should not be or do you know for sure because you checked it? doug On 07/31/2014 10:42 AM, bbr...@bidmc.harvard.edu wrote: > Hi Doug, > > For the functional runs, it's the same task during each run, so the volumes > shouldn't be changing. > > Ben > > > Benjamin Brent, M.D., M.S. > Massachusetts Mental Health Center > 75 Fenwood Road, Room 618 > Boston, MA 02115 > 617-754-1262 > > This message is intended for the use of the person(s) to whom it may be > addressed. It may contain information that is privileged, confidential, or > otherwise protected from disclosure under applicable law. If you are not the > intended recipient, any dissemination, distribution, copying, or use of this > information is prohibited. If you have received this message in error, please > permanently delete it and immediately notify the sender. Thank you. > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, July 30, 2014 4:53 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Preprocessing Error > > Is the size of the volume (row, cols, or slices) changing between the runs? > > On 07/30/2014 04:18 PM, bbr...@bidmc.harvard.edu wrote: >> Hi Doug, >> >> I have been getting an error message when preprocessing data on 2 subjects >> in stable 4 (using the same command worked fine, however, with several >> others). >> >> The command I ran was: preproc-sess -smout fmcsm6 -fwhm 6 -s Con7_self -df >> sesspar >> >> The error message I get is pasted below. >> >> Any suggestions about how to fix this would be much appreciated! >> >> Thanks, >> >> Ben >> >> /autofs/space/tyra_001/users/gcoombs/self/subjects/Con7_self/bold >> 3dvolreg -verbose -dfile 003/fmc.mcdat -base >> 003/tmp.mc-afni2.6069/tempvol.nii.gz -prefix >> 003/tmp.mc-afni2.6069/outvol.nii.gz 003/tmp.mc-afni2.6069/invol.nii.gz >> ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] >> ++ Authored by: RW Cox >> *+ WARNING: If you are performing spatial transformations on an oblique >> dset, >> such as 003/tmp.mc-afni2.6069/tempvol.nii.gz, >> or viewing/combining it with volumes of differing obliquity, >> you should consider running: >> 3dWarp -deoblique >> on this and other oblique datasets in the same session. >> See 3dWarp -help for details. >> ++ Oblique dataset:003/tmp.mc-afni2.6069/tempvol.nii.gz is 12.500000 degrees >> from plumb. >> ++ Reading in base dataset 003/tmp.mc-afni2.6069/tempvol.nii.gz >> ++ Oblique dataset:003/tmp.mc-afni2.6069/invol.nii.gz is 17.700005 degrees >> from plumb. >> ++ centers of base and input datasets are 26.86 mm apart >> ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base >> 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same dimensions! >> Input: nx=64 ny=64 nz=33 >> Base: nx=256 ny=256 nz=128 >> ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base >> 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same grid spacing! >> Input: dx= 2.969 dy= 2.969 dz= 3.000 >> Base: dx= 1.000 dy=-1.000 dz= 1.330 >> ** Input 003/tmp.mc-afni2.6069/invol.nii.gz and base >> 003/tmp.mc-afni2.6069/tempvol.nii.gz don't have same orientation! >> Input: R-L A-P I-S >> Base: A-P S-I R-L >> ** FATAL ERROR: perhaps you could make your datasets match? >> ERROR: 3dvolreg >> Invalid null command. >> ERROR: mc-sess failed >> >> >> Benjamin Brent, M.D., M.S. >> Massachusetts Mental Health Center >> 75 Fenwood Road, Room 618 >> Boston, MA 02115 >> 617-754-1262 >> >> This message is intended for the use of the person(s) to whom it may be >> addressed. It may contain information that is privileged, confidential, or >> otherwise protected from disclosure under applicable law. If you are not the >> intended recipient, any dissemination, distribution, copying, or use of this >> information is prohibited. If you have received this message in error, >> please permanently delete it and immediately notify the sender. Thank you. >> >> _______________________________________________ >> 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. > > > _______________________________________________ > 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
