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trac-all running -jobs issue error
by Daniel Callow 19 Apr '19

19 Apr '19

External Email - Use Caution Hello, After running trac-all -prep -jobs file -c /homes/dcallow/dmrirc.long.example.parallel.sh I am trying to submit the jobs for parallel computing. However, when running the following #!/bin/tcsh -f #SBATCH --time=300:00:00 #SBATCH --mem=24000 #SBATCH --output=results #SBATCH --cores=6 set subj= ($argv[1]) trac-preproc -c /homes/dcallow/dti_freesurf/trac/Ex.${subj}.long.base_${subj}/scripts/dmrirc.local -log /homes/dcallow/dti_freesurf/trac/Ex.${subj}.long.b$ trac-preproc -c /homes/dcallow/dti_freesurf/trac/Rest.${subj}.long.base_${subj}/scripts/dmrirc.local -log /homes/dcallow/dti_freesurf/trac/Rest.${subj}.lo$ trac-preproc -c /homes/dcallow/dti_freesurf/trac/base_${subj}/scripts/dmrirc.local -log /homes/dcallow/dti_freesurf/trac/base_${subj}/scripts/trac-all.log$ changing the input for ${subj} for each subject I run I get the following error. FileName /homes/dcallow/diffusion_recons//AES137.Ex/image000001.dcm Identification syngo MR B17 N umarisVeScannerModel TrioTimPatientName Date and time 20180119 S tudyDateStudyTime 103151.312000 SeriesTime 113039.437000 AcqTime 113030.842500 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_diff_mddw_D64 PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 106 InversionTime -1 RepetitionTime 6300 PhEncFOV 210 ReadoutFOV 210 Image information RunNo 169 SeriesNo 170 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 65 NFrames 65 SliceArraylSize 35 IsMosaic 1 ImgPos 106.0489 107.8193 -44.0513 VolRes 1.6406 1.6406 3.6000 VolDim 128 128 Vc -1.0000 -0.0000 0.0000 Vr -0.0000 -1.0000 0.0000 Vs -0.0000 -0.0000 1.0000 VolCenter 1.0489 2.8193 18.9487 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 0 Vs = -0 -0 1 INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mv -f /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dwi_orig.voxel_space.bvecs /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES$ mri_probedicom --i /homes/dcallow/diffusion_recons//AES136.Ex/image000001.dcm > /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dcminfo.d$ mv -f /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/bvecs.tmp /homes/dcallow/dti_freesurf/trac/Ex.AES136.long.base_AES136/dmri/dwi_orig$ R=6300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) Reslicing using nearest writing to /homes/dcallow/dti_freesurf/trac/Rest.AES127.long.base_AES127/dmri/dwi_orig_las.nii.gz... INFO: found /homes/dcallow/dti_freesurf/trac/Rest.AES127.long.base_AES127/dmri/dwi_orig.bvals, copying INFO: found /homes/dcallow/dti_freesurf/trac/Rest.AES127.long.base_AES127/dmri/dwi_orig.bvecs, converting to LAS mv -f /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/dmri/dwi_orig_las.bvecs /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/$mv -f /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/dmri/dwi_orig_las.bvals /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/$eddy_correct /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base_AES120/dmri/dwi_orig_las.nii.gz /homes/dcallow/dti_freesurf/trac/Rest.AES120.long.base$9/sys:/cell_root/software/fsl/new/sys/bin/remove_ext: No such file or directory /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: [: -eq: unary operator expected Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> fslroi <input> <output> <tmin> <tsize> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Cannot open volume _tmp for reading! /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 95: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$ Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value /bin/rm: cannot remove `_tmp????.*': No such file or directory /bin/rm: cannot remove `_ref*': No such file or directory /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 83: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/ ys:/cell_root/software/fsl/new/sys/bin/remove_ext: No such file or directory /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 84: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$/cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 87: [: -eq: unary operator expected Usage: fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> fslroi <input> <output> <tmin> <tsize> fslroi <input> <output> <xmin> <xsize> <ymin> <ysize> <zmin> <zsize> <tmin> <tsize> Note: indexing (in both time and space) starts with 0 not 1! Inputting -1 for a size will set it to the full image extent for that dimension. Cannot open volume _tmp for reading! /cell_root/software/fsl/5.0.11/sys/bin/eddy_correct: line 95: /cell_root/software/fsl/5.0.11/sys:/cell_root/software/fsl/5.0.9/sys:/cell_root/software/fsl$ Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value /bin/rm: cannot remove `_tmp????.*': No such file or directory /bin/rm: cannot remove `_ref*': No such file or directory Linux compute-4-28.bswift.umd.edu 2.6.32-696.30.1.el6.x86_64 #1 SMP Fri May 18 11:50:44 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Fri Apr 19 15:45:56 EDT 2019 Any idea why the script might be throwing this error? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Lazy binding problem
by Wang, Lingyan 19 Apr '19

