Dear Freesurfer Developers,

I am working remotely from my Windows notebook through the NoMachine Linux. I have been trying to recon-all without success.

Please see below the scripts. Thank you!


epimetheus:alz14[994] recon-all -i /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134 -subject BIO-ALS-701-043-post -all -brainstem-structures
Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /autofs/cluster/atassigp/ALSspeech/FS/Subjects
Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0
Linux epimetheus.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
'/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/scripts/recon-all.local-copy'
/autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post

 mri_convert /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134 /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/mri/orig/001.mgz

mri_convert.bin /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134 /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/mri/orig/001.mgz
$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
reading from /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355976815813134...
Getting Series No
INFO: Found 216 files in /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004
INFO: Scanning for Series Number 4
Scanning Directory
INFO: found 209 files in series
INFO: loading series header info.

RunNo = 3
WARNING: Run 1 appears to be truncated
  Files Found: 209, Files Expected (lRep+1): 1
FileName /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2015072216183223733750182
Identification
NumarisVer        syngo MR B17
ScannerModel      TrioTim
PatientName       HUP_PBR03_ALS701-043_150722
Date and time
StudyDate         20150722
StudyTime         161523.709000
SeriesTime        161832.316000
AcqTime           161824.385000
Acquisition parameters
PulseSeq          epfid2d1_64
Protocol          ge_fun_WholeBrain_64_1
PhEncDir          COL
EchoNo            1
FlipAngle         90
EchoTime          30
InversionTime     -1
RepetitionTime    2000
PhEncFOV          200
ReadoutFOV        200
Image information
RunNo             3
SeriesNo          4
ImageNo           1
NImageRows        448
NImageCols        448
NFrames           209
SliceArraylSize   37
IsMosaic          1
ImgPos            828.1392 504.4394 162.4422
VolRes              3.1250   3.1250   3.6000
VolDim             64       64       37
Vc                 -0.9480   0.0638   0.3118
Vr                 -0.2544  -0.7403  -0.6223
Vs                  0.1911  -0.6693   0.7180
VolCenter           0.0000   0.0000   0.0000
TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: sorting.
WARNING: files are not found to be different and cannot be sorted
File1: /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2015072216183223733750182
File2: /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2016092913355233033411124
INFO: ( 64  64  37), nframes = 209, ismosaic=1
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
Could not parse NUMARIS version string syngo MR B17
found in dicom tag 18,1020 (len = 3 != 6)
Repetition Time = 2000, TR = 2000 ms
PE Dir COL COL
AutoAlign matrix detected
AutoAlign Matrix ---------------------
 0.98571   0.04965  -0.16097  -1.09341;
-0.02565   0.98867   0.14788   15.43880;
 0.16649  -0.14164   0.97582  -11.39330;
 0.00000   0.00000   0.00000   1.00000;

FileName /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-043-BL/MPRAGE1/004/MR.1.3.12.2.1107.5.2.32.35101.2015072216183223733750182
Identification
NumarisVer        syngo MR B17
ScannerModel      TrioTim
PatientName       HUP_PBR03_ALS701-043_150722
Date and time
StudyDate         20150722
StudyTime         161523.709000
SeriesTime        161832.316000
AcqTime           161824.385000
Acquisition parameters
PulseSeq          epfid2d1_64
Protocol          ge_fun_WholeBrain_64_1
PhEncDir          COL
EchoNo            1
FlipAngle         90
EchoTime          30
InversionTime     -1
RepetitionTime    2000
PhEncFOV          200
ReadoutFOV        200
Image information
RunNo             3
SeriesNo          4
ImageNo           1
NImageRows        448
NImageCols        448
NFrames           209
SliceArraylSize   37
IsMosaic          1
ImgPos            106.6647  98.5294 -23.8684
VolRes              3.1250   3.1250   3.6000
VolDim             64       64       37
Vc                 -0.9480   0.0638   0.3118
Vr                 -0.2544  -0.7403  -0.6223
Vs                  0.1911  -0.6693   0.7180
VolCenter          -0.8517 -13.6964  -7.1010
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
ERROR: VolSS2MosSS: number of columns in the mosaic (280)
is not an integer multiple of the number of columns in
the image (64)
Linux epimetheus.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s BIO-ALS-701-043-post exited with ERRORS at Mon Sep 14 14:43:43 EDT 2020

For more details, see the log file /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-043-post/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



Ana Luiza Zaninotto, B.A, MSc, Ph.D.

Speech and Feeding Disorders Lab

MGH Institute of Health Professions - MGHIHP

+1 (617) 724-6347, +1(857)294-2080