Hi Doug,

It is the same command left by spmregister
freeview orig.mgz pcals.nii 

Just i excluded the flag -f /surf/?h.orig

what is your freeview command?

 

 

On 07/14/2017 08:46 AM, John Anderson wrote:

> 

>> Dear Freesurfer experts,

>> I want to derive registration matrix between pcasl image and the

>> structural space in Freesurfer (i.e. orig.mgz) If I open orig.mgz and

>> the pcasl image in Freesurefr I see overlap between the images

>> (attached Figure1).

>> When I use "spmregister" as follow:

>> spmregister --mov perfusion_calib.nii.gz --s SUBJ --reg reg.dat

>> --fsvol orig --o CBF_T1.nii

>> 

>> Then visualize "CBF_T1" using freeview I see mis-registration

>> (attached Figure2)

>> 

>> Please what I am doing wrong?

>> Thank you for any guidance

>> Jon

>> 

> 

> 

> 

> _______________________________________________

> 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

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/

 

_______________________________________________

Freesurfer mailing list

Freesurfer@nmr.mgh.harvard.edu

https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer *�k��