recon-all -s BIO-ALS-701-005-BL exited with ERRORS - Freesurfer

14 Sep 2020


      Dear developers,
I have been trying to run the recon-all without success. I am working remotely using my Windows laptop through NoMachine Linux.
Please see below the scripts and the error message. Thank you.
epimetheus:alz14[854] recon-all -i /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm -subject BIO-ALS-701-005-BL -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-701-005-BL/scripts/recon-all.local-copy'
/autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL
mri_convert /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz
mri_convert.bin /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/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-701-005-BL/MPRAGE/005/78000-000005-000001.dcm...
Getting Series No
INFO: Found 719 files in /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005
INFO: Scanning for Series Number 5
Scanning Directory
INFO: found 704 files in series
INFO: loading series header info.
RunNo = 4
INFO: sorting.
sdfiSameSlicePos() eps = 0.000001
INFO: (256 256 176), nframes = 4, ismosaic=0
sdfi->UseSliceScaleFactor 0
datatype = 4, short=4, float=3
PE Dir ROW ROW
AutoAlign matrix detected
AutoAlign Matrix ---------------------
 0.98640   0.09502  -0.13409  -22.58164;
-0.07808   0.98890   0.12638   16.16202;
 0.14461  -0.11420   0.98288  -7.16005;
 0.00000   0.00000   0.00000   1.00000;
FileName /autofs/cluster/atassigp/ALSspeech/BIO-ALS-701-005-BL/MPRAGE/005/78000-000005-000001.dcm
Identification
NumarisVer        syngo MR B13 4VB13A
ScannerModel      TrioTim
PatientName       HUP_PBR03_ALS701-005_120604
Date and time
StudyDate         20120604
StudyTime         104553.448000
SeriesTime        110830.078000
AcqTime           110221.415000
Acquisition parameters
PulseSeq          tfl3d4_ns
Protocol          MEMPRAGE_4e_p3_1mm_iso
PhEncDir          ROW
EchoNo            1
FlipAngle         7
EchoTime          1.64
InversionTime     1200
RepetitionTime    2530
PhEncFOV          256
ReadoutFOV        256
Image information
RunNo             4
SeriesNo          5
ImageNo           1
NImageRows        256
NImageCols        256
NFrames           4
SliceArraylSize   1
IsMosaic          0
ImgPos            137.3315  96.1324 107.3163
VolRes              1.0000   1.0000   1.0000
VolDim            256      256      176
Vc                 -0.0950  -0.9889  -0.1142
Vr                 -0.1341   0.1264  -0.9829
Vs                 -0.9864   0.0781   0.1446
VolCenter          21.2017  -7.3992 -20.3829
TransferSyntaxUID 1.2.840.10008.1.2.1
UseSliceScaleFactor 0 (slice 0: 1)
IsDWI = 0
INFO: no Siemens slice order reversal detected (good!).
TR=2530.00, TE=1.64, TI=1200.00, flip angle=7.00
i_ras = (-0.095018, -0.988904, -0.114196)
j_ras = (-0.134094, 0.126384, -0.982876)
k_ras = (-0.986403, 0.078078, 0.144615)
writing to /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz...
#--------------------------------------------
#@# MotionCor Mon Sep 14 14:11:28 EDT 2020
Found 1 runs
/autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz
Checking for (invalid) multi-frame inputs...
ERROR: input(s) cannot have multiple frames!
/autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/mri/orig/001.mgz has 4 frames
If this is a multi-frame MEMPRAGE image,
use mri_concat --rms to combine echo frames.
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-701-005-BL exited with ERRORS at Mon Sep 14 14:11:29 EDT 2020
For more details, see the log file /autofs/cluster/atassigp/ALSspeech/FS/Subjects/BIO-ALS-701-005-BL/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) 724-6347https://www.google.com/search?q=speech+and+feeding+disorders+lab&rlz=1C1GCEU_enUS821US821&oq=speech+and+feeding+&aqs=chrome.1.69i57j0l5.11462j0j7&sourceid=chrome&ie=UTF-8#, +1(857)294-2080
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