fmcpr.nii.gz --o fmcpr.native.nii.gz > --fstarg orig.mgz --reg register.dof6.dat --no-save-reg > --interp trilin > > in my mind, it is equivalent of what preproc-sess does > when we use -mni305 flag (it uses mri_vol2vol to map fmcpr to > mni space). > > Am I right? > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > > -- > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School -- 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.
