Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30089 discussions

Masking cortical thickness
by James Hobart 13 Feb '18

13 Feb '18

Hi all, I am looking to mask out a small region of the GM when calculating the cortical thickness of ROIs across the brain. Essentially I have a couple of cases with small GM lesions where the cortical thickness is less likely to be meaningful for my analysis. I have binary lesion masks and also full recon-all s for these cases. I was thinking I would need to mask the cortical thickness map somehow (potentially mapping the mask volume to a surface?) before using the mris_anatomical_stats to calculate cortical thickness. Is this the best way to go about this? Many thanks James

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Re: [Freesurfer] map values to vertices {Disarmed}
by Frederick Barrett 13 Feb '18

13 Feb '18

Thank you, Bruce. I did reconstruct the surfaces from that subject. These are the steps that I've taken: recon-all -s <subid> -i <mprage> -all mris_register <subid>/surf/<hemi>.sphere fsaverag5/<hemi>.?reg.template.tif <subid>/surf/<hemi>.fsaverage5.sphere.reg mri_surf2surf -s <subid> -h <hemi> --sval-xyz <hemi>.pial --trgsubject fsaverage5 --tval <hemi> mri_surf2surf -s <subid --hemi <hemi> --sval-xyz <hemi>.pial --trgsubject fsaverage5 --tval <hemi>.pial.<subid> --tval-xyz <subid>/mri/orig.mgz mris_convert fsaverage5/surf/<hemi>.pial.<subid> fsaverage5/surf/<hemi>.pial.<subid>.asc this final file (fsaverage5/surf/<hemi>.pial.<subid>.asc) was read into MATLAB and MATLAB code generates a continuous value for each vertex (n=10242) for a given subject. I want to map these values back to the surface, but it sounds like if you're recommending mri_vol2surf, that you are saying I should represent these continuous values in a voxel in 3D space, is that correct? Is there an easy way to map the values for each vertex without having to go through a 3D representation? Best, Fred Hi Fred we usually use mri_vol2surf for this kind of thing. Did you reconstruct surfaces from that subject? cheers Bruce On Tue, 13 Feb 2018, Frederick Barrett wrote: Greetings all, I apologize in advance for what may (or may not) be a basic question. I want to map values from a continuous variable (non-integer) to each vertex on a surface so that I can visualize these values on the surface (or an inflated brain), but I can't figure out how to do this. I've projected the pial surface of fsaverage5 to native space within a volunteer, then exported the xyz coordinates of each vertex (10242 * 2, lh & rh) for that volunteer to an .asc file using mris_convert. These xyz coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD scan in native space for the subject were read into MATLAB, and I've used a separate toolbox in Matlab to generate weights from the BOLD data that map to each vertex (a continuous variable, one weight per vertex per subject), and these weights can be written to a text file in the following format for each hemisphere: x1 y1 z1 weight1 x2 y2 z2 weight2 ... x10242 y10242 z10242 weight10242 or vertex1 weight1 vertex2 weight2 ... vertex10242 weight10242 or another format if that would be helpful. How can I map these weights back to a surface and visualize it? Please advise. I began to think this fell into the realm of annotation, but it seems that annotations are categorial rather than continuous. Thank you so much for your time. Best, Fred ---------------------------------------------------------- Frederick Barrett, Ph.D Assistant Professor of Psychiatry and Behavioral Sciences Behavioral Pharmacology Research Unit Johns Hopkins School of Medicine 5510 Nathan Shock Dr / Rm 3048 Baltimore, MD 21224 Voice/mail: (410) 550-9777 Email: fbarr...(a)jhmi.edu | frederick.barr...(a)gmail.com NCBI: https://goo.gl/mUKEZm Google Scholar: MailScanner has detected a possible fraud attempt from "scholar.google.com" claiming to be http://goo.gl/vjrrsl _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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map values to vertices {Disarmed}
by Frederick Barrett 13 Feb '18

