Thank you so much Bruce, it now works like a charm!
Best, Muriel
On Jul 12, 2012, at 2:30 AM, Bruce Fischl wrote:
Hi Muriel
not sure what your second frame is, but you should be able to do this:
cd $SUBJECTS_DIR/<subject id>/mri/orig mv 001.mgz multiframe.mgz mri_convert -nth 0 multiframe.mgz 001.mgz recon-all -s <subject id> -all
cheers Bruce
On Thu, 12 Jul 2012, Muriel Bruchhage wrote:
Maybe this is easiest:
Best, Muriel
On Jul 12, 2012, at 12:54 AM, Bruce Fischl wrote:
did it have 2 frames? If so, what is the difference between them?
On Thu, 12 Jul 2012, Muriel Bruchhage wrote:
Hi Bruce,
I tried to send the .mgz file to you, but it apparently exceeded the limit. Nevertheless, I thought that it looked fine (I compared it to the bert data freesurfer came with).
Thank you very much again for all your efforts!
Best,
Muriel
On Jul 11, 2012, at 11:51 PM, Bruce Fischl wrote:
you can run freeview on the 001.mgz and see what is in it. If it has more than one frame freeview will include a slider that lets you change from one to the other. Or you can email it to me and I'll take a look.
On Wed, 11 Jul 2012, Muriel Bruchhage wrote:
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 >> >> >>
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Muriel Bruchhage