Re: [Freesurfer] run preproc-sess with -nomc
Thanks Doug! This indeed worked. (Just had to run mktemplate-sess and mkbrainmask-sess separately.) Evelina On Dec 13, 2011, at 5:48 PM, Douglas N Greve wrote: You can try specifying the functional stem in mkanalysis-sess with -funcstem yourfuncstem (assuming your data are yourfuncstem.nii). This will cause selxavg3-sess to bypass the preprocessing. doug Thunell Evelina wrote: Hi Doug, I might try to do it in SPM but it requires some more work I think - The Freesurfer retinotopic mapping analysis is automatic and easy to use. Evelina On Dec 12, 2011, at 10:51 PM, Douglas N Greve wrote: Hi Evelina, why don't you do the whole analysis in SPM then map the results to the surface? doug Thunell Evelina wrote: Hi Douglas, I do most of my analysis in matlab and SPM. For this one part of my experiment - it's a retinotopic mapping that I will use to ensure that my ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, motion correction and coregistration between functional runs and of the structural image already in SPM. I thought that since these flags exist they would just skip a step in the processing and send the data directly to the next step. But since it's not the case I'll have to do it some other way instead, maybe just redo the whole preprocessing in Freesurfer on the already preprocessed data. (Running the analysis with selxavg3-sess -analysis retlh -s SessXX *-no-preproc *doesn't work.) Anyway, the important thing is that the retinotopic mapping data stay coregistered with the rest of the functional data. If I can do this step in Freesurfer instead (and the rest of the preprocessing) that would be an option. Thanks a lot, Evelina On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote: Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface. doug Thunell Evelina wrote: Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@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 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. -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- 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: 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
Re: [Freesurfer] run preproc-sess with -nomc
Hi Doug, I might try to do it in SPM but it requires some more work I think - The Freesurfer retinotopic mapping analysis is automatic and easy to use. Evelina On Dec 12, 2011, at 10:51 PM, Douglas N Greve wrote: Hi Evelina, why don't you do the whole analysis in SPM then map the results to the surface? doug Thunell Evelina wrote: Hi Douglas, I do most of my analysis in matlab and SPM. For this one part of my experiment - it's a retinotopic mapping that I will use to ensure that my ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, motion correction and coregistration between functional runs and of the structural image already in SPM. I thought that since these flags exist they would just skip a step in the processing and send the data directly to the next step. But since it's not the case I'll have to do it some other way instead, maybe just redo the whole preprocessing in Freesurfer on the already preprocessed data. (Running the analysis with selxavg3-sess -analysis retlh -s SessXX *-no-preproc *doesn't work.) Anyway, the important thing is that the retinotopic mapping data stay coregistered with the rest of the functional data. If I can do this step in Freesurfer instead (and the rest of the preprocessing) that would be an option. Thanks a lot, Evelina On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote: Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface. doug Thunell Evelina wrote: Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@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 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. -- 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: 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
Re: [Freesurfer] run preproc-sess with -nomc
You can try specifying the functional stem in mkanalysis-sess with -funcstem yourfuncstem (assuming your data are yourfuncstem.nii). This will cause selxavg3-sess to bypass the preprocessing. doug Thunell Evelina wrote: Hi Doug, I might try to do it in SPM but it requires some more work I think - The Freesurfer retinotopic mapping analysis is automatic and easy to use. Evelina On Dec 12, 2011, at 10:51 PM, Douglas N Greve wrote: Hi Evelina, why don't you do the whole analysis in SPM then map the results to the surface? doug Thunell Evelina wrote: Hi Douglas, I do most of my analysis in matlab and SPM. For this one part of my experiment - it's a retinotopic mapping that I will use to ensure that my ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, motion correction and coregistration between functional runs and of the structural image already in SPM. I thought that since these flags exist they would just skip a step in the processing and send the data directly to the next step. But since it's not the case I'll have to do it some other way instead, maybe just redo the whole preprocessing in Freesurfer on the already preprocessed data. (Running the analysis with selxavg3-sess -analysis retlh -s SessXX *-no-preproc *doesn't work.) Anyway, the important thing is that the retinotopic mapping data stay coregistered with the rest of the functional data. If I can do this step in Freesurfer instead (and the rest of the preprocessing) that would be an option. Thanks a lot, Evelina On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote: Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface. doug Thunell Evelina wrote: Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@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 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. -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- 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: 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
Re: [Freesurfer] run preproc-sess with -nomc
Hi Douglas, I do most of my analysis in matlab and SPM. For this one part of my experiment - it's a retinotopic mapping that I will use to ensure that my ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, motion correction and coregistration between functional runs and of the structural image already in SPM. I thought that since these flags exist they would just skip a step in the processing and send the data directly to the next step. But since it's not the case I'll have to do it some other way instead, maybe just redo the whole preprocessing in Freesurfer on the already preprocessed data. (Running the analysis with selxavg3-sess -analysis retlh -s SessXX -no-preproc doesn't work.) Anyway, the important thing is that the retinotopic mapping data stay coregistered with the rest of the functional data. If I can do this step in Freesurfer instead (and the rest of the preprocessing) that would be an option. Thanks a lot, Evelina On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote: Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface. doug Thunell Evelina wrote: Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:gr...@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 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] run preproc-sess with -nomc
Hi Evelina, why don't you do the whole analysis in SPM then map the results to the surface? doug Thunell Evelina wrote: Hi Douglas, I do most of my analysis in matlab and SPM. For this one part of my experiment - it's a retinotopic mapping that I will use to ensure that my ROIs are in V1 - I'm using Freesurfer. I have done slice time correction, motion correction and coregistration between functional runs and of the structural image already in SPM. I thought that since these flags exist they would just skip a step in the processing and send the data directly to the next step. But since it's not the case I'll have to do it some other way instead, maybe just redo the whole preprocessing in Freesurfer on the already preprocessed data. (Running the analysis with selxavg3-sess -analysis retlh -s SessXX *-no-preproc *doesn't work.) Anyway, the important thing is that the retinotopic mapping data stay coregistered with the rest of the functional data. If I can do this step in Freesurfer instead (and the rest of the preprocessing) that would be an option. Thanks a lot, Evelina On Dec 9, 2011, at 7:06 PM, Douglas N Greve wrote: Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface. doug Thunell Evelina wrote: Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:gr...@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 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. -- 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: 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
Re: [Freesurfer] run preproc-sess with -nomc
Hi Evelina, why do you want to run it without MC? I'm not sure it will run that way. When you run it with -noreg, it causes it not to run the registration. For the preprocessing you have set up, it requires that the registration be run at some point because it needs it to map the fmri to the surface. doug Thunell Evelina wrote: Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ 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: 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] run preproc-sess with -nomc
Hi, Does anyone know how to correctly use the -nomc and -noreg flags? When I run: preproc-sess -fwhm 0 -surface self lhrh -s SessLP -fsd bold -nomc I get the error message: ERROR: could not determine file for /Applications/freesurfer/sessions/retinotopy/SessLP/bold/001/fmcpr I also tried preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold -noreg which gives the error: ERROR: cannot find /Applications/freesurfer/sessions/retinotopy/SessLPpolar/bold/001/register.dof6.dat Try running register-sess with -per-run When I do preproc-sess -fwhm 0 -surface self lhrh -s SessLPpolar -fsd bold it works fine and finishes without errors (preproc-sess done) (I'm using freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 on Mac OS X 10.6.8) Thanks a lot for any help, Evelina ___ 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.
