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:
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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
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Date: Mon, 30 Sep 2013 17:48:15 -0400 From: Douglas N Greve greve@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask To: freesurfer@nmr.mgh.harvard.edu Message-ID: 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
