Hi Pedro, thanks for your reply. I think, the MPRAGE data is ok with 1mm³ isotropic voxelsize aquired on a Trio system. The orientation is probably a problem because i just feed the images the way they come from the scanner direct into freesurfer. Even that freesurfer is not multithreaded, the higher processor 3GHz with higer RAM should run freesurfer faster than the lower 1.6GHz, isn´t it? Cheers, Thomas ----- Original Message ----- From: Pedro Paulo Oliveira Jr To: 'Thomas Doering' Cc: freesurfer@nmr.mgh.harvard.edu Sent: Monday, October 22, 2007 10:31 AM Subject: RE: [Freesurfer] intrasubject segmentation variance
Thomas,
There are some comments on your question.
Freesurfer is not multithreaded so it won't benefit from multicore unless you start one analysis on each core.
Your running times are high. My Opteron usually takes 23 hs to perform the recon-all in 3.0.5 version of FreeSurfer. One issue that can make the running time much higher is a poor SPGR/MPRAGE data. Maybe if you send one slice. Other issue that can raise the time is wrong volume orientation..
Best Regards,
Pedro Paulo Oliveira Jr
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Thomas Doering Sent: segunda-feira, 22 de outubro de 2007 09:05 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] intrasubject segmentation variance
Dear freesurfers,
i was running Freesurfer on the same subject on two independent Computers.
The first Computer PC1has 2 physical Intel processors with 2 logical each - (dual core) - 1.6GHz with 4Gb Ram and the second PC2 has 2 physical Intel processors with 4 logical - (quad core) - 3 GHz with 8 Gb Ram.
After running on these two Computers - i start at the exactly same time - i got a surprising result: My faster Computer PC2 took 41h to run the subject and the slower Computer took 31h.
I wonder if somebody have some comment on this, because i have no idea what is wrong ( When i have the Linux System Monitor on, watching the CPU History, it seems that the slower PC hat a more effective occupation/usage than the faster - switching faster between one CPU and the other one...)
Another small question:
In the final segmentation table, i noticed that there are some small diferences between the results of PC1 and PC2: for ex.:
PC1:ctx - rh-caudalmiddle frontal = 5029 5029
PC2:ctx - -"- 5360 5360
, so a diference of ~6%. I guess these are variations due to the algorithm..
Are there some established limits for that diferences?
Thanks for help,
Thomas