Whereever there are spaces in the pathname, add a "\" in front of the space and try again, e.g. instead of:
tkregisterfv --mov /Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001-0001.dcm --reg /Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001-0001.dcm --surfs use: tkregisterfv --mov /Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET\ BRAIN\ TOF\ STATIC 2/2016004A/IM-0001-0001.dcm --reg /Users/djsandoval/Desktop/Selwyn/M87127996-2016004/Baseline/PETCT/PET/PET\ BRAIN\ TOF\ STATIC\ 2/2016004A/IM-0001-0001.dcm --surfs I hope this is helpful - Don > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer- > boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Wednesday, January 25, 2017 4:53 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Registration: Variable Must Begin with a Letter > Error > <Repost> > > In the terminal output it says that your movable volume is > > > /Users/djsandoval/Desktop/Selwyn/M87127996- > 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001- > 0001.dcm > > not template.nii.gz. In principle, that should be fine, except that there are > spaces in the path > > On 01/25/2017 04:34 PM, Anderson Napolitano wrote: > > > > Hello Experts! > > > > > > I am having trouble checking the registration per step 2 of the pet > > surfer tutorial: http://freesurfer.net/fswiki/PetSurfer. The line: > > mri_coreg --s subject --mov template.nii.gz --reg template.reg.lta > > worked just fine but when checking the registration using the line: > > tkregisterfv --mov template.nii.gz --reg template.reg.lta --surfs I > > get the following output: set: Variable name must begin with a letter > > As suggested by Dr. Greve, I've attached a text file documenting the > > input, the output and the output with the debug flag on. > > Please let me know if I can provide you any further details and I will > > get to it as soon as I can. > > Thank you very much for your time. > > Warmest Regards, > > Anderson > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > /**************************************************************** > ************** > Terminal Input > **************************************************************** > **************/ > > tkregisterfv --mov /Users/djsandoval/Desktop/Selwyn/M87127996- > 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001- > 0001.dcm --reg /Users/djsandoval/Desktop/Selwyn/M87127996- > 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001- > 0001.dcm --surfs > > /**************************************************************** > ************** > Terminal Output > **************************************************************** > **************/ > > set: Variable name must begin with a letter > > /**************************************************************** > ************** > Terminal Output with Debug Flag On > **************************************************************** > **************/ > > set echo = 1 ; > breaksw > breaksw > > end > end > while ( $#argv != 0 ) > while ( 5 != 0 ) > > set flag = $argv[1] ; shift ; > set flag = --mov > shift > > switch ( $flag ) > switch ( --mov ) > if ( $#argv < 1 ) goto arg1err ; > if ( 4 < 1 ) goto arg1err > set movvol = $argv[1] ; shift ; > set movvol = > /Users/djsandoval/Desktop/Selwyn/M87127996- > 2016004/Baseline/PETCT/PET/PET BRAIN TOF STATIC 2/2016004A/IM-0001- > 0001.dcm > set: Variable name must begin with a letter. > shift > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu<mailto: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<http://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<mailto: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 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.
