Hi,
I have just installed Freesurfer and I am now following the steps in the preprocessing tutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/ FsFastTutorial) but for some reason preproc-sess is not generating (1) the motion corrected & smoothed volume fmcsm5.nii, and (2) the brain mask masks/brain.nii volume, as it should.
Inspecting the terminal output, I couldn't see any potential source of problems apart from a warning generated by Matlab which says:
Warning: Duplicate directory name: /Users/eiji/matlab.
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
Warning: Executing startup failed in matlabrc. This indicates a potentially serious problem in your MATLAB setup, which should be resolved as soon as possible. Error detected was: MATLAB:UndefinedFunction Undefined command/function 'setenv'.
In matlabrc at 224
>> >> >> >> >> >> >> >> >> >> INFO: northog = 6, pct = 100 >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >>
------------------------------------------
In spite of that, preproc-sess seems to exit without errors, later displaying 'spatiallysmooth-sess Done' and 'mkbrainmask-sess done'. So it looks that technically there wasn't an error?
Checking the mailing lists archives, I found a recent thread discussing a similar problem but it is not very clear to me how it was solved in the end (Balaji? Doug?). Directory permissions looks fine (755). Could anyone help? (Link to the thread: http://www.mail-archive.com/ freesurfer@nmr.mgh.harvard.edu/msg07826.html. I am using the same subject line in this post...)
I am attaching as a text file the terminal output of the command I am executing (' preproc-sess -s mgh-101.1 -fwhm 5 ' ). I also installed AFNI and FSL as I tried to advance in the tutorial.
This is surely not a bug report, but for the record the description of my platform is as follows:
---------------------------------------------------------------------
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5
Kernel info: Darwin 8.11.0 Power Macintosh
--------------------------------------------------------------------- Please include the following additional information in your report:
1) subject name -> mgh-101.1 (I suppose) 2) the entire command-line executed -> preproc-sess -s mgh-101.1 - fwhm 5 3) the error message generated -> No obvious error message, but fmcsm5.nii and masks/brain.nii are not generated 4) optionally include the subject's /script/recon-all.log -> (OK, now you got me, I see there are several recon-all.log's but none in the vicinity of the preproc tutorial directory...)
----
Any help will be greatly appreciated! If there is anything unclear, please, let me know.
Thank you very much in advance.
Eiji