On Jul 11, 2012, at 11:23 PM, Muriel Bruchhage wrote: > I added the -all at the end and skipped the -i flag, but I still get an error > message: > > Checking for (invalid) multi-frame inputs... > ERROR: input(s) cannot have multiple frames! > /Applications/freesurfer/subjects/MRI_04_2012/GID02/2_T1_3DSAG/DICOM/GID02/mri/orig/001.mgz > has 2 frames > > I am so sorry to bother you with these probably very amateur questions - but > how can I have multiple frames when I just got one .mgz file and just one T1? > > Best, > Muriel > > On Jul 11, 2012, at 10:55 PM, Bruce Fischl wrote: > >> 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
