Thanks for the clarification, Sebastian! (I am sending this to the ML hoping that your reply might be useful to other newbies like me!)
E.
On 2008/08/26, at 16:41, Sebastian Moeller wrote:
Hi Eiji,
On Aug 26, 2008, at 3:22 AM, freesurfer-request@nmr.mgh.harvard.edu wrote:
Message: 2 Date: Tue, 26 Aug 2008 10:21:30 +0900 From: "N. Eiji Nawa" eiji@atr.jp Subject: Re: [Freesurfer] Preproc-sess: Spatial smoothing and brain masking To: freesurfer@nmr.mgh.harvard.edu Cc: Doug Greve greve@nmr.mgh.harvard.edu Message-ID: 8400CC61-80F1-488D-8CE8-BB0C4463A598@atr.jp Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
A follow-up to my own post. I found a post that suggested that executing 'spatialsmooth-sess' with the '-update' could prevent the generation of fmcsm5.nii (https://mail.nmr.mgh.harvard.edu/ pipermail// freesurfer/2008-July/008081.html).
Nah, the July result was that OSX's "test" command does not behve like the gnu "test" used in Linux, and therefore -update will not work properly on macs. So running without the -update flag is one possible work around.
Well, actually running "preprocess-sess" with the "-noupdate" command line option should solve your problems for now...
In fact, running:
spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd bold -s mgh-101.1 -d $FSFTUTDIR/my-study -noinorm
worked fine!
As expected...
Likewise with 'mkbrainmask-sess':
mkbrainmask-sess -maskstem brain -fsd bold -s mgh-101.1 -d $FSFTUTDIR/ my-study
_without_ the '-update' correctly generated the masks/brain.nii volume.
I just wonder if preproc-sess only has this behavior in systems like mine, since it does not look like it is a general problem (I am using Mac OS 10.4.11 in a PowerPC G5).
It seems Macos 10.4.11 as well as Macos 10.5.4 are affected. I would not be amazed, if all versions of MacosX are affected, as of their BSD origin compared to Linux's gnu core utilities. The details: While "test $infile -nt $outfile" returns 0 under Linux, if $outfile does not exist, it returns 1 under Macosx. This is hard to generically care for...
In any case, running spatialsmooth-sess and mkbrainmask-sess manually after executing preproc-sess seems to generate all the volumes!
A (potentially incomplete) list of affected fs-fast scripts: /fsfast/bin/mc-sess ./fsfast/bin/mkbrainmask-sess ./fsfast/bin/mktemplate-sess ./fsfast/bin/preproc-sess ./fsfast/bin/spatialsmooth-sess ./fsfast/bin/stc-sess
Ahoi Sebastian
E.
-- Sebastian Moeller
Tel.: 04 21 - 2 18 - 90 96 Fax.: 04 21 - 2 18 - 90 04 GSM: 0 15 77 - 1 90 31 41 moeller@neuro.uni-bremen.de
AG Kreiter / FB 2 Institut fuer Hirnforschung III Abteilung Theoretische Neurobiologie Universitaet Bremen Biogarten Hochschulring 16a Postfach 33 04 40 28359 Bremen
freesurfer@nmr.mgh.harvard.edu
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N. Eiji Nawa