Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

Problems with recon-all -s soft and hard fallures
by Camerino, .I.L. (Ileana) 22 Apr '19

22 Apr '19

External Email - Use Caution Dear Freesurfer experts, I am running recon all from the terminal of a linux machine: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I tried recon all on an image dataset of small vessel disease patients. I tried the command on several subjects and I got the same outcome: a soft fallure. Please, find the recon all log in the attachment. Even though in the "recon all.log": it says: recon-all -s sub025 finished without errors, after checking the pial and white matter segmentations, very clear misplacement failures and part of dura mater are present (see attachment: segmenation misplacement and dura). I am also wandering how to avoid that white matter lesions are taken into the aseg segmentation? I checked the documentation and this kind of errors is not mentioned anywhere. Can be the case, that this error is due to the fact that these are clinical images? Can this problem be fixed? For sake of curiosity, I tried the recon all command on another dataset (stroke) and with these data I got an hard failure. recon all exited with errors: ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0573, pval=0.0034 < threshold=0.0050). (see second recon all o35403143 with errors) Please, can anyone give me some ideas how to fix both errors? Thank you in advance Ileana

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Re: [Freesurfer] Lazy binding problem {Disarmed}
by fsbuild 21 Apr '19

21 Apr '19

External Email - Use Caution Hello Lingyan, You can download an updated Mac freesurfer distribution from the following link,https://drive.google.com/file/d/1v2WwPg68id42NqfMeBTI3zijjto69_C1/view… After the download, you can uncompress the freesurfer_Mac.zip archive and put the freesurfer tree anywhere as long as you change the FREESURFER_HOME environment variable to point to it.  Then you would run the freesurfer script to setup the environment using that location.  For example, you can put the ../freesurfer tree under your home directory which you always have privileges to read/write to. $ cd $HOME$ pwd/Users/lwang  <— I am making up this path for this example ... then uncompress the zip archive in to your home directory, here assuming the archive was downloaded into your Downloads folder, $ unzip -d $HOME  $HOME/Downloads/freesurfer_Mac.zip … then in Bourne shell or bash shell you could do….  $ export FREESURFER_HOME=$HOME/Mac/freesurfer … and then to setup the environment… $ source $FREESURFER_HOME/SetUpFreeSurfer.sh Then you should no longer see the lazy evaluation error or be concerned with doing an install that needs admin privileges or whether or not SIP is on/off..(Setup instructions for the environment are also here, https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) - R. On Apr 19, 2019, at 15:17, Wang, Lingyan <Lingyan.Wang(a)bcm.edu> wrote:        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.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibdyld: 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.dylibdyld: Symbol not found: ___emutls_get_address  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib  Expected in: /usr/lib/libSystem.B.dylibAnd 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]: yrsync -zbrlv --progress --suffix=.1555625828_bak rsync://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c/* /Applications/freesurferreceiving 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 considersent 4 bytes  received 9 bytes  26.00 bytes/sectotal size is 0  speedup is 0.00rsync 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-v6.0.0-2beb96cI was wondering if you have any suggestions to fix this problem. Many thanks!Wang, Lingyan Yau LabDepartment of NeuroscienceBaylor College of Medicine_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Extracting mean of values within a lable
by Sims, Sara A (Campus) 21 Apr '19

21 Apr '19

External Email - Use Caution Hello! I have a surface overlay that I want to extract the mean of the values within a label and export to a text file. How can I do that? I was looking into mris_anatomical_stats, but does mris_anatomical_stats let you tell it what file to pull the data from instead of just doing the standard extractions? Alternatively, I would be fine with just extracting all the values within the label and then finding the mean on my own. How could I extract all the values within the label and exporting to a text file? Thanks, Sara Sims

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epidewarp.fsl error in trac-all script
by Daniel Callow 20 Apr '19

