Hi Muriel

the -s switch should be followed by a subject identifier (e.g. subject0001), not the 001.mgz file. Note that you don't need to convert your dicom to mgz either, just point recon-all at one slice in the correct (T1-weighted) dicom series with -i <path to dicom file>. And one acquisition is usually sufficient these days depending on the coil and field strength. We don't use T2s at the moment.

cheers Bruce

On Wed, 11 Jul 2012, Muriel Bruchhage wrote:

Hi, 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/

source $FREESURFER_HOME/SetUpFreeSurfer.csh

source $FREESURFER_HOME

setenv SUBJECTS_DIR /Applications/freesurfer/subjects/MRI_04_2012/

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/    andwith $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. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion 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,

Muriel Bruchhage