19 Apr '19

External Email - Use Caution Hi, I had this lazy binding problem described in the FS6 releasenotes and couldn't solve it. This is the error message I got when using @SUMA_Make_Spec_Fs: dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib And I've disabled SIP. When I tried use sudo -E fs_update, here is the message I got: Build is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Running this will update some of your freesurfer binaries. Shall I proceed? [y/n/Abort]: y rsync -zbrlv --progress --suffix=.1555625828_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-D… /Applications/freesurfer receiving file list ... rsync: change_dir "/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c" (in pub) failed: No such file or directory (2) 0 files to consider sent 4 bytes received 9 bytes 26.00 bytes/sec total size is 0 speedup is 0.00 rsync error: some files could not be transferred (code 23) at /BuildRoot/Library/Caches/com.apple.xbs/Sources/rsync/rsync-51/rsync/main.c(1404) [receiver=2.6.9] The MacOS system is macOS Sierra 10.12.5 and freesurfer is freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I was wondering if you have any suggestions to fix this problem. Many thanks! Wang, Lingyan Yau Lab Department of Neuroscience Baylor College of Medicine

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xhemi Longitudinal Comparison
by Wang, Xiaoyu 19 Apr '19

19 Apr '19

External Email - Use Caution Dear FreeSurfer Experts, We are trying to compare the early onset hemisphere vs Late onset hemisphere of PD patients. I am trying to use Xhemi in order to reorganize all early onset hemisphere to the left hemisphere and the late onset to the right hemisphere. I am following the Xhemi wiki tutorial as well as the freesurfer archives messages between Doug and Paula with Subject: [Filipping issue] from 2014. I saw that Doug had told Paula to run mris_preproc twice, first do the left normally >>> mris_preproc --hemi lh --meas thickness --surfreg >>> fsaverage_sym.sphere.reg --s subject1 --s subject2 --o >> subjects.lh.sm00.mgh and then run the right hemisphere subjects with --s subject/xhemi in the command line. >>> mris_preproc --hemi lh --meas thickness --surfreg >>> fsaverage_sym.sphere.reg --s subject3/xhemi --s subject4/xhemi --o >>> subjects.rh.sm00.mgh Then use mri_concat to fuse the two outputs together. 1) My question for this is how do you then compare to the right hemisphere? From the wiki, you need the --xhemi and --paired-diff in the command line to do a cross hemisphere comparison. the above is great to compare to healthy control, but how do I adapt that to do a cross hemisphere comparison. 2) The question I have is how to do a longitudinal comparison between Left and right hemispheres with the xhemi data. Would it be possible to use xhemi together with Mass-Univariate LME? If not, do I need to use Xhemi to generate thickness and volume data? Can't I just use the regular stat data from the regular reconstruction? Sincerely, Xiaoyu Wang

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issue running trac-all longitudinal
by Daniel Callow 19 Apr '19

19 Apr '19

External Email - Use Caution Hello, trac-all -prep -c /Volumes/DANIEL/dmrirc.long.example.single.sh with the attached configuration file. I get the following error message INFO: no Siemens slice order reversal detected (good!). TR=6300.00, TE=106.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, -1, 0) k_ras = (-0, -0, 1) writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz... Saving bvals and bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.voxel_space.bvecs /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/image000001.dcm > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dcminfo.dat mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvecs.tmp /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvecs mv -f /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/bvals.tmp /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.bvals orientLAS /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_orig_las.nii.gz dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer//bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: input file must be in NIfTI format Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Apr 18 15:16:47 EDT 2019 and after that I get ------------------------------ SUBJECT base_AES101 DATE Thu Apr 18 15:11:44 EDT 2019 USER amos HOST 255a-280.umd.edu PROCESSOR x86_64 OS Darwin Darwin 255a-280.umd.edu 18.2.0 Darwin Kernel Version 18.2.0: Thu Dec 20 20:46:53 PST 2018; root:xnu-4903.241.1~1/RELEASE_X86_64 x86_64 $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ /Applications/freesurfer//bin/trac-preproc PWD /Volumes/DANIEL/dti_freesurf CMD cp /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/mni2anatorig.mat /Volumes/DANIEL/dti_freesurf/trac/Ex.AES101.long.base_AES101/dmri/xfms/anatorig2mni.mat /Volumes/DANIEL/dti_freesurf/trac/base_AES101/dmri/xfms Any idea what might be causing the issue? Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Extract the ROI mapping
by 2016102110043＠whu.edu.cn 18 Apr '19

18 Apr '19

External Email - Use Caution Hello Freesurfer developers, After I recon-all my subjects, the label files are generated. Could you please kindly help me how can I extract the special brain region from these label files by matlab: But I don't know if it is the mean thickness for brain region BA1. Where can I get the detail information for these label files, such as 'lh.BA1.label'. Best Regards and thanks, Henry 2016102110043(a)whu.edu.cn

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MRI RA position available at Ohio State Buckeye Brain Aging Lab
by Hayes, Scott M. 18 Apr '19

