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) 724-6347https://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:4de4da5b-f7a4-4390-807a-af47efc8af46]
It looks like you are passing it a functional volume? You have to pass it a T1-weighted volume with resolution around 1mm
On 9/14/2020 2:52 PM, Zaninotto, Ana Luiza Costa wrote:
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 https://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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Zaninotto, Ana Luiza Costa