Freesurfer December 2020

freesurfer@nmr.mgh.harvard.edu

97 participants
131 discussions

Converting a binary volume roi.nii file to a label for roi analysis in Freesurfer
by Paul Dhami 23 Dec '20

23 Dec '20

External Email - Use Caution Dear Freesurfer community, I have a volumetric roi.nii file created with spm, based on MNI coordinates from the literature. My goal is to do a roi analysis in Freesurfer, as I am interested in correlating the thickness values of this roi with a behavioral measurer. However, I am lost as to how I can appropriately convert this volumetric roi.nii file to a label. I hate to ask for too much, but can anyone briefly share the commands or steps as to how to convert this roi.nii file to a label so I can conduct an roi analysis within Freesurfer? Thank you very much, Paul

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error in running tkregisterfv
by Peter de Best 23 Dec '20

23 Dec '20

External Email - Use Caution What am I trying to do: I am trying to register my functional resting state scan to the MPRAGE scan (which is saved in the freesurfer subjects directory under ‘subject _30_8_2020’ after running recon-al on a MPRAGE that was aligned to AC PC). The mgz file brain.mgz and the functional scan aligned. What are the commands I use bbregister --s subject_30_8_2020 --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGE.dat --init-header –bold tkregisterfv --mov subject_motion_corrected_func_4D_RestingState.nii --reg affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat –surfs (bbregister works, tkregisterfv does not; I only provide the bbregistercode for context) What is the error? When I try to run tkregisterfv, I get the following output: “cd /Users/me/Documents/30_8_2020/subject_REST_CF freeview -transform-volume -viewport cor -v /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/mri/orig.mgz:visible=0:name=orig.mgz(targ) /Users/me/Documents/30_8_2020/subject_REST_CF/subject_motion_corrected_func_4D_RestingState.nii:name=subject_motion_corrected_func_4D_RestingState.nii(mov):reg=/Users/me/Documents/30_8_2020/subject_REST_CF/affine_TESTTESTTEST6July2337_1_matrix_AVERAGEbbb.dat --surface /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/lh.white:edgecolor=yellow --surface /Applications/freesurfer/7.1.1/subjects/subject_30_8_2020/surf/rh.white:edgecolor=yellow /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: conditional binary operator expected /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: syntax error near `FS_ALLOW_VGLRUN' /Applications/freesurfer/7.1.1/bin/fsvglrun: line 20: `if [[ ! -v FS_ALLOW_VGLRUN ]]; then'” My platform: macOS Mojave, version 10.14.6 There is no recon-al log. What I tried to do/ checked: 1) FSL is installed. 2) the fsvglrun text describes fsvgl as a necessary file, and I found that VirtualGL is supposed to contained that, and I tried to install that. It also says that FS_ALLOW_VGLRUN should be set to 1, but I have no idea how to do that. 3) make sure to reboot after every potential solution. None of that worked/ resolved the issue.

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error message when running mri_info
by Jonathan Lynn 23 Dec '20

23 Dec '20

External Email - Use Caution Hello, I've been using a software to process SWI data that includes an option to save the output as nifti files. When I attempt to use either the mri_info or mri_convert commands on these nifti files I receive the following error message: niiRead(): unknown space units 7 in /pfc/common_area/high_pass_1750_1910.nii Where "high_pass_1750_1910.nii" is the name of my nifti file. This leads me to believe there is a problem in how my SWI processing software saves nifti files which makes them incompatible with FreeSurfer. I am curious if it is a problem with some aspect of the nifti header information that is causing me to receive this error and if so, which aspect? Using the fsl program fslhd I have gotten the header info for one of these nifti files and pasted it below: filename high_pass_1750_1910.nii sizeof_hdr 348 data_type INT16 dim0 4 dim1 232 dim2 256 dim3 176 dim4 1 dim5 0 dim6 0 dim7 0 vox_units Unknown time_units rad/s datatype 4 nbyper 2 bitpix 16 pixdim0 0.000000 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 0.000000 pixdim5 -nan pixdim6 6445431373862396660923732403945472.000000 pixdim7 6445014188069157487771091399081984.000000 vox_offset 352 cal_max 3253932511416847943508928692748288.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 6444907725225778945067450074398720.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code -99 slice_start 30622 slice_end -1814 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 73 ´õtent_name ëh`0 intent_p1 0.000000 intent_p2 6444907725225778945067450074398720.000000 intent_p3 68507965883187986432.000000 qform_name Unknown qform_code 0 qto_xyz:1 1.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 1.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 1.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Unknown sform_code 0 sto_xyz:1 0.000000 0.000000 0.000000 0.000000 sto_xyz:2 0.000000 0.000000 0.000000 0.000000 sto_xyz:3 0.000000 0.000000 0.000000 0.000000 sto_xyz:4 0.000000 0.000000 0.000000 0.000000 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descrip aux_file ¤ô I am hoping someone can help me understand why I am receiving this error from mri_info. Thank you, John

