It does include those steps, but you won't need to re-run them manually. Just run register-sess, then run preproc-sess as you normally would. It should see that the most recent files are the registration files and then perform all the steps afterwards. You should double check that it does not rerun the registration, but it should not. doug
On 10/16/2014 12:54 PM, Xiaomin Yue wrote:
Is it right that the prep roc-sess includes the following steps: 1) mktemplate-sess; 2) mkbrainmask-sess; 3)register-sess; 4) mc-sess; 5) rawfunc2surf-sess. So, I need to rerun step3, 4, and 5 manually, is that right?
Thanks, Xiaomin
Date: Thu, 16 Oct 2014 12:12:23 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] volume to surface registration problem
I have not tested it with spm12, so use spm8. There is not currently a way to run the spm init from preproc-sess, so you'll have to run it
from
register-sess.
On 10/16/2014 12:04 PM, Xiaomin Yue wrote:
Hi Doug,
Thanks for the promptly response. I do have spm8 and spm12b installed. Which version should I use? Also, how to change the spm as the inital registration method in the preproc-sess?
Xiaomin
Date: Thu, 16 Oct 2014 12:00:04 -0400 From: greve@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] volume to surface registration problem
The problem is probabably that the fsl flirt registration failed and that caused bbr to fail. If you have spm and matlab installed,
running
it with
cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514 bbregister --s field --init-spm --6 --bold --mov bold/template.nii
--reg bold/register.dof6.dat --init-reg-out
bold/init.register.dof6.dat
On 10/16/2014 11:14 AM, Xiaomin Yue wrote:
Hi,
When I used preproc-sess processing my data, the registration
output
is off a great of deal. The functional data was collected
using 7T,
and the surface was reconstructed successfully from 3T data
and was
checked visually multiple times. I am using fs5.3 installed on a linux system. Attached is the registration log file.
Any suggestions will be appreciated.
Xiaomin Yue
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