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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-

> bounces@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

> > 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

> 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

> greve@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/

> _______________________________________________

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