2 1

Extracted mean timecourse from FS label
by Mason Wells 23 Dec '20

23 Dec '20

External Email - Use Caution Hi Experts, I have pre-processed some resting-state date using fMRI prep. I have the functional data on the fs_native surface in bold.func.gii format for each hemisphere. I have created some FS labels and I would like to extract the mean time course from vertices within these labels. Is it possible to use FreeSurfer tools to do this? I have a feeling mri_segstats might be the correct option, but I don't believe this can be used with GIFTI functional data. I tried the command below * mri_segstats --slabel sub-0006 lh /home/masontwells/Documents/freesurfer/subjects/sub-0006/label/lh.wang2015atlas.V1v.label --avgwf out.dat --id 1 --i ../../post-fmriprep/sub-0006_ses-1_task-rest_acq-TR2000_space-fsnative_hemi-L_bold.func.gii However, the terminal produces serval of these messages when the command runs: * ** DA[599] has coordsys with intent NIFTI_INTENT_TIME_SERIES (should be NIFTI_INTENT_POINTSET) I assume this is a sign that the command and data format are not compatible? If this is the case, can you advise on the best way to extract the mean time courses from my functional data? Will I have to resample the volume data to the surface with mri_vol2surf to get it into MGH format and then run mri_segstats? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://secure-web.cisco.com/1qzj6G102Hp0-GTfeJ6322xQNXQcW4GkqaH5liYvjrdTN9…><http://secure-web.cisco.com/1wKqfPd1L9yGr-NK1MFwwQm3aX2SenX1VtTlRgPt0wLl12m…> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

