I apologize, the csh file is located in the home directory, /homes/14/jake/AnalysisPrograms
Thanks
Hi,
Thanks for the bugr command. Here is my information, Thank you!
Please include the following additional information in your report:
- subject name:
CD_aftbotox_ctrl5
- the entire command-line executed
csh CD_aftbotox_ctrl5_ContrastAnalysis.csh
- the error message generated (please see below, our preprocessing
step is built into our csh file.)
- optionally include the subject's /script/recon-all.log
**The logfile for preprocessing can be found in:
/autofs/space/meso_018/users/ablood/cerv/log striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log
FREESURFER_HOME: /usr/local/freesurfer/stable3
Build stamp: freesurfer-Linux-centos4-stable-v3.0.5-20070717
RedHat release: CentOS release 5 (Final)
Kernel info: Linux 2.6.18-8.1.15.el5 i686
NMR Center info (/space/freesurfer exists):
machine: striatum
SUBJECTS_DIR: /space/sake/3/users/inverse/subjects
***(this is set to be /space/meso/18/users/ablood/cerv by the .csh script)
PWD: /homes/14/jake/AnalysisPrograms
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] Error From: "Pratap Kunwar" pkunwar@nmr.mgh.harvard.edu Date: Fri, March 28, 2008 12:00 pm To: jake@nmr.mgh.harvard.edu
Jake,
Are you doing preprocessing or stxgrinder, and are you running from
*running from the following directory /autofs/homes/014/jake/AnalysisPrograms
or /autofs/space/meso_018/users/ablood/cerv/ ?
it will be nice if you provide more info. use "bugr" to get report and send to freesurfer. about bugreporting, https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting?action=highlight&...
pratap
Hi,
We are getting an error where our preprocessing step seems to be failing, any help would be greatly appreciated, thank you!
*using the following command (which sources /usr/local/freesurfer/nmr-stable3-env) striatum:jake[85] csh CD_aftbotox_ctrl5_ContrastAnalysis.csh
*error: --- Parsing Config File: /autofs/space/meso_018/users/ablood/cerv/tap_rh_short_CD_aftbotox_ctrl5_sm4/analysis.cfg
-gammafit 2.25 1.25 -timewindow 25.0000 -prestim 0 -polyfit 1 -TER 2.5000 -nskip 0 -fwhm 0 -rescale 1000 ERROR: 022/fmcsm4 does not have a .meanval file, run inorm ERROR (/autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5): selxavg failed ERROR: cannot find tap_rh_short_CD_aftbotox_ctrl5_sm4/h.dat
stxgrinder-sess logfile is /autofs/space/meso_018/users/ablood/cerv/log/stxgrinder-sess.080328112804.log
ERROR: analysis tap_rh_short_CD_aftbotox_ctrl5_sm4 does not exist for /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5
**The logfile for preprocessing can be found in: /autofs/space/meso_018/users/ablood/cerv/log striatum:jake[107] more preproc-CD_aftbotox_ctrl5-bold.log
***Here is the error from the logfile: to3d WARNING: Significant outliers detected in these sub-bricks: 60 103 104 105 106 107 108 120 122 You should inspect the dataset for possible corruption. [Outliers are defined as in program 3dToutcount. ] [Outliers early in an EPI time series may be due to ] [the longitudinal magnetization equilibration effect.] [Other causes are subject movement, scanner problems,] [or anything that makes a time series look irregular.] [ 3dToutcount -save outnam dataset | 1dplot -stdin ] [can be used to make a dataset 'outnam' that marks ] [outlier voxels; see 3dToutcount -help for details. ]
++ 3D dataset written to disk -------------- Motion Correcting --------------------------- /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ctrl5/bold/mctmp set VR = 3dvolreg 3dvolreg -verbose -dfile /autofs/space/meso_018/users/ablood/cerv/CD_aftbotox_ct rl5/bold/018/fmc4.mcdat -prefix 6776.volreg -base targ-6776+orig[0] 6776+orig ++ Program 3dvolreg: AFNI version=AFNI_2006_03_21_1314 [32-bit] ++ Authored by: RW Cox ++ Reading in base dataset ./targ-6776+orig.BRIK ** Input ./6776+orig.HEAD and base ./targ-6776+orig.HEAD don't have same dimensi ons! Input: nx=64 ny=64 nz=30 Base: nx=64 ny=64 nz=16 ** FATAL ERROR: perhaps you could make your datasets match? set st = 1 if ( 1 ) then echo ERROR: 3dvolreg existed with status 1 ERROR: 3dvolreg existed with status 1 exit 1 ERROR: mc-sess failed
Thanks,
Jake
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