It worked! Thank you so so much!
Best, Muriel On Jul 11, 2012, at 6:34 PM, Muriel Bruchhage wrote: > Hi Bruce, > > Thank you very much for your fast response. > > Unfortunately though, I still get an error response when typing in "recon-all > -i /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ > -subjid GID02" > > recon-all -i > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/ -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/GID02/2_T1_3DSAG/DICOM > Actual FREESURFER_HOME /Applications/freesurfer > 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 > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02 > \n mri_convert > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz > \n > mri_convert > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz > > corRead(): can't open file > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/COR-.info > $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > reading from > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM... > 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 18:32:26 CEST 2012 > > For more details, see the log file > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > Thank you very much in advance for all your help! > > Best, > Muriel > > > On Jul 11, 2012, at 6:20 PM, Bruce Fischl wrote: > >> 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 >>> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
