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
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 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
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.edumailto: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
greve@nmr.mgh.harvard.edumailto:greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
www.nmr.mgh.harvard.edu/facility/filedrop/index.htmlhttp://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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-
Anderson Napolitano -
Douglas N Greve -
Krieger, Donald N.