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. >>> >> >> >> >>
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