20 Apr '19

External Email - Use Caution Hello freesurfer developers, When running trac-all the script seems to be getting tripped up on the epidewarp.fsl portion of the script and throwing a weird error about the fsl version? I am running trac-all -prep with bo homogeneity correction included in the configuration file. I get the following error. writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... orientLAS /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 10 mri_convert -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz mri_convert.bin -oni 96 -onj 96 -onk 53 -oid -0.998405 -0.0247418 0.0507528 -ojd 4.61648e-10 0.898878 0.438199 -okd 0.0564624 -0.4375 0.897444 -oc 2.21634 10.523 31.9495 -rt nearest /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz normalizing out_i_direction: (-0.998405, -0.0247418, 0.0507528) -> (-0.998405, -0.0247418, 0.0507528) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... TR=560.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998405, -0.0247418, 0.0507528) j_ras = (-4.61648e-10, -0.898878, -0.438199) k_ras = (0.0564624, -0.4375, 0.897444) Reslicing using nearest writing to /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz... mri_probedicom --i /Volumes/DANIEL/dti_freesurf/diffusion_recons//AES101.Rest/phase/TE7.38_image000001.dcm > /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0info.dat fslroi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz 0 1 epidewarp.fsl --mag /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0mag.nii.gz --dph /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/b0pha.nii.gz --exf /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/lowb.nii.gz --epi /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi_eddy.nii.gz --tediff 2.46000000000000000000 --esp 0.7 --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz --epidw /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/dwi.nii.gz FSLVersion 6.0.1 FSLVerMaj 6 FSL Version is 6.0.1, must be 3.X or 4.X or 5.X 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 Sat Apr 20 14:56:02 EDT 2019 Does this mean there is an issue with the trac-all script that makes it incompatable with fsl? I notice the --vsm /Volumes/DANIEL/dti_freesurf/trac/Rest.AES101.long.base_AES101/dmri/vsm.nii.gz portion of the epidewarp.fsl script was not created. Everything else that should go into it was created. Can anyone give me some guidance on why this might be happening? 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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fsgd creation
by Amrita Bedi 20 Apr '19

20 Apr '19

External Email - Use Caution Hi Freesurfer developers, My question is related to creation of an fsgd file for glm analysis. I have approximately 500 subjects and 10 variables. I was wondering whats the most time efficient way of creating an fsgd file given my data currently resides in an excel file. Best Amrita

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Senior Research Scientist position at Penn
by Satterthwaite, Theodore 20 Apr '19

20 Apr '19

External Email - Use Caution Hi All, We have an open Senior Research Scientist position; see info below. Feel free to email me directly. Thanks!! Ted Full post: https://jobs.hr.upenn.edu/postings/45503 Ted Satterthwaite and the Lifespan Brain Institute at Penn are seeking to recruit a Senior Research Scientist to lead the analytic efforts of a multi-institution initiative in developmental data science. This initiative will create a large-scale public resource for developmental human neuroscience. In collaboration with collaborators at Child Mind Institute (Mike Milham) we will aggregate, process, harmonize, and publicly share >10,000 structural and functional images for youth ages 5-22. Using this massive data resource, we will seek to develop normative patterns of brain network development, and identify how abnormal network development is associated with specific patterns of psychopathology. This position will involve working as part of a highly-interdisciplinary research team that includes experts in diverse fields such as network science (Danielle S. Bassett), multivariate pattern analysis (Christos Davatzikos), and imaging statistics (Taki Shinohara). To work effectively in this highly collaborative environment, the applicant must have superior communication, language, and writing skills. The applicant must have completed their Ph.D. in neuroscience, engineering, psychology, or statistics with an established record of high productivity; post-doctoral training is desirable. Expertise in using neuroimaging software (e.g., FSL, FreeSurfer, ANTs, AFNI), statistical packages (e.g., R), and scripting languages (e.g., nipype , python, bash) are required. Flexible salary, based upon experience. Theodore D. Satterthwaite, M.D. Assistant Professor of Psychiatry University of Pennsylvania Perelman School of Medicine **NOTE NEW EMAIL: sattertt(a)pennmedicine.upenn.edu<mailto:sattertt@pennmedicine.upenn.edu> ** www.satterthwaitelab.com<http://www.satterthwaitelab.com>

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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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