The two have different dimensions. One has 256^3, the other 160^3 doug
On 04/01/2015 12:31 PM, sha...@nmr.mgh.harvard.edu wrote: > I emailed them! > >> 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/ >> >> >> > -- 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. 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