On Tue, Oct 4, 2011 at 1:22 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Hi Michell, you appear to have two FreeSurfer analysis for this subject:
/usr/local/freesurfer/subjects/ld12

/usr/local/freesurfer/subjects/retinotopy/sj12

Can you verify that these are *exactly* the same?

doug

Michelle Umali wrote:

Hi Doug and Freesurfers,
No matter what I try I am still getting the Dimension mismatch error when running fieldsign-sess. I even ran recon-all -s sj12 -make all.
I don't think it's a problem with the directories (below). The subjectname file is correct, and when I run field-sign-sess it sees the anatomical directory.

What else do you recommend?

Thanks.
Michelle

On Mon, Oct 3, 2011 at 4:36 PM, Michelle Umali <mumali01@gmail.com <mailto:mumali01@gmail.com>> wrote:

Hi Doug,
I keep my retinotopy (sj) and anatomical (ld) data separate. I
named the retinotopy directory sj12 with the subjectname file
says ld12, which is the anatomical directory for the same subject.

-Michelle

On Mon, Oct 3, 2011 at 4:31 PM, Douglas N Greve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

Can you check that the subjectname file is correct? In some
cases, it looks like it is using subject sj12, in others it
looks like it is using subject ld12.
doug

Michelle Umali wrote:

Hi Doug,

I re-ran from preproc-sess using the -force flag, and I
still get the same dimension mismatch error.

I'm attaching the terminal output starting from pre-proc-sess.

What's the next step?

Thanks.
Michelle

On Mon, Oct 3, 2011 at 3:23 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:

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

<mailto: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>>>
<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
<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>
<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
<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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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
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<mailto:greve@nmr.mgh.harvard.edu>>

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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>>>
Phone Number: 617-724-2358
<tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>>
<tel:617-724-2358 <tel:617-724-2358>
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<tel:617-724-2358 <tel:617-724-2358>>>> Fax:

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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
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<mailto:greve@nmr.mgh.harvard.edu>>>
Phone Number: 617-724-2358 <tel:617-724-2358>
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<tel:617-724-2358 <tel:617-724-2358>
<tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422
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<tel:617-726-7422 <tel:617-726-7422>>
<tel:617-726-7422 <tel:617-726-7422>
<tel:617-726-7422 <tel:617-726-7422>>>

Bugs:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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-- Douglas N. Greve, Ph.D.
MGH-NMR Center
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<mailto:greve@nmr.mgh.harvard.edu>
<mailto:greve@nmr.mgh.harvard.edu
<mailto:greve@nmr.mgh.harvard.edu>>
Phone Number: 617-724-2358 <tel:617-724-2358>
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<tel:617-726-7422>
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
FileDrop:
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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-- Douglas N. Greve, Ph.D.
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Phone Number: 617-724-2358 <tel:617-724-2358> Fax:
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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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