Dear freesurfers,
I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In the preprocessing the functional images are registered to the anatomical ones using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the preproc-sess registration fails it is possible to achieve a proper registration using various options of bbregister. Does it suffice to replace the register files created during the preprocessing with the ones received during the registration correction in order to attain proper preprocessed data or are there routines in steps 4 to 8 in the preprocessing which rely on the registration?
Thanks in advance
pfannmoe
They rely on the registration. What is failing? It is usually the initialization that fails. If you're using FSL, you can try using the SPM registration (though it's a little trickier to set up). doug
On 06/04/2012 05:20 AM, Jörg Pfannmöller wrote:
Dear freesurfers,
I have a simple question concerning the freesurfer 5.1 FSFAST preprocessing. In the preprocessing the functional images are registered to the anatomical ones using bbregister. This is the 3rd in a series of 8 preprocessing steps. If the preproc-sess registration fails it is possible to achieve a proper registration using various options of bbregister. Does it suffice to replace the register files created during the preprocessing with the ones received during the registration correction in order to attain proper preprocessed data or are there routines in steps 4 to 8 in the preprocessing which rely on the registration?
Thanks in advance
pfannmoe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm
before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5');
doug
ps. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Dear Doug,
I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly?
Cheers pfannmoe
On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm
before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5');
doug
ps. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug
On 6/5/12 6:03 AM, Jörg Pfannmöller wrote:
Dear Doug,
I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly?
Cheers pfannmoe
On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Grevegreve@nmr.mgh.harvard.edu wrote:
You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm
before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5');
doug
ps. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Dear Doug,
I have tested the various options of register-sess. The result was a succesful registration of the functional to the anatomical image. This registration with register-sess is performed after preproc-sess failed to achieve a proper registration. The register.dof6.dat file is updated by register-sess. I would like to ask a last thing just in order to make it definite. Can I now use those data for example with selxavg3-sess in order to compute the activated areas for this subject?
Greets pfannmoe
On Tue, 05 Jun 2012 18:30:42 -0400 Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug
On 6/5/12 6:03 AM, Jörg Pfannmöller wrote:
Dear Doug,
I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly?
Cheers pfannmoe
On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Grevegreve@nmr.mgh.harvard.edu wrote:
You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm
before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5');
doug
ps. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
You should run preproc-sess again to make sure that all the files that need to be updated after the registration are properly updated. This should not change the registration -- it should just look at the time stamps of the files and update any that need updating. However, if the files earlier in the stream were changed at some point, then it might try to regenerate the registration, so just in case make a backup of your registration files before running preproc-sess. doug
On 06/27/2012 08:08 AM, Jörg Pfannmöller wrote:
Dear Doug,
I have tested the various options of register-sess. The result was a succesful registration of the functional to the anatomical image. This registration with register-sess is performed after preproc-sess failed to achieve a proper registration. The register.dof6.dat file is updated by register-sess. I would like to ask a last thing just in order to make it definite. Can I now use those data for example with selxavg3-sess in order to compute the activated areas for this subject?
Greets pfannmoe
On Tue, 05 Jun 2012 18:30:42 -0400 Douglas Grevegreve@nmr.mgh.harvard.edu wrote:
You can't do directly from preproc-sess, but you can do it from register-sess if you have an additional whole brain acquisition in the same session. This can be any acquisition (BOLD, MPRAGE, low-b DTI, etc) as long as it is whole brain. If your anatomical was acquired in the same session, then it is even easier because you can run register-sess with the -init-header option (instead of using fsl or spm). This assumes that the subject did not move more than 5mm between EPI and MPRAGE (usually the case). Let me know if this works for you. doug
On 6/5/12 6:03 AM, Jörg Pfannmöller wrote:
Dear Doug,
I am having a partial field of view and a full brain scan. How can I integrate the results in the preproc-sess sequence in order to complete the preprocessing correctly?
Cheers pfannmoe
On Mon, 04 Jun 2012 11:42:32 -0400 Douglas N Grevegreve@nmr.mgh.harvard.edu wrote:
You can try running register-sess outside of preproc-sess, something like register-sess -s session -fsd bold -per-run -init-spm
before you do that, you need to have spm5 and matlab, and change your matlab/startup.m to add the spm5 path path(path,'/usr/pubsw/common/spm/spm5');
doug
ps. Is this whole brain coverage or are you chopping off some of the brain
On 06/04/2012 11:36 AM, Jörg Pfannmöller wrote:
Dear Doug,
indeed the initialization fails. I was able to initiate bbregister manually, giving a good registration result. Can you give me a hint how to modify the registration and keeping the preproc-sess stream intact?
Cheers
pfannmoe
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
P.S.:I executed the following sequence to achieve the first level analysis with a correct registration.
preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run
register-sess -s session_id -fsd bold -per-run -init-header
preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -noreg -regfile session_id/bold/001/register.dof6.dat -force
selxavg3-sess -s session_id -analysis stim.sm0.lh -no-preproc
As far as I can see this is the right procedure. Do you agree or is there another or simpler way to correct the registration and proceed with a first level analysis?
No, that looks correct. doug
On 06/27/2012 12:05 PM, Jörg Pfannmöller wrote:
P.S.:I executed the following sequence to achieve the first level analysis with a correct registration.
preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run
register-sess -s session_id -fsd bold -per-run -init-header
preproc-sess -s session_id -fsd bold -sliceorder siemens -surface fsaverage lhrh -mni305 -fwhm 0 -per-run -noreg -regfile session_id/bold/001/register.dof6.dat -force
selxavg3-sess -s session_id -analysis stim.sm0.lh -no-preproc
As far as I can see this is the right procedure. Do you agree or is there another or simpler way to correct the registration and proceed with a first level analysis? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Douglas N Greve
-
Jörg Pfannmöller