Re: [Freesurfer] volume to surface registration problem
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. > > > > > > > > > > > > > ___
Re: [Freesurfer] volume to surface registration problem
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 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.
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
Re: [Freesurfer] volume to surface registration problem
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 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.
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] volume to surface registration problem
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 Logfile for bbregister Thu Oct 16 10:54:36 EDT 2014 setenv SUBJECTS_DIR /misc/data41/yuex/human_anat cd /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514 /opt/freesurfer-530/bin/bbregister --s field --init-fsl --6 --bold --mov bold/template.nii --reg bold/register.dof6.dat --init-reg-out bold/init.register.dof6.dat $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ Linux konis 2.6.32-431.20.5.el6.x86_64 #1 SMP Fri Jul 25 08:34:44 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /opt/freesurfer-530 mri_convert bold/template.nii bold/tmp.bbregister.16782/template.nii mri_convert bold/template.nii bold/tmp.bbregister.16782/template.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from bold/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999653, -0.00336006, -0.0261388) j_ras = (-2.83047e-08, -0.991839, 0.127499) k_ras = (-0.0263539, 0.127455, 0.991494) writing to bold/tmp.bbregister.16782/template.nii... fslregister --s field --mov bold/tmp.bbregister.16782/template.nii --reg bold/tmp.bbregister.16782/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/tmp.bbregister.16782/fslregister --dof 6 --fsvol brainmask.mgz Log file is bold/tmp.bbregister.16782/reg.init.dat.fslregister.log Thu Oct 16 10:54:37 EDT 2014 --s field --mov bold/tmp.bbregister.16782/template.nii --reg bold/tmp.bbregister.16782/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp bold/tmp.bbregister.16782/fslregister --dof 6 --fsvol brainmask.mgz $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $ konis Linux konis 2.6.32-431.20.5.el6.x86_64 #1 SMP Fri Jul 25 08:34:44 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux nIters 1 -- /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514 mri_convert /misc/data41/yuex/human_anat/field/mri/brainmask.mgz bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii mri_convert /misc/data41/yuex/human_anat/field/mri/brainmask.mgz bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /misc/data41/yuex/human_anat/field/mri/brainmask.mgz... TR=6.88, TE=2.72, TI=725.00, flip angle=10.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to bold/tmp.bbregister.16782/fslregister/refvol.fslregister.nii... -- /misc/data41/yuex/humanfMRI/human_curvature/subjdata/field090514 mri_convert bold/tmp.bbregister.16782/template.nii bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii --frame 0 mri_convert bold/tmp.bbregister.16782/template.nii bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii --frame 0 $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from bold/tmp.bbregister.16782/template.nii... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999653, -0.00336006, -0.0261388) j_ras = (-2.83047e-08, -0.991839, 0.127499) k_ras = (-0.0263539, 0.127455, 0.991494) keeping frame 0 writing to bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii... Mov determinant is 2.94386 Swapping dims for pos det WARNING:: Flipping Left/Right orientation (as det < 0) tkregister_tcl /opt/freesurfer-530/tktools/tkregister2.tcl target volume bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii movable volume bold/tmp.bbregister.16782/template.nii reg file bold/tmp.bbregister.16782/fslregister/swapreg.dat LoadVol0 ZeroCRAS 0 $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ Diagnostic Level -1 INFO: loading target bold/tmp.bbregister.16782/fslregister/movvol.fslregister.nii INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable bold/tmp.bbregister.16782/template.nii Tmov: -1.408 0.000 0.000 100.000; 0.000 0.000 1.484 -30.422; 0.000 -1.408 0.000 100.000; 0.000 0.000 0.000 1.000; mkheaderreg = 1, float2int = 0 Computing reg from header (and possibly input matrix) Input registration matrix (computed) 1.000 0.003 0.026 1.408; -0.026 0.127 0.991 0.000; 0.000 0.992 -0.127 -0.000; 0.000 0.000 0.000 1.000; --- Input registration matrix 1.000 0.003 0.026 1.408;
