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/ 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. 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