Hello Christopher, Perhaps you could upload a data set for which mri_convert is segfaulting so that we can take a closer look?
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange -Zeke On 06/13/2016 02:19 PM, Christopher Finuf wrote: > I'm trying to convert the dicom to the original 001.mgz file using the > following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR > is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current > working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The > following is the output and error that I get. I'm running the latest > version v 5.3.0 of freesurfer. Any suggestions on what the problem is? > What is strange that it works with half my data set but the other has > this error. I've run this command in the exact way many times before and > have never had this issue. > > > > > > bash-3.2$ recon-all -i > /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm > -subjid Bigler_Repeatability_0005Ad_M1 > > > Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects > > Actual FREESURFER_HOME /Applications/freesurfer > > Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin > Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; > root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 > > /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1 > > \n mri_convert > /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm > /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz > \n > > mri_convert > /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm > /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz > > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from > /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm... > > Getting Series No > > INFO: Found 178 files in > /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1 > > INFO: Scanning for Series Number 2 > > Scanning Directory > > INFO: found 176 files in series > > INFO: loading series header info. > > > RunNo = 1 > > INFO: sorting. > > INFO: (224 256 176), nframes = 1, ismosaic=0 > > PE Dir ROW ROW > > AutoAlign matrix detected > > AutoAlign Matrix --------------------- > > 1.000 0.000 0.000 0.000; > > 0.000 1.000 0.000 0.000; > > 0.000 0.000 1.000 0.000; > > 0.000 0.000 0.000 1.000; > > > FileName > /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm > > Identification > > NumarisVer syngo MR B17 > > ScannerModel TrioTim > > PatientName Bigler_Repeatability_AD_M > > Date and time > > StudyDate 20160512 > > StudyTime 075942.531000 > > SeriesTime 081401.859000 > > AcqTime 080647.620000 > > Acquisition parameters > > PulseSeq *tfl3d1_ns > > Protocol t1_mpr_sag_iso_ave2_ipat2_(mprage) > > PhEncDir ROW > > EchoNo 1 > > FlipAngle 9 > > EchoTime 2.26 > > InversionTime 900 > > RepetitionTime 1900 > > PhEncFOV 218.75 > > ReadoutFOV 250 > > Image information > > RunNo 1 > > SeriesNo 2 > > ImageNo 1 > > NImageRows 256 > > NImageCols 224 > > NFrames 1 > > SliceArraylSize 1 > > IsMosaic 0 > > ImgPos 75.8389 136.8499 125.0000 > > VolRes 0.9766 0.9766 1.0000 > > VolDim 224 256 176 > > Vc 0.0767 -0.9971 0.0000 > > Vr -0.0000 0.0000 -1.0000 > > Vs -0.9971 -0.0767 0.0000 > > VolCenter -3.5106 21.0460 0.0000 > > TransferSyntaxUID 1.2.840.10008.1.2.1 > > UseSliceScaleFactor 0 (slice 0: 1) > > Segmentation fault > > Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin > Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; > root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 > > > recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed > Jun 8 13:39:08 MDT 2016 > > > For more details, see the log file > /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log > > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > _______________________________________________ > 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 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.