2 4

Multiple Frames
by Hsieh, Stephanie 23 Dec '20

23 Dec '20

Hi FreeSurfer Developers, I am trying to process a few MPRAGE sequences (different sessions), so I can edit the scans. And I am having trouble reconning the .mgz files. I have looked into why my job terminated early and I have attached the message below. The error states that 'input(s) cannot have multiple frames'. And I then looked into the mri_info, which I have also attached below, and based off of some similar questions I found in the archive, my dimensions seem to be incorrect for freesurfer to process. My dimensions are 240 x 256 x 176 x 2, and I believe they should be 240 x 256 x 176 in order for it to work. How do I go about fixing my dimensions? Does it have to do with how I unpacked the DICOMS? I have not run into this issue before so I would love to learn what caused this error. Thanks in advance, Stephanie Early termination error: 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/brutha/FS6 Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0 Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/autofs/cluster/freesurfer/centos6_x86_64/stable6_0_0/bin/recon-all' -> '/autofs/cluster/brutha/FS6/SCD_021_BL/scripts/recon-all.local-copy' /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-1.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz... /autofs/cluster/brutha/FS6/SCD_021_BL mri_convert /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz mri_convert.bin /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/brutha/FS6/SCD_021_BL-2.mgz... TR=2300.00, TE=2.95, TI=900.00, flip angle=9.00 i_ras = (0.108201, -0.990984, 0.079018) j_ras = (0.0145467, -0.0778978, -0.996855) k_ras = (-0.994023, -0.10901, -0.00598659) writing to /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Dec 10 21:00:24 EST 2020 Found 2 runs /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /autofs/cluster/brutha/FS6/SCD_021_BL/mri/orig/001.mgz has 2 frames Linux compute-0-85.nmr.mgh.harvard.edu<http://compute-0-85.nmr.mgh.harvard.edu/>3.10.0-1160.6.1.el7.x86_64 #1 SMP Tue Nov 17 13:59:11 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s SCD_021_BL exited with ERRORS at Thu Dec 10 21:00:25 EST 2020 mri_info on the session I am trying to run: Volume information for SCD_021_BL-1.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000 Volume information for SCD_021_BL-2.mgz type: MGH dimensions: 240 x 256 x 176 x 2 voxel sizes: 1.054688, 1.054688, 1.200000 type: SHORT (4) fov: 270.000 dof: 0 xstart: -126.6, xend: 126.6 ystart: -135.0, yend: 135.0 zstart: -105.6, zend: 105.6 TR: 2300.00 msec, TE: 2.95 msec, TI: 900.00 msec, flip angle: 9.00 degrees nframes: 2 PhEncDir: ROW FieldStrength: 3.000000 ras xform present xform info: x_r = 0.1082, y_r = 0.0145, z_r = -0.9940, c_r = 9.2070 : x_a = -0.9910, y_a = -0.0779, z_a = -0.1090, c_a = 36.6058 : x_s = 0.0790, y_s = -0.9969, z_s = -0.0060, c_s = -29.9521 talairach xfm : Orientation : PIL Primary Slice Direction: sagittal voxel to ras transform: 0.1141 0.0153 -1.1928 98.5179 -1.0452 -0.0822 -0.1308 184.0548<tel:184.0548> 0.0833 -1.0514 -0.0072 95.2548 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1.33484 ras to voxel transform: 0.1026 -0.9396 0.0749 155.6942<tel:155.6942> 0.0138 -0.0739 -0.9452 102.2669<tel:102.2669> -0.8284 -0.0908 -0.0050 98.8026 -0.0000 -0.0000 -0.0000 1.0000

2 1

FREESURFER AND NEURONAVIGATOR IMAGE
by marco.muti＠tin.it 23 Dec '20

23 Dec '20

External Email - Use Caution I need to use freesurfer brain_anat.nii T1 and path.pd.nii (CST WM tract ) in the navigator for neurosurgery. It is necessary to merge the two volume images and to transform it in dicom.Exist a command for that or a procedure in Fressurfer? Or same other software?Thanks!!!!!

2 1

fspalm error : --sig2p-max unknown
by Marina Fernández 23 Dec '20

23 Dec '20

External Email - Use Caution Dear experts, When I was running permutations with fspalm an error appeared because it couldn't find the --sig2p-max option when using mri_surfcluster internally. You can find below the terminal output. How can I fix this error? Thank you in advance Marina. *Terminal output: ... >> >> palm processing complete - running the surface cluster analysis... /usr/local/freesurfer/subjects/merchi182_thickness_stats/stats/thickness/permutation/lctx/across/across_age_cov_none_0.05/pos/lh.fsgd_subj_gauss003/palm mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030 --subject merchi182_thickness_average --hemi lh --annot aparc --sum contrast.clustertable.summary --no-fixmni --surf white --ocn contrast.ocn.mgz --oannot ./contrast.ocn.annot --sig2p-max ERROR: Option --sig2p-max unknown error: mri_surfcluster failed fspalm --glmdir /usr/local/freesurfer/subjects/merchi182_thickness_stats//stats/thickness/permutation/lctx/across//across_age_cov_none_0.05/pos//lh.fsgd_subj_gauss003 --cft 1.301 --name palm --iters 100 --cwp .05 --onetail: Signal 127 ans = 255

