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, +1(857)294-2080
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