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 greve@nmr.mgh.harvard.edumailto: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

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.

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 greve@nmr.mgh.harvard.edu mailto: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

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 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

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 greve@nmr.mgh.harvard.edu mailto: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

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 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

-- 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