Re: [Freesurfer] longitudinal TRACULA -prep error
Hi Carissa – Don’t set variables to “None” in the config file. Just remove those lines from the config file altogether – that’s the same as not having any inputs for them. Hope this helps, a.y From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Carissa Nicole Weis mailto:cnw...@uwm.edu>> Reply-To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, September 27, 2018 at 4:28 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] longitudinal TRACULA -prep error External Email - Use Caution Hello, I’m running into an error in the longitudinal TRACULA pipeline that I’m not sure how to resolve. I saw this error in the message board but there was no resolution to the problem so I thought I’d ask again. I’ve successfully run the recon-all longitudinal pipeline and am trying to run the trac-all –prep step with a longitudinal configuration file. Here’s the error, it happens for both time points listed in my configuration file: #@# Image corrections Thu Sep 27 12:59:31 CDT 2018 mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1... crypt_gkey = *CyXds2s6sOqQ Starting DICOMRead2() dcmfile = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI Ref Series No = 6 Found 2666 files, checking for dicoms Found 2660 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 38 nslices = 70 ndcmfiles = 2660 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=1.00, TE=57.70, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz... crypt_gkey = *CyXds2s6sOqQ mri_probedicom --i /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals flip4fsl /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x -y z /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals eddy_correct /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004 processing /bigraid-
[Freesurfer] longitudinal TRACULA -prep error
External Email - Use Caution Hello, I'm running into an error in the longitudinal TRACULA pipeline that I'm not sure how to resolve. I saw this error in the message board but there was no resolution to the problem so I thought I'd ask again. I've successfully run the recon-all longitudinal pipeline and am trying to run the trac-all -prep step with a longitudinal configuration file. Here's the error, it happens for both time points listed in my configuration file: #@# Image corrections Thu Sep 27 12:59:31 CDT 2018 mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz mri_convert /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ reading from /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1... crypt_gkey = *CyXds2s6sOqQ Starting DICOMRead2() dcmfile = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 dcmdir = /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI Ref Series No = 6 Found 2666 files, checking for dicoms Found 2660 dicom files in series. First Sorting Computing Slice Direction Vs: 0 0 2 Vs: 0 0 1 Second Sorting Counting frames nframes = 38 nslices = 70 ndcmfiles = 2660 PE Dir = COL (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=1.00, TE=57.70, TI=0.00, flip angle=90.00 i_ras = (-1, 0, 0) j_ras = (0, -1, 0) k_ras = (-0, -0, 1) writing to /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz... crypt_gkey = *CyXds2s6sOqQ mri_probedicom --i /bigraid-03/LS/RawData/iSTAR/106_6mo/106_6mo/p516/e584/DTI_all/DTI/i10760738.MRDC.1 > /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dcminfo.dat cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvecs.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs cp /bigraid-03/LS/Scripts/iStar/DTI_CWEIS_MS/istar_bvals.txt /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals.tmp /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals flip4fsl /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 2 fslswapdim /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.nii.gz x -y z /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: left-right orientation was flipped by fslswapdim fslorient -forceradiological /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvecs /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvecs mv -f /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.mghdti.bvals /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/bvals eddy_correct /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_orig_flip.nii.gz /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi.nii.gz 0 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0001 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0002 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0003 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0004 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0005 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0006 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0007 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0008 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0009 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0010 processing /bigraid-03/LS/Data/istar/freesurfer/106_6mo.fs.long.106/dmri/dwi_tmp0011 process
