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>>
> Subject: Re: [Freesurfer] Question about preproc-sess -no-subcort-mask
> To: 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>>
> 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
Phone Number: 617-724-2358
Fax: 617-726-7422

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