18 Apr '19

External Email - Use Caution Research Assistant Position The Buckeye Brain Aging Lab (B-BAL) Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position in the Buckeye Brain Aging Lab (B-BAL; https://u.osu.edu/bbal/) directed by Dr. Scott Hayes. The B-BAL studies the relationships among aging, physical activity, cognition and the brain [using Magnetic Resonance Imaging (MRI) metrics]. We also examine neural correlates of memory in healthy and clinical populations. The Research Assistant 1 assists in the general coordination and conduct of research in the B-BAL, including administration of neuropsychological tests and/or questionnaires to young and older adults; recruits, screens, and schedules human subjects, including coordination of subject appointments (cognitive, MRI, and physical fitness assessments), subject payments, and submission of IRB amendments; assists with participant recruitment efforts between the laboratory and community partners; assists with research lab purchases and maintains lab supplies; assists with cognitive, MRI, and physical fitness data collection, including obtaining informed consent, cognitive testing (computer and paper and pencil based testing), MRI data acquisition, and record keeping; assists with cognitive and MRI data processing and analyses, supervises undergraduate research assistants. Desired qualifications include: Bachelor's degree in psychology, neuroscience, computer science, engineering, or physics; programming experience in unix, python, matlab, as well as experience in neuroimaging data analyses; knowledge of software packages, such as FreeSurfer, FSL, AFNI, SPM, CONN, R. The position is available for one year with the possibility of extension for additional years based on satisfactory performance and availability of funds. If you are interested in being considered for the position, please apply online at https://www.jobsatosu.com,under job listing #448534 (application portal opens this weekend) and submit a cover letter, writing sample (research paper from course, poster presented at a conference), current CV and arrange to have two reference letters emailed to bbal(a)osu.edu<mailto:bbal@osu.edu> . If you have questions about the position or the lab, please email bbal(a)osu.edu<mailto:bbal@osu.edu> . To build a diverse workforce, The Ohio State University encourages applications from all individuals. Ohio State is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to age, race, color, religion, sex, sexual orientation, gender identity, national origin, disability status, or protected veteran status. Best, Scott __________________ Scott M. Hayes, Ph.D. Assistant Professor Department of Psychology Chronic Brain Injury, Discovery Themes The Ohio State University <http://u.osu.edu/>http://u.osu.edu/bbal/

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fixing errors with pial boundary
by Morgan Botdorf 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Experts, I asked about this a few months ago, but didn't receive a reply so thought I would ask again! We have come across several subjects where the pial boundary line does not extend far enough outward and misses some gray matter. We know that control points can be used to fix a similar issue with white matter boundaries. Are there any tools that can be used to fix this type of gray matter error? Thank you, Morgan Botdorf -- Morgan Botdorf, M.S. Graduate Student Neurocognitive Development Lab University of Maryland, College Park mbotdorf(a)terpmail.umd.edu Office: 301.405.5922

2 1

convert aseg to functional space
by Sam W. 18 Apr '19

18 Apr '19

External Email - Use Caution Hi, I just finished reconall and now I'd like to convert the aseg.mgz to native functional space. My first thought was to simply convert the aseg.mgz to native functional space with mri_vol2vol: mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o aseg-in-rawavg.nii --regheader Is this a valid procedure to convert the aseg to functional space? I think the recommended way is to register the example_func to anatomical first: bbregister --mov example_func.nii.gz --s sub001 --reg reg.dat and then use mri_vol2vol with the --inv flag mri_vol2vol --mov sub001/mri/aseg.mgz --targ example_func.nii.gz --o aseg-in-rawavg.nii --regheader --inv But I'm not sure... Could someone confirm which of the above (or maybe none of them) is correct? Best regards, Sam

2 4

mri_glmfit-sim error correcting for MC for LGI analysis
by C.P.E. Rollins 18 Apr '19

18 Apr '19

External Email - Use Caution Dear Freesurfer Developers, I have a 2-part question: 1) I was advised to use permutation to control for multiple comparisons in an LGI analysis, would you mind elaborating how to do this in command line (in terms of command and parameters)? 2) In running "mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 1.3 pos --cwp 0.05 --2spaces --debug", I receive the following error (attached). I was wondering if you might have any advice? The file /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white exists and I can view it in freeview. Many thanks, Colleen

3 4

Issue with longitudinal surfaces
by maxime GUILLAUME 18 Apr '19

18 Apr '19

External Email - Use Caution Dear freesurfer experts, I re-send this question because i didn't received (or missed) the answer from the first time i sent it. I am performing a longitudinal study (2 time points, 1 year apart) in patients with Multiple Sclerosis using freesurfer 6.0. After following the tutorial for the CROSS, the BASE (where I only performed few manual edits of the surfaces) and the LONG steps, I am facing a problem with the results of the longitudinal pipeline: If I overlay the final surfaces of the different time points (the white and pial surfaces of the LONG step) on the BASE template using the command given in the fs tutorial, there are important differences between the two time points (see figure attached). This happened only on a subset of my subjects. One of our collaborators in this study suggested that this might be because the patient was positioned differently in the two time points, in particular with respect to the z axis (and indeed the major differences between the two surfaces are in the topmost area of the brain). Does anybody have experienced the same problem? And how can I correct for it? Thank you in advance for your help. (*in the captures surfaces of the first visit are in red and blue and in lighter tones for the second visit)

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