Hi Maria Gabriela - This does not look like a diffusion dicom: PulseSeq tfl_me3d4_16ns Protocol T1

a.y ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Figueiro Longo, Maria Gabriela MFIGUEIROLONGO@mgh.harvard.edu Sent: Monday, April 27, 2020 9:49 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Tracula error: ERROR: Must specify input table of gradient vectors

Hi,

I have been trying different ways to troubleshooting this error without success. I am pasting here the whole error when I try to run "trac-all -prep -c" in the Dev version:

INFO: SUBJECTS_DIR is /autofs/cluster/guptagp/LLLT/fsrecon INFO: Diffusion root is /autofs/cluster/guptagp/gabi/tracula/Output Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/dev INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-linux-centos7_x86_64-dev-20200422-b097f6b Current Stamp: freesurfer-linux-centos7_x86_64-dev-20200427-0e41864 trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/scripts/trac-all.cmd ; trac-preproc -c /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/dmrirc.local -log /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.log -cmd /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/scripts/trac-all.cmd ; #------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Image corrections Mon Apr 27 09:37:59 EDT 2020 mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz mri_convert --bvec-voxel /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz reading from /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010... Getting Series No INFO: Found 5211 files in /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715 INFO: Scanning for Series Number 102 Scanning Directory INFO: found 140 files in series INFO: loading series header info.

RunNo = 101 INFO: sorting. sdfiSameSlicePos() eps = 0.000001

WARNING: file /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ...

INFO: (256 256 140), nframes = 1, ismosaic=0 sdfi->UseSliceScaleFactor 0 INFO: rescale not needed datatype = 4, short=4, float=3 PE Dir ROW ROW FileName /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 Identification NumarisVer syngo MR E11 ScannerModel Prisma_fit PatientName 3LT050_s1_170715 Date and time StudyDate 20170715 StudyTime 092536.870000 SeriesTime 100956.320000 AcqTime 093429.902500 Acquisition parameters PulseSeq tfl_me3d4_16ns Protocol T1 PhEncDir ROW EchoNo 1 FlipAngle 7 EchoTime 1.69 InversionTime 1100 RepetitionTime 2530 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 101 SeriesNo 102 ImageNo 139 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 54.1349 92.6115 176.0819 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 140 Vc 0.0934 -0.9338 -0.3453 Vr 0.0226 0.3487 -0.9370 Vs 0.4326 0.3520 -0.8301 VolCenter 99.2585 42.3521 -46.1506 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=1.69, TI=1100.00, flip angle=7.00 i_ras = (0.0933703, -0.933839, -0.345291) j_ras = (0.0225973, 0.348705, -0.93696) k_ras = (0.432568, 0.35197, -0.830061) writing to /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dwi_orig.nii.gz... mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat ERROR: Must specify input table of gradient vectors Linux deqi.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

trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020

#------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Inter-subject registration (base template) Mon Apr 27 09:39:14 EDT 2020 cp /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory Linux deqi.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

trac-preproc exited with ERRORS at Mon Apr 27 09:39:14 EDT 2020

[deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat [deqi:Scripts] (nmr-dev-env) mri_probedicom --i /autofs/cluster/guptagp/LLLT/raw_data/3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.30000017071500164627700002010 > /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/dcminfo.dat [deqi:Scripts] (nmr-dev-env) autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat: Command not found. [deqi:Scripts] (nmr-dev-env) cp autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat /autofs/cluster/guptagp/gabi/tracula/Output/3LT050/dmri/xfms cp: cannot stat \u2018autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/mni2anatorig.mat\u2019: No such file or directory cp: cannot stat \u2018/autofs/cluster/guptagp/gabi/tracula/Output/3LT050_s1_170715.long.3LT050/dmri/xfms/anatorig2mni.mat\u2019: No such file or directory

Thanks for the help, Gabriela ________________________________ From: Figueiro Longo, Maria Gabriela Sent: Friday, April 24, 2020 10:47 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Tracula error: ERROR: Must specify input table of gradient vectors

Hello Dear Freesurfer Developers,

I am attempting to run Tracula in the last to subject of my study (I had processed all the other subjects using the same script without problems). However, when I try to run the scrip bellow, I am having the error:

" ERROR: Must specify input table of gradient vectors "

I am reviewed the associated DICOM images and couldn't find any problem with the images. I reviewed a couple emails in the list, but couldn't find a clear reason for keeping having this error.

I am using the Freesurfer Dev version.

I really appreciate any help.

Thank you, Gabriela

# FreeSurfer SUBJECTS_DIR # T1 images and FreeSurfer segmentations are expected to be found here # setenv SUBJECTS_DIR /autofs/cluster/guptagp/LLLT/fsrecon

# Output directory where trac-all results will be saved # Default: Same as SUBJECTS_DIR # set dtroot = /autofs/cluster/guptagp/gabi/tracula/Output

# Subject IDs (one per time point per subject) # set subjlist = ( 3LT050_s1_170715 )

# Longitudinal base template subject IDs (one for each time point above) # set baselist = ( 3LT050 )

# In case you want to analyze only Huey and Louie # Default: Run analysis on all time points and subjects # # set runlist = (1 2 5 6)

# Input diffusion DICOMs (file names relative to dcmroot) # If original DICOMs don't exist, these can be in other image format # but then bvecfile and bvalfile must be specified (see below) # set dcmroot = /autofs/cluster/guptagp/LLLT/raw_data set dcmlist = ( 3LT050_s1_170715/MR.1.3.12.2.1107.5.2.43.67026.20170715092715598296003 )

Gabriela Longo, MD, MSc.

Emergency Radiology Clinical Fellow, Emergency Radiology Division

Massachusetts General Hospital (MGH)

mfigueirolongo@mgh.harvard.edu

Phone: +1 857 214 0568