I have to say that I'm stumped. Do you really need to resolve this question?
doug


On 10/01/2013 12:27 PM, Leila Reddy wrote:
> Hi Doug,
>
> Here it is.
>
> cheers,
> Leila
>
> ------------------------------------------------------------------------
> *From:* Douglas N Greve <greve@nmr.mgh.harvard.edu>
> *To:* Leila Reddy <leils@yahoo.com>
> *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Sent:* Tuesday, October 1, 2013 5:53 PM
> *Subject:* Re: Question about preproc-sess -no-subcort-mask
>
>
> Hmmm, not sure what to say. CAn you send me $FREESURFER_HOME/fsfast/bin/preproc-sess  ?
>
>
>
> On 10/01/2013 07:45 AM, Leila Reddy wrote:
> > Hi Doug,
> >
> > I don't think that could have happened as I only found out about the no-subcort-mask option yesterday (after I had done all the original analysis).
> >
> > I have just re-run all the analyses for the same subject with the same commands on the two machines (output of bugr for the 2 machines is below). I had deleted everything from this subject's bold directory except the f.nii and para.para files for each run, so that everything is re-analyzed. I get the same problem as before. I attach a screen capture of freeview with my bold/analysis.mni/mask.nii overlaid on freesurfer/average/mni305.cor.mgz from the two machines. As you can see, they are different. They only look the same if I re-run the analysis on snowleopardv5.3.0 with preproc-sess -no-subcort-mask.
> >
> > Thanks again,
> > Leila
> >
> > Machine 1:
> > ---------------------------------------------------------------------
> >
> > FREESURFER_HOME: /APPLICATIONS/freesurfer
> >
> > Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
> >
> > Kernel info: Darwin 10.8.0 i386
> >
> > ---------------------------------------------------------------------
> > Machine 2:
> > ---------------------------------------------------------------------
> >
> > FREESURFER_HOME: /APPLICATIONS/freesurfer
> >
> > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0
> >
> > Kernel info: Darwin 12.0.0 x86_64
> >
> > ---------------------------------------------------------------------
> >
> >
> > ------------------------------------------------------------------------
> >
> > Date: Mon, 30 Sep 2013 17:48:15 -0400
> > From: 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>>>
> > Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask
> > To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>>
> > Message-ID: <5249F19F.3070503@nmr.mgh.harvard.edu <mailto:5249F19F.3070503@nmr.mgh.harvard.edu> <mailto:5249F19F.3070503@nmr.mgh.harvard.edu <mailto:5249F19F.3070503@nmr.mgh.harvard.edu>>>
> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >
> > They do have the same default. Note that if you run preproc-sess with
> > -no-subcort-mask and then run it again without -no-subcort-mask it will
> > not generate a new file. Could that have happened?
> > doug
> >
> >
> >
>
> -- Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
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> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
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>

-- Douglas N. Greve, Ph.D.
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/