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Hi FreeSurfer Developers,
I'm attempting to perform a full recon-all on the dicom/nifti file for test my freesurfer installation as described on the website https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall but I have an error like this;
recon-all -s file1 -i /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm -all
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/file1
mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz
mri_convert /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm... Starting DICOMRead2() dcmfile = /home/ebru/Desktop/den01_org/T1_1/IM-0002-0001.dcm dcmdir = /home/ebru/Desktop/den01_org/T1_1 Ref Series No = 201 Found 182 files, checking for dicoms Found 180 dicom files in series. First Sorting Computing Slice Direction Vs: -0.0462818 0.24329 0.968857 Vs: -0.0462815 0.243288 0.968849 Second Sorting Counting frames nframes = 1 nslices = 180 ndcmfiles = 180 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=8.39, TE=3.86, TI=0.00, flip angle=8.00 i_ras = (-0.996607, -0.0773363, 0.0281873) j_ras = (0.0680693, -0.966865, -0.246046) k_ras = (0.0462815, -0.243288, 0.968849) writing to /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz... #-------------------------------------------- #@# MotionCor Çrş Nis 24 11:45:57 +03 2019 Found 1 runs /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue.
cp /usr/local/freesurfer/subjects/file1/mri/orig/001.mgz /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz
/usr/local/freesurfer/subjects/file1
mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform
mri_convert /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/file1/mri/rawavg.mgz... TR=8.39, TE=3.86, TI=0.00, flip angle=8.00 i_ras = (-0.996607, -0.0773363, 0.0281873) j_ras = (0.0680693, -0.966865, -0.246046) k_ras = (0.0462815, -0.243288, 0.968849) Original Data has (0.976562, 0.976562, 1) mm size and (256, 256, 180) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from short to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /usr/local/freesurfer/subjects/file1/mri/orig.mgz...
mri_add_xform_to_header -c /usr/local/freesurfer/subjects/file1/mri/transforms/talairach.xfm /usr/local/freesurfer/subjects/file1/mri/orig.mgz /usr/local/freesurfer/subjects/file1/mri/orig.mgz
INFO: extension is mgz #-------------------------------------------- #@# Talairach Çrş Nis 24 11:46:09 +03 2019 /usr/local/freesurfer/subjects/file1/mri
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s file1 exited with ERRORS at Çrş Nis 24 11:46:11 +03 2019
For more details, see the log file /usr/local/freesurfer/subjects/file1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one?
1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Ubuntu version:18.10 3) uname -a: Linux sid 4.18.0-17-generic #18-Ubuntu SMP Wed Mar 13 14:34:40 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
DownloadAndInstall - Free Surfer Wikihttps://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. surfer.nmr.mgh.harvard.edu