Hi Bruce, To be quite honest, I am not sure, but I used the same data on a fsl segmentation task (using a nifti format though) and I never got any error messages back there.
Best, Muriel On Jul 11, 2012, at 11:26 PM, Bruce Fischl wrote: > Hi Muriel > > what was the scan that you are trying to run FreeSurfer on? Did it have more > than one echo? > > Bruce > > > > On Wed, 11 Jul 2012, Muriel Bruchhage wrote: > >> >> 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 >> >> >> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
