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> 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> 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>> 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>>> 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>>>> 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>>>>> 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>
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