2 1

Error During Fix Topology and Brain Usability
by Angel Hammond 23 Dec '20

23 Dec '20

External Email - Use Caution Dear Experts, I have a brain that I have been getting an error for during fix topology during recon-all using Freesurfer 6.0 on macOS Catalina. I have read a couple of threads on this same kind of error on the Freesurfer list and it seems this is due to some error in wm segmentation, cerebellum, or skull. However, being new with Freesurfer I am not sure what to check and how to fix such a large defect (or if it's even worth fixing - is this usable?). Just a few notes on this scan, it has heavy motion and was flagged by our radiologist as having 'excessive white matter changes'. I uploaded the subject to the FTP named '088.tar.gz' to take a look at. Thank you! The recon-all.log error message here: INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ before topology correction, eno=-788 (nv=159056, nf=319688, ne=479532, g=395) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 101024 ambiguous faces found in tessellation segmenting defects... 166 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 8 into 3 -merging segment 14 into 3 -merging segment 48 into 3 -merging segment 7 into 4 -merging segment 6 into 5 -merging segment 1 into 10 -merging segment 20 into 16 -merging segment 19 into 18 -merging segment 10 into 23 -merging segment 32 into 29 -merging segment 37 into 30 -merging segment 75 into 45 -merging segment 62 into 64 -merging segment 109 into 92 -merging segment 127 into 92 -merging segment 128 into 92 -merging segment 141 into 92 -merging segment 159 into 92 -merging segment 157 into 92 -merging segment 125 into 121 -merging segment 123 into 122 -merging segment 139 into 133 144 defects to be corrected 0 vertices coincident reading input surface /study3/midus3/data/freesurfer/subjects/088/surf/rh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.4365 (-4.7182) -vertex loglikelihood: -6.8975 (-3.4488) -normal dot loglikelihood: -3.5115 (-3.5115) -quad curv loglikelihood: -6.1828 (-3.0914) Total Loglikelihood : -26.0283 CORRECTING DEFECT 0 (vertices=115, convex hull=128, v0=113) After retessellation of defect 0 (v0=113), euler #=-112 (102634,295350,192604) : difference with theory (-141) = -29 CORRECTING DEFECT 1 (vertices=43, convex hull=79, v0=2438) After retessellation of defect 1 (v0=2438), euler #=-111 (102656,295448,192681) : difference with theory (-140) = -29 CORRECTING DEFECT 2 (vertices=3335, convex hull=1683, v0=2597) XL defect detected... After retessellation of defect 2 (v0=2597), euler #=-113 (103831,299911,195967) : difference with theory (-139) = -26 CORRECTING DEFECT 3 (vertices=108, convex hull=48, v0=2938) After retessellation of defect 3 (v0=2938), euler #=-111 (103837,299955,196007) : difference with theory (-138) = -27 CORRECTING DEFECT 4 (vertices=1336, convex hull=711, v0=3387) XL defect detected... After retessellation of defect 4 (v0=3387), euler #=-109 (104350,301857,197398) : difference with theory (-137) = -28 CORRECTING DEFECT 5 (vertices=162, convex hull=218, v0=4667) After retessellation of defect 5 (v0=4667), euler #=-108 (104432,302198,197658) : difference with theory (-136) = -28 CORRECTING DEFECT 6 (vertices=18, convex hull=48, v0=5608) After retessellation of defect 6 (v0=5608), euler #=-107 (104444,302251,197700) : difference with theory (-135) = -28 CORRECTING DEFECT 7 (vertices=562, convex hull=419, v0=5682) L defect detected... After retessellation of defect 7 (v0=5682), euler #=-106 (104704,303262,198452) : difference with theory (-134) = -28 CORRECTING DEFECT 8 (vertices=44, convex hull=101, v0=5705) After retessellation of defect 8 (v0=5705), euler #=-105 (104716,303339,198518) : difference with theory (-133) = -28 CORRECTING DEFECT 9 (vertices=37, convex hull=38, v0=8189) After retessellation of defect 9 (v0=8189), euler #=-104 (104719,303364,198541) : difference with theory (-132) = -28 CORRECTING DEFECT 10 (vertices=180, convex hull=169, v0=8978) After retessellation of defect 10 (v0=8978), euler #=-103 (104772,303609,198734) : difference with theory (-131) = -28 CORRECTING DEFECT 11 (vertices=12, convex hull=25, v0=9633) After retessellation of