On Mon, Oct 3, 2011 at 3:23 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

You can an asynchrony between your fmri data and the anatomical:
Anatomical: num vertices: 146530
fMRI: 158944 vertices

re-run the fMRI starting from preproc-sess. You will need to make sure that preproc-sess actually re-runs at least the sample-to-surface. By default, it just looks to see if things are up-to-date (but does not check the anatomical). So, you can run it with -force. This will cause it to re-run everything. Or you can delete the surface files in the bold directories and re-run without -force.

doug

Michelle Umali wrote:

Hi Doug,

I've attached the mri_info output on the eccen and polar images as well as the mris_info on the lh.sphere surface

Thanks.
Michelle

On Mon, Oct 3, 2011 at 2:38 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Can you send me the result of running mri_info on
eccen/real.nii
eccen/imag.nii
polar/real.nii
polar/imag.nii
in the
/usr/local/freesurfer/subjects/retinotopy/sj12/bold/rtopy.self.lh
directory?

And the result of
mris_info
/usr/local/freesurfer/subjects/retinotopy/sj12/surf/lh.sphere

doug

Michelle Umali wrote:

Hi Doug,
I've attached the output from running fieldsign-sess.

Thanks for all your help.
Michelle

On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu

<mailto:greve@nmr.mgh.harvard.edu>>> wrote:

Michelle, before you do that, can you run the offending program
with -debug and send me the (copious) terminal output? Your
anat
should not have to be re-run.

doug

Michelle Umali wrote:

Hi Bruce,
Will this undo my wm and pial edits?

Thanks.
Michelle

On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl
<fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>
<mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>
<mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>

<mailto:fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>>> wrote:

try running

recon-all -s subject -make all

and leave the -dontrun off. It should bring
everything up
to date

Bruce

On Sat, 1 Oct 2011, Michelle Umali wrote:

Dear Freesurfers,
I'm still getting a MRISripZeros() and
MRIScopyMRI Surf/src
mismatch error
when running fieldsign-sess. You suggested that
this
problem
was due to the
surfaces being out of synch. When I ran
recon-all -s
subject
-make all
-dontrun, I saw that several steps had not run.
The data
looked alright and
the number of vertices matched when I ran
-vno-check.

The mismatch error is still occurring, and I
don't know
how to
proceed.

Please suggest steps that I should take.

Thanks.
Michelle

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