I am new to freesurfer and tried to run recon-all on it (I am using a MacBook Pro with Lion if that is of any importance).

What I have been done so far:

1) I set my Freesurfer environment in my .tcshrc file to:

setenv FREESURFER_HOME /Applications/freesurfer/

2) I converted my original T1 DICOM files into one MGZ file using the mri_convert command (mri_convert <first dicom>.dcm 001.mgz). Both files can be found under $SUBJECTS_DIR/GID02/2_T1_3DSAG - the MGZ file under a MGZ folder and the DICOMs under a DICOM folder ($SUBJECTS_DIR/GID02/2_T1_3DSAG/MGZ or $SUBJECTS_DIR/GID02/2_T1_3DSAG/DICOM respectively).

3) I tried the recon-all command with both the setenv $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/ and with $SUBJECTS_DIR//Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ where the MGZ file actually lies.

Does the fact that I only have one .mgz file have an influence on my data processing? Would a T2 scan count as a second structural scan?

As I always get this error message:

1) for running it with recon-all -all -subjid GID02 on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/

[Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% ls

GID02 GID251 GID51_2 GID70 GID753

GID100 GID28 GID53 GID701 GID76

GID117 GID33 GID549 GID710 VBM

GID12 GID47 GID61 GID72 fsaverage

GID140 GID51 GID62 GID75

[Muriels-MacBook-Pro:freesurfer/subjects/MRI_04_2012] mbruchhage% cd GID02/2_T1_3DSAG/MGZ/

[Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% ls

001.mgz

[Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz

ERROR: cannot find /Applications/freesurfer/subjects/MRI_04_2012/001.mgz

[Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid GID02

Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0

Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012

Actual FREESURFER_HOME /Applications/freesurfer

-rw-rw-r-- 1 mbruchhage wheel 33313 Jul 11 12:13 /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log

Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64

#--------------------------------------------

#@# MotionCor Wed Jul 11 17:54:17 CEST 2012

ERROR: no run data found in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri. Make sure to

have a volume called 001.mgz in /Applications/freesurfer/subjects/MRI_04_2012/GID02/mri/orig.

If you have a second run of data call it 002.mgz, etc.

Darwin Muriels-MacBook-Pro.local 11.3.1 Darwin Kernel Version 11.3.1: Thu Feb 16 19:05:38 PST 2012; root:xnu-1699.25.42~1/RELEASE_X86_64 x86_64

recon-all -s GID02 exited with ERRORS at Wed Jul 11 17:54:17 CEST 2012

For more details, see the log file /Applications/freesurfer/subjects/MRI_04_2012/GID02/scripts/recon-all.log

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2) for running it with recon-all -all -subjid 001.mgz on setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ

[Muriels-MacBook-Pro:GID02/2_T1_3DSAG/MGZ] mbruchhage% recon-all -all -subjid 001.mgz

mkdir: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory

cp: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/scripts/build-stamp.txt: Not a directory

cat: /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz/scripts/build-stamp.txt: Not a directory

INFO: FreeSurfer build stamps do not match

Subject Stamp:

Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0

INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ

Actual FREESURFER_HOME /Applications/freesurfer

/Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/MGZ/001.mgz: Not a directory.

Thank you very much in advance and greetings from Oslo,