defect 11 (v0=9633), euler #=-102 (104774,303621,198745) : difference with theory (-130) = -28 CORRECTING DEFECT 12 (vertices=243, convex hull=275, v0=9655) After retessellation of defect 12 (v0=9655), euler #=-100 (104899,304141,199142) : difference with theory (-129) = -29 CORRECTING DEFECT 13 (vertices=223, convex hull=157, v0=12134) After retessellation of defect 13 (v0=12134), euler #=-99 (104986,304474,199389) : difference with theory (-128) = -29 CORRECTING DEFECT 14 (vertices=27, convex hull=65, v0=12681) After retessellation of defect 14 (v0=12681), euler #=-98 (104995,304521,199428) : difference with theory (-127) = -29 CORRECTING DEFECT 15 (vertices=914, convex hull=491, v0=12900) L defect detected... After retessellation of defect 15 (v0=12900), euler #=-96 (105241,305518,200181) : difference with theory (-126) = -30 CORRECTING DEFECT 16 (vertices=85, convex hull=105, v0=13658) After retessellation of defect 16 (v0=13658), euler #=-95 (105291,305713,200327) : difference with theory (-125) = -30 CORRECTING DEFECT 17 (vertices=53, convex hull=86, v0=14037) After retessellation of defect 17 (v0=14037), euler #=-94 (105321,305842,200427) : difference with theory (-124) = -30 CORRECTING DEFECT 18 (vertices=255, convex hull=132, v0=14332) After retessellation of defect 18 (v0=14332), euler #=-93 (105393,306128,200642) : difference with theory (-123) = -30 CORRECTING DEFECT 19 (vertices=38, convex hull=80, v0=17657) After retessellation of defect 19 (v0=17657), euler #=-92 (105417,306235,200726) : difference with theory (-122) = -30 CORRECTING DEFECT 20 (vertices=8, convex hull=28, v0=17757) After retessellation of defect 20 (v0=17757), euler #=-91 (105418,306249,200740) : difference with theory (-121) = -30 CORRECTING DEFECT 21 (vertices=538, convex hull=333, v0=18109) After retessellation of defect 21 (v0=18109), euler #=-89 (105554,306832,201189) : difference with theory (-120) = -31 CORRECTING DEFECT 22 (vertices=262, convex hull=253, v0=18458) After retessellation of defect 22 (v0=18458), euler #=-87 (105680,307339,201572) : difference with theory (-119) = -32 CORRECTING DEFECT 23 (vertices=7, convex hull=32, v0=20614) After retessellation of defect 23 (v0=20614), euler #=-86 (105681,307353,201586) : difference with theory (-118) = -32 CORRECTING DEFECT 24 (vertices=36, convex hull=55, v0=20986) After retessellation of defect 24 (v0=20986), euler #=-85 (105689,307400,201626) : difference with theory (-117) = -32 CORRECTING DEFECT 25 (vertices=1348, convex hull=596, v0=21154) XL defect detected... After retessellation of defect 25 (v0=21154), euler #=-84 (106133,309038,202821) : difference with theory (-116) = -32 CORRECTING DEFECT 26 (vertices=59, convex hull=109, v0=24677) After retessellation of defect 26 (v0=24677), euler #=-83 (106173,309205,202949) : difference with theory (-115) = -32 CORRECTING DEFECT 27 (vertices=18, convex hull=22, v0=26139) After retessellation of defect 27 (v0=26139), euler #=-82 (106173,309212,202957) : difference with theory (-114) = -32 CORRECTING DEFECT 28 (vertices=22, convex hull=15, v0=28505) After retessellation of defect 28 (v0=28505), euler #=-81 (106175,309222,202966) : difference with theory (-113) = -32 CORRECTING DEFECT 29 (vertices=47, convex hull=33, v0=28568) After retessellation of defect 29 (v0=28568), euler #=-80 (106179,309245,202986) : difference with theory (-112) = -32 CORRECTING DEFECT 30 (vertices=33, convex hull=68, v0=29152) After retessellation of defect 30 (v0=29152), euler #=-79 (106199,309331,203053) : difference with theory (-111) = -32 CORRECTING DEFECT 31 (vertices=23, convex hull=31, v0=29620) After retessellation of defect 31 (v0=29620), euler #=-78 (106200,309346,203068) : difference with theory (-110) = -32 CORRECTING DEFECT 32 (vertices=36, convex hull=69, v0=29653) After retessellation of defect 32 (v0=29653), euler #=-77 (106213,309410,203120) : difference with theory (-109) = -32 CORRECTING DEFECT 33 (vertices=32, convex hull=69, v0=30231) After retessellation of defect 33 (v0=30231), euler #=-76 (106232,309497,203189) : difference with theory (-108) = -32 CORRECTING DEFECT 34 (vertices=26, convex hull=69, v0=31159) After retessellation of defect 34 (v0=31159), euler #=-75 (106240,309544,203229) : difference with theory (-107) = -32 CORRECTING DEFECT 35 (vertices=1193, convex hull=611, v0=33216) XL defect detected... After retessellation of defect 35 (v0=33216), euler #=-73 (106607,310974,204294) : difference with theory (-106) = -33 CORRECTING DEFECT 36 (vertices=25, convex hull=54, v0=33352) After retessellation of defect 36 (v0=33352), euler #=-72 (106621,311037,204344) : difference with theory (-105) = -33 CORRECTING DEFECT 37 (vertices=106, convex hull=128, v0=33930) After retessellation of defect 37 (v0=33930), euler #=-71 (106682,311280,204527) : difference with theory (-104) = -33 CORRECTING DEFECT 38 (vertices=47, convex hull=35, v0=35396) After retessellation of defect 38 (v0=35396), euler #=-70 (106688,311309,204551) : difference with theory (-103) = -33 CORRECTING DEFECT 39 (vertices=88, convex hull=39, v0=35775) After retessellation of defect 39 (v0=35775), euler #=-69 (106697,311351,204585) : difference with theory (-102) = -33 CORRECTING DEFECT 40 (vertices=45, convex hull=21, v0=36715) After retessellation of defect 40 (v0=36715), euler #=-68 (106697,311358,204593) : difference with theory (-101) = -33 CORRECTING DEFECT 41 (vertices=83, convex hull=81, v0=36730) After retessellation of defect 41 (v0=36730), euler #=-68 (106724,311487,204695) : difference with theory (-100) = -32 CORRECTING DEFECT 42 (vertices=35, convex hull=75, v0=37712) After retessellation of defect 42 (v0=37712), euler #=-67 (106741,311570,204762) : difference with theory (-99) = -32 CORRECTING DEFECT 43 (vertices=66, convex hull=96, v0=38608) After retessellation of defect 43 (v0=38608), euler #=-66 (106780,311725,204879) : difference with theory (-98) = -32 CORRECTING DEFECT 44 (vertices=59, convex hull=35, v0=42853) After retessellation of defect 44 (v0=42853), euler #=-65 (106784,311748,204899) : difference with theory (-97) = -32 CORRECTING DEFECT 45 (vertices=31, convex hull=68, v0=43693) After retessellation of defect 45 (v0=43693), euler #=-64 (106800,311817,204953) : difference with theory (-96) = -32 CORRECTING DEFECT 46 (vertices=100, convex hull=159, v0=44412) After retessellation of defect 46 (v0=44412), euler #=-63 (106860,312071,205148) : difference with theory (-95) = -32 CORRECTING DEFECT 47 (vertices=2008, convex hull=765, v0=44793) XL defect detected... After retessellation of defect 47 (v0=44793), euler #=-63 (107570,314609,206976) : difference with theory (-94) = -31 CORRECTING DEFECT 48 (vertices=21, convex hull=63, v0=45597) After retessellation of defect 48 (v0=45597), euler #=-62 (107584,314672,207026) : difference with theory (-93) = -31 CORRECTING DEFECT 49 (vertices=5, convex hull=9, v0=46164) After retessellation of defect 49 (v0=46164), euler #=-61 (107585,314677,207031) : difference with theory (-92) = -31 CORRECTING DEFECT 50 (vertices=141, convex hull=53, v0=46378) After retessellation of defect 50 (v0=46378), euler #=-60 (107603,314756,207093) : difference with theory (-91) = -31 CORRECTING DEFECT 51 (vertices=89, convex hull=130, v0=47463) After retessellation of defect 51 (v0=47463), euler #=-59 (107666,315008,207283) : difference with theory (-90) = -31 CORRECTING DEFECT 52 (vertices=99, convex hull=86, v0=48729) After retessellation of defect 52 (v0=48729), euler #=-57 (107690,315116,207369) : difference with theory (-89) = -32 CORRECTING DEFECT 53 (vertices=23, convex hull=53, v0=49690) After retessellation of defect 53 (v0=49690), euler #=-56 (107701,315168,207411) : difference with theory (-88) = -32 CORRECTING DEFECT 54 (vertices=28, convex hull=61, v0=51301) After retessellation of defect 54 (v0=51301), euler #=-55 (107719,315249,207475) : difference with theory (-87) = -32 CORRECTING DEFECT 55 (vertices=10, convex hull=21, v0=53334) After retessellation of defect 55 (v0=53334), euler #=-54 (107721,315261,207486) : difference with theory (-86) = -32 CORRECTING DEFECT 56 (vertices=53, convex hull=85, v0=54650) After retessellation of defect 56 (v0=54650), euler #=-53 (107740,315353,207560) : difference with theory (-85) = -32 CORRECTING DEFECT 57 (vertices=65, convex hull=27, v0=58847) After retessellation of defect 57 (v0=58847), euler #=-52 (107744,315372,207576) : difference with theory (-84) = -32 CORRECTING DEFECT 58 (vertices=20, convex hull=32, v0=59115) After retessellation of defect 58 (v0=59115), euler #=-51 (107747,315391,207593) : difference with theory (-83) = -32 CORRECTING DEFECT 59 (vertices=41, convex hull=73, v0=60478) After retessellation of defect 59 (v0=60478), euler #=-50 (107763,315466,207653) : difference with theory (-82) = -32 CORRECTING DEFECT 60 (vertices=356, convex hull=211, v0=61182) After retessellation of defect 60 (v0=61182), euler #=-49 (107897,315966,208020) : difference with theory (-81) = -32 CORRECTING DEFECT 61 (vertices=8, convex hull=18, v0=61319) After retessellation of defect 61 (v0=61319), euler #=-48 (107898,315975,208029) : difference with theory (-80) = -32 CORRECTING DEFECT 62 (vertices=44, convex hull=71, v0=61429) After retessellation of defect 62 (v0=61429), euler #=-47 (107921,316072,208104) : difference with theory (-79) = -32 CORRECTING DEFECT 63 (vertices=29, convex hull=56, v0=63923) After retessellation of defect 63 (v0=63923), euler #=-46 (107936,316142,208160) : difference with theory (-78) = -32 CORRECTING DEFECT 64 (vertices=22, convex hull=36, v0=64851) After retessellation of defect 64 (v0=64851), euler #=-45 (107943,316174,208186) : difference with theory (-77) = -32 CORRECTING DEFECT 65 (vertices=156, convex hull=196, v0=65023) After retessellation of defect 65 (v0=65023), euler #=-44 (108028,316519,208447) : difference with theory (-76) = -32 CORRECTING DEFECT 66 (vertices=43, convex hull=50, v0=65760) After retessellation of defect 66 (v0=65760), euler #=-43 (108043,316582,208496) : difference with theory (-75) = -32 CORRECTING DEFECT 67 (vertices=46, convex hull=29, v0=67556) After retessellation of defect 67 (v0=67556), euler #=-42 (108048,316605,208515) : difference with theory (-74) = -32 CORRECTING DEFECT 68 (vertices=68, convex hull=85, v0=67614) After retessellation of defect 68 (v0=67614), euler #=-41 (108076,316725,208608) : difference with theory (-73) = -32 CORRECTING DEFECT 69 (vertices=232, convex hull=165, v0=69771) After retessellation of defect 69 (v0=69771), euler #=-41 (108175,317105,208889) : difference with theory (-72) = -31 CORRECTING DEFECT 70 (vertices=391, convex hull=190, v0=70249) After retessellation of defect 70 (v0=70249), euler #=-40 (108275,317488,209173) : difference with theory (-71) = -31 CORRECTING DEFECT 71 (vertices=24, convex hull=32, v0=70287) After retessellation of defect 71 (v0=70287), euler #=-39 (108279,317507,209189) : difference with theory (-70) = -31 CORRECTING DEFECT 72 (vertices=32, convex hull=53, v0=71355) After retessellation of defect 72 (v0=71355), euler #=-38 (108285,317547,209224) : difference with theory (-69) = -31 CORRECTING DEFECT 73 (vertices=178, convex hull=148, v0=72699) After retessellation of defect 73 (v0=72699), euler #=-37 (108302,317664,209325) : difference with theory (-68) = -31 CORRECTING DEFECT 74 (vertices=7, convex hull=30, v0=72932) After retessellation of defect 74 (v0=72932), euler #=-36 (108304,317678,209338) : difference with theory (-67) = -31 CORRECTING DEFECT 75 (vertices=177, convex hull=117, v0=73659) After retessellation of defect 75 (v0=73659), euler #=-35 (108386,317978,209557) : difference with theory (-66) = -31 CORRECTING DEFECT 76 (vertices=24, convex hull=56, v0=74392) After retessellation of defect 76 (v0=74392), euler #=-34 (108400,318044,209610) : difference with theory (-65) = -31 CORRECTING DEFECT 77 (vertices=26, convex hull=51, v0=74882) After retessellation of defect 77 (v0=74882), euler #=-33 (108409,318088,209646) : difference with theory (-64) = -31 CORRECTING DEFECT 78 (vertices=203, convex hull=159, v0=76388) After retessellation of defect 78 (v0=76388), euler #=-32 (108491,318401,209878) : difference with theory (-63) = -31 CORRECTING DEFECT 79 (vertices=30159, convex hull=7767, v0=78672) Segmentation fault (core dumped) Linux c139.keck.waisman.wisc.edu 3.10.0-1127.19.1.el7.x86_64 #1 SMP Thu Aug 20 14:39:03 CDT 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 088 exited with ERRORS at Sat Nov 7 18:24:33 CST 2020 Angel Hammond Research Specialist Center for Healthy Minds University of Wisconsin-Madison

