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.
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