Re: [Freesurfer] Dimension Mismatch Error

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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