Re: [Freesurfer] Error: if: Expression Syntax.

2017-02-06 Thread Anderson Napolitano
Hi Dr. Greve, Thank you very much. That worked beautifully. For those who are having the same problem as I did, the command: mri_coreg --s subject_name --mov static_template.nii.gz --reg registration_matrix.reg.lta creates a text file named registration_matrix.reg.lta on your current

Re: [Freesurfer] Error: if: Expression Syntax.

2017-02-06 Thread Douglas N Greve
It should have created a file called registration_matrix (though you should add a .lta extension). Run it with --help to get more info On 02/06/2017 11:24 AM, Anderson Napolitano wrote: > > Hi Dr. Greve, > > > Ah I see. If that's the case, is the command: > > > mri_coreg --s subject_name --move

Re: [Freesurfer] Error: if: Expression Syntax.

2017-02-06 Thread Anderson Napolitano
Hi Dr. Greve, Ah I see. If that's the case, is the command: mri_coreg --s subject_name --move dicom_template --reg registration_matrix generating the registration matrix? I have ran a search on the subject folder for any *.reg* file and has only found lh.sphere.reg and rh.sphere.reg on the

Re: [Freesurfer] Error: if: Expression Syntax.

2017-02-02 Thread Douglas Greve
Why are you passing a dicom file as the registration file? The reg file is a FS-specific text file used to store the registration matrix. On 2/2/17 6:35 PM, Anderson Napolitano wrote: Hello Experts! I am having trouble running the following command: tkregisterfv --mov

[Freesurfer] Error: if: Expression Syntax.

2017-02-02 Thread Anderson Napolitano
Hello Experts! I am having trouble running the following command: tkregisterfv --mov /Users/djsandoval/Desktop/Selwyn/M87151031-2016002/Followup/PETCT/PET/STATICBRAINPET/2016002B/IM-0001-0001.dcm --reg