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.eduwrote:
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.**edugreve@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<greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.**edu <greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.**edu <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 <fischl@nmr.mgh.harvard.edu>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu><mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <fischl@nmr.mgh.harvard.edu>> <mailto:fischl@nmr.mgh.**harvard.edu<fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.**harvard.edu <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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ------------------------------**------------------------------**------------
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