sure, glad it worked out Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote:
> > 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