2 1

How to remove clusters less than 50 vertex/voxels in FreeSurfer during visualisation
by Sunil Khokhar 23 Dec '20

23 Dec '20

External Email - Use Caution Dear Experts! After doing the statistics I want to remove clusters that are less than 50 voxels/vertices from sig.mgh file which contains the visualisation of the results. Looking forward to your advices. Thanks in advance!

2 1

Recon-all error: MatrixMultiply: m1 is null!
by Boa Sorte Silva, Narlon 23 Dec '20

23 Dec '20

External Email - Use Caution Hi there, Hope this finds you well I have noticed the following error for some of my runs: @# Cortical ribbon mask Mon Dec 14 15:43:24 PST 2020 /Applications/freesurfer/7.1.1/subjects/BT_long/BT_055_base/mri \n mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --parallel BT_055_base \n SUBJECTS_DIR is /Applications/freesurfer/7.1.1/subjects/BT_long loading input data... Running hemis in parallel Processing left hemi Processing right hemi computing distance to right white surface computing distance to left white surface error: MatrixMultiply: m1 is null! Darwin PHTH-CDM-NBOASORT 18.5.0 Darwin Kernel Version 18.5.0: Mon Mar 11 20:40:32 PDT 2019; root:xnu-4903.251.3~3/RELEASE_X86_64 x86_64 recon-all -s BT_055_base exited with ERRORS at Mon Dec 14 15:43:27 PST 2020 Here are details of the computer and FS version I am using: * OS: macOS Mojave (10.14.4) * FS: 7.1.1 It seems to happen at random, whenever I run recon-all on the same subject again, the error doesn’t occur. This is true for cross-sectional, base, and long processing steps in my machine. I have seen an email relating to this issue before, but I wasn’t able to access the attachment file which would fix the problem. I was wondering if you guys would be able to help? Thank you Nárlon Cássio Nárlon Cássio Boa Sorte Silva, PhD CIHR/MSFHR Postdoctoral Research Fellow Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health University of British Columbia Twitter: @BoaNarlon

2 1

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Freesurfer December 2020