13 Feb '18

Greetings all, I apologize in advance for what may (or may not) be a basic question. I want to map values from a continuous variable (non-integer) to each vertex on a surface so that I can visualize these values on the surface (or an inflated brain), but I can't figure out how to do this. I've projected the pial surface of fsaverage5 to native space within a volunteer, then exported the xyz coordinates of each vertex (10242 * 2, lh & rh) for that volunteer to an .asc file using mris_convert. These xyz coordinates (and the vertex #) and a 3D summary volume (NIfTI) for a BOLD scan in native space for the subject were read into MATLAB, and I've used a separate toolbox in Matlab to generate weights from the BOLD data that map to each vertex (a continuous variable, one weight per vertex per subject), and these weights can be written to a text file in the following format for each hemisphere: x1 y1 z1 weight1 x2 y2 z2 weight2 ... x10242 y10242 z10242 weight10242 or vertex1 weight1 vertex2 weight2 ... vertex10242 weight10242 or another format if that would be helpful. How can I map these weights back to a surface and visualize it? Please advise. I began to think this fell into the realm of annotation, but it seems that annotations are categorial rather than continuous. Thank you so much for your time. Best, Fred ---------------------------------------------------------- Frederick Barrett, Ph.D Assistant Professor of Psychiatry and Behavioral Sciences Behavioral Pharmacology Research Unit Johns Hopkins School of Medicine 5510 Nathan Shock Dr / Rm 3048 Baltimore, MD 21224 Voice/mail: (410) 550-9777 Email: fbarret2(a)jhmi.edu<mailto:fbarret2@jhmi.edu> | frederick.barrett(a)gmail.com<mailto:frederick.barrett@gmail.com> NCBI: https://goo.gl/mUKEZm Google Scholar: http://goo.gl/vjrrsl<http://scholar.google.com/citations?user=KCtXPmAAAAAJ>

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Problems running LGI
by Dusan Hirjak 13 Feb '18

13 Feb '18

Dear Freesurfer Experts, I am currently trying to run LGI. I have the 2017b Matlab version, Mac OS Sierra and I already set up the freesurfer PATH in Matlab. However, I am getting the following error after starting recon all -s localGI : Dusans-MacBook-Pro:NSS_Analysis_01 dusan$ recon-all -s SP002 -localGI Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/NSS_Analysis_01 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 dusan wheel 508655 Jul 29 2017 /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/scripts/recon-all.log Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf #-------------------------------------------- #@# Local Gyrification Index lh Sat Feb 10 21:59:13 CET 2018 \n mris_compute_lgi --i lh.pial \n ================= rm -Rf /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... 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: mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/NSS_Analysis_01/SP002/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Darwin Dusans-MBP 16.7.0 Darwin Kernel Version 16.7.0: Thu Jun 15 17:36:27 PDT 2017; root:xnu-3789.70.16~2/RELEASE_X86_64 x86_64 Any help would be greatly appreciated! Many thanks, Dusan

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quantifyHAsubregions.sh , HBT/FS60/CA
by Eva Hilland 13 Feb '18

13 Feb '18

Hi Eugenio, Is it possible to use *quantifyHAsubregions.sh* to write out the three different hippocampal subfield outputs ? - HBT: the hippocampus is subdivided into head, body and tail. - FS60: it mimics the FreeSurfer 6.0 hippocampal module, i.e., no head/body subdivision for the hippocampal subregions. - CA: the "internal" labels (GC-ML-DG and molecular layer) are absorbed by the CA subfields: GC-ML-DG is absorbed by CA4, and the voxels in the molecular layer are assigned the label of the closest voxel that is neither molecular layer nor background Best Eva

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Read 13, expected 64, could not read .nii.gz as type 24
by Ben Smith 11 Feb '18

