Dear all, I am trying to convert the curv surface into a volume by using the following command: mri_surf2vol –surf curv –hemi lh –template $subj/mri/T1.mgz –surfval $subj/surf/lh.curv –projfrac 0 –volregidentity $subj –o CurvatureVolume.nii I get the following error: the lh.curv has many more faces than vertices! If the curv file is not a surface, is it possible at all to convert it into a volume?
Thanks a lot for your help. Best, Roberta
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
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
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
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/
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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.
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
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/
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The information in this e-mail is intended only for the person to
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contains patient information, please contact the Partners Compliance
HelpLine at
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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
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 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
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
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
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 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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
the curv file is not a surface. A surface has a list of vertices, the xyz at each vertex, and the neighboring vertices. lh.white and rh.pial are example surface files. The curv file just has a curv value at each vertex with no info about xyz etc. If you do not specify a --surf, then it will use white by default (which is probably what you want).
On 10/16/2014 10:52 AM, Roberta Santoro wrote:
Dear all,
I am trying to convert the curv surface into a volume by using the following command:
mri_surf2vol –surf curv –hemi lh –template $subj/mri/T1.mgz –surfval $subj/surf/lh.curv –projfrac 0 –volregidentity $subj –o CurvatureVolume.nii
I get the following error: the lh.curv has many more faces than vertices!
If the curv file is not a surface, is it possible at all to convert it into a volume?
Thanks a lot for your help.
Best,
Roberta
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Roberta Santoro -
Xiaomin Yue