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: gr...@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: gr...@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 > > > > > > > > > > > > > > > _______________________________________________ > > > > > 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 > > > > gr...@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 > > > > > > > > > > > > The information in this e-mail is intended only for the person to > > > whom it is > > > > addressed. If you believe this e-mail was sent to you in error and > > > the e-mail > > > > contains patient information, please contact the Partners > Compliance > > > HelpLine at > > > > http://www.partners.org/complianceline . If the e-mail was sent to > > > you in error > > > > but does not contain patient information, please contact the sender > > > and properly > > > > dispose of the e-mail. > > > > > > > > > > > > > _______________________________________________ > > > 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 > > gr...@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 > > > _______________________________________________ > 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 gr...@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