11 Feb '18

I'm attempting to run preproc-sess and have got an error - it seems while running mri_vol2surf. I've included the full output of preproc-sess below, but I think the key information will be right at the end where the error message is. A couple of comments that may be relevant: - The raw data I've placed in the directory are links to the files that were created using the bash ln -s command - They are in nii.gz format really briefly, the key information seems to be: ------- niiRead(): error reading from /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 ERROR: Read 13, expected 64 ERROR: could not read /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz as type 24 ------ Any ideas? Thanks very much in advance for your help! Ben -------------------------------------------------------------- preproc-sess logfile is log/preproc-sess.20592.log -------------------------------------------------------------- $Id: preproc-sess,v 1.64.2.1 2016/08/02 21:19:09 greve Exp $ bensmith setenv FREESURFER_HOME /opt/fmritools/freesurfer setenv SUBJECTS_DIR /opt/fmritools/freesurfer/subjects Linux msm2 4.12.0-1-amd64 #1 SMP Debian 4.12.6-1 (2017-08-12) x86_64 GNU/Linux /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed /opt/fmritools/freesurfer/fsfast/bin/preproc-sess -sf sessid -fsd bold -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Sun Feb 11 14:19:19 PST 2018 instem f mc 1 f fmcpr stc 0 fmcpr sm 0 mask 1 brain sub106sess Template ----------------------------- mktemplate-sess -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -update Session: /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess ---------------- Sun Feb 11 14:19:20 PST 2018 Detected input format at nii.gz sub106sess Update not needed Run: 001 ---------------- Sun Feb 11 14:19:20 PST 2018 sub106sess 001 Update not needed Run: 002 ---------------- Sun Feb 11 14:19:20 PST 2018 sub106sess 002 Update not needed Sun Feb 11 14:19:20 PST 2018 mktemplate-sess completed sub106sess Registration ----------------------------- register-sess -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg -------------------------------------------------------------- register-sess logfile is /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/log/register-sess.sub106sess.log -------------------------------------------------------------- Sun Feb 11 14:19:20 PST 2018 setenv SUBJECTS_DIR /opt/fmritools/freesurfer/subjects cd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed /opt/fmritools/freesurfer/fsfast/bin/register-sess -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -delete-dat -dof 6 -bold -per-run -update -init-coreg freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux msm2 4.12.0-1-amd64 #1 SMP Debian 4.12.6-1 (2017-08-12) x86_64 GNU/Linux Session: /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess ---------------- Sun Feb 11 14:19:20 PST 2018 /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess Run: 001 ---------------- Sun Feb 11 14:19:20 PST 2018 Update not needed Run: 002 ---------------- Sun Feb 11 14:19:21 PST 2018 Update not needed Sun Feb 11 14:19:21 PST 2018 register-sess completed sub106sess Mask ------------------------ mkbrainmask-sess -maskstem brain -fsd bold -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -per-run -update ------------------------------------------------ /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess Sun Feb 11 14:19:21 PST 2018 sub106sess Update not needed for session-level mask sub106sess Update not needed for run 001 mask sub106sess Update not needed for run 002 mask sub106sess Update not needed for run 001 meanval sub106sess Update not needed for run 002 meanval Sun Feb 11 14:19:21 PST 2018 mkbrainmask-sess done sub106sess MC ----------------------------- mc-sess -fstem f -fmcstem fmcpr -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -per-run -update Logfile is /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/log/mc-sub106sess-bold.log ------------------------------------------- /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess RunList: 001 002 sub106sess 001 Update not needed ------- ************************** ----------- ------- Motion Correcting Run 002 ----------- ------- ************************** ----------- sess = sub106sess Sun Feb 11 14:19:22 PST 2018 mc-afni2 --i 002/f.nii.gz --t 002/template.nii.gz --o 002/fmcpr.nii.gz --mcdat 002/fmcpr.mcdat /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold mri_info --nframes --o /tmp/mriinfo.21157 002/template.nii.gz log file is 002/fmcpr.nii.gz.mclog mcdat file is 002/fmcpr.mcdat tmp dir is 002/tmp.mc-afni2.21157 #@# -------------------------------- /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold mri_convert 002/template.nii.gz 002/tmp.mc-afni2.21157/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float mri_convert.bin 002/template.nii.gz 002/tmp.mc-afni2.21157/tempvol.nii.gz --nskip 0 --ndrop 0 -odt float nskip = 0 ndrop = 0 $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 002/template.