Thanks Bruce and Joerg,

How can I create symlink to the fsaverage? I recently have installed freesurfer and I was able to run a subject last week without any error not sure why all the subjects I ran now over the weekend ended up with same error.

Thanks

-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2011 8:48 AM To: Ayaz, Muhammad Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] fsaverage error with recon-all

Hi Ayaz

you need to create a symlink to the fsaverage subject we distribute in your SUBJECTS_DIR if you want to get the estimate Brodmann area labels.

cheers Bruce

On Tue, 31 May 2011, Ayaz, Muhammad wrote:

Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage. Thanks Ayaz #@# BA Labels lh Fri May 27 21:47:56 CDT 2011 INFO: fsaverage subject does not exist in SUBJECTS_DIR INFO: Creating symlink to fsaverage subject...

ln -s /usr/local/freesurfer/subjects/fsaverage /usr/local/subjects/fsaverage

ln: creating symbolic link `/usr/local/subjects/fsaverage': Permission denied

mri_label2label --srcsubject fsaverage --srclabel /usr/local/subjects/fsaverage/label/lh.BA1.label --trgsubject 3t3999_3_1_MPRAGE --trglabel ./lh.BA1.label --hemi lh --regmethod surface

No such file or directory mri_label2label: could not open label file /usr/local/subjects/fsaverage/label/lh.BA1.label

srclabel = /usr/local/subjects/fsaverage/label/lh.BA1.label srcsubject = fsaverage trgsubject = 3t3999_3_1_MPRAGE trglabel = ./lh.BA1.label regmethod = surface

srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0

SUBJECTS_DIR /usr/local/subjects FREESURFER_HOME /usr/local/freesurfer Loading source label. Invalid argument ERROR reading /usr/local/subjects/fsaverage/label/lh.BA1.label Linux MRI-WorkStation 2.6.32-31-generic #61-Ubuntu SMP Fri Apr 8 18:25:51 UTC 2011 x86_64 GNU/Linux

recon-all -s 3t3999_3_1_MPRAGE exited with ERRORS at Fri May 27 21:47:56 CDT 2011

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