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
[cid:9097102c-a1f0-4411-8009-6508f44e67d6]
