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
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Douglas N. Greve, Ph.D.
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