I don't think there was a file attached. Have you been able to processes any
subjects in FreeSurfer? Or does it fail in this way on all subjects?
On 4/24/2019 4:59 AM, Ebru Ayyürek wrote:
External Email - Use Caution
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
Wiki<https://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
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