oh, you need to specify what you want it to do. Add -all at the end of the command line and it will do everything. Note that if you are rerunning, you can leave out the -i <path to dicom>
cheers Bruce On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > Hei, > > Thanks you very much again for your help! > > Nevertheless, even though I got the message that the recon-all has been done > without any errors, no talaraich transform, skull stripping or segmentation > has been done. I placed my fsaverage folder in the same folder where all my > participant-folders are - could that have been the problem? (this is also the > same place where my $SUBJECTS_DIR is directed to) > > Best, > > Muriel > > > On Jul 11, 2012, at 10:39 PM, Bruce Fischl wrote: > >> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
