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> 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
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/
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 . 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.