External Email - Use Caution

Yes I have been try to processes other subjects in Freesurfer,I have installed freesurfer a little while ago and to test my installation,I did full recon-all to single subject T1w data but I get an error like this.But I solved the problem.I used freesurfer 5.3 version.But I get an error then I downloaded latest version of freesurfer and processing worked succesfully.I think it is about version of your linux and freesurfer.

________________________________ Gönderen: Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu adına freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Gönderildi: 24 Nisan 2019 Çarşamba 20:15 Kime: freesurfer@nmr.mgh.harvard.edu Konu: Re: [Freesurfer] recon-all error

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 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

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