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.946649, 0.322266) k_ras = (0, -0.322266, 0.946649) writing to 002/tmp.mc-afni2.21157/tempvol.nii.gz... #@# -------------------------------- /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold mri_convert 002/f.nii.gz 002/tmp.mc-afni2.21157/invol.nii.gz -odt float mri_convert.bin 002/f.nii.gz 002/tmp.mc-afni2.21157/invol.nii.gz -odt float $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 002/f.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0.946649, 0.322266) k_ras = (0, -0.322266, 0.946649) writing to 002/tmp.mc-afni2.21157/invol.nii.gz... #@# -------------------------------- /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold 3dvolreg.afni -verbose -dfile 002/fmcpr.mcdat -1Dmatrix_save 002/fmcpr.mat -base 002/tmp.mc-afni2.21157/tempvol.nii.gz -prefix 002/tmp.mc-afni2.21157/outvol.nii.gz 002/tmp.mc-afni2.21157/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 002/tmp.mc-afni2.21157/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:002/tmp.mc-afni2.21157/tempvol.nii.gz is 18.799990 degrees from plumb. ++ Reading in base dataset 002/tmp.mc-afni2.21157/tempvol.nii.gz ++ Oblique dataset:002/tmp.mc-afni2.21157/invol.nii.gz is 18.799990 degrees from plumb. ++ Reading input dataset 002/tmp.mc-afni2.21157/invol.nii.gz ++ Edging: x=3 y=3 z=2 ++ Creating mask for -maxdisp + Automask has 55699 voxels + 7724 voxels left in -maxdisp mask after erosion ++ Initializing alignment base ++ Starting final pass on 360 sub-bricks: 0..1..2..3..4..5..6..7..8..9..10..11..12..13..14..15..16..17..18..19..20..21..22..23..24..25..26..27..28..29..30..31..32..33..34..35..36..37..38..39..40..41..42..43..44..45..46..47..48..49..50..51..52..53..54..55..56..57..58..59..60..61..62..63..64..65..66..67..68..69..70..71..72..73..74..75..76..77..78..79..80..81..82..83..84..85..86..87..88..89..90..91..92..93..94..95..96..97..98..99..100..101..102..103..104..105..106..107..108..109..110..111..112..113..114..115..116..117..118..119..120..121..122..123..124..125..126..127..128..129..130..131..132..133..134..135..136..137..138..139..140..141..142..143..144..145..146..147..148..149..150..151..152..153..154..155..156..157..158..159..160..161..162..163..164..165..166..167..168..169..170..171..172..173..174..175..176..177..178..179..180..181..182..183..184..185..186..187..188..189..190..191..192..193..194..195..196..197..198..199..200..201..202..203..204..205..206..207..208..209..210..211..212..213..214..215..216..217..218..219..220..221..222..223..224..225..226..227..228..229..230..231..232..233..234..235..236..237..238..239..240..241..242..243..244..245..246..247..248..249..250..251..252..253..254..255..256..257..258..259..260..261..262..263..264..265..266..267..268..269..270..271..272..273..274..275..276..277..278..279..280..281..282..283..284..285..286..287..288..289..290..291..292..293..294..295..296..297..298..299..300..301..302..303..304..305..306..307..308..309..310..311..312..313..314..315..316..317..318..319..320..321..322..323..324..325..326..327..328..329..330..331..332..333..334..335..336..337..338..339..340..341..342..343..344..345..346..347..348..349..350..351..352..353..354..355..356..357..358..359.. ++ CPU time for realignment=0 s [=0 s/sub-brick] ++ Min : roll=-0.118 pitch=-1.217 yaw=-0.225 dS=-0.601 dL=-0.394 dP=-0.185 ++ Mean: roll=+0.020 pitch=-0.177 yaw=-0.055 dS=-0.097 dL=-0.042 dP=+0.235 ++ Max : roll=+0.197 pitch=+0.404 yaw=+0.051 dS=+0.947 dL=+0.210 dP=+1.071 ++ Max displacements (mm) for each sub-brick: 1.72 1.45 1.25 1.22 1.08 1.07 1.20 0.97 0.84 0.77 0.89 0.77 0.79 0.50 0.56 0.58 0.53 0.42 0.51 0.61 0.68 0.54 0.55 0.42 0.42 0.33 0.38 0.33 0.35 0.30 0.30 0.27 0.30 0.27 0.37 0.22 0.57 0.32 0.32 0.38 0.28 0.66 0.58 0.54 0.53 0.51 0.38 0.45 0.37 0.28 0.23 0.28 0.29 0.52 0.35 0.38 0.48 0.25 0.29 0.33 0.32 0.37 0.43 0.39 0.51 0.57 0.39 0.45 0.47 0.68 0.90 0.74 0.78 0.55 0.58 0.65 1.17 1.00 0.58 0.50 0.88 0.75 0.69 0.65 0.45 0.44 0.46 0.28 0.22 0.36 0.25 0.29 0.36 0.55 0.50 0.35 0.34 0.49 0.34 0.37 0.54 0.60 0.72 0.31 0.30 0.28 0.34 0.43 0.46 0.33 0.47 0.35 0.50 0.50 0.51 0.57 0.62 0.54 0.51 0.57 0.45 0.47 0.51 0.52 0.37 0.32 0.37 0.29 0.26 0.34 0.35 0.34 0.42 0.51 0.46 0.41 0.34 0.27 0.27 0.15 0.21 0.26 0.10 0.10 0.08 0.09 0.17 0.13 0.10 0.11 0.15 0.10 0.12 0.10 0.21 0.17 0.16 0.17 0.17 0.20 0.22 0.15 0.17 0.15 0.19 0.14 0.15 0.15 0.17 0.24 0.18 0.23 0.25 0.25 0.26 0.25 0.31 0.25 0.15 0.12 0.00 0.07 0.11 0.08 0.07 0.17 0.29 0.18 0.16 0.16 0.15 0.17 0.14 0.18 0.27 0.25 0.17 0.19 0.16 0.18 0.41 0.33 0.29 0.34 0.37 0.37 0.39 0.39 0.39 0.39 0.32 0.24 0.26 0.22 0.21 0.20 0.21 0.17 0.22 0.46 0.25 0.42 0.32 0.28 0.30 0.23 0.20 0.29 0.27 0.32 0.30 0.19 0.24 0.25 0.47 0.45 0.43 0.35 0.29 0.29 0.32 0.32 0.31 0.32 0.32 0.33 0.37 0.29 0.30 0.29 0.26 0.29 0.48 0.45 0.52 0.81 0.59 0.59 0.62 0.59 0.53 0.58 0.61 0.64 0.63 0.61 0.61 0.63 0.66 0.62 0.75 0.81 0.86 0.97 0.94 0.94 0.87 0.89 0.92 0.91 0.91 0.91 0.94 0.84 0.85 0.86 0.83 0.98 0.99 0.99 1.01 0.92 1.00 1.07 1.23 1.42 1.44 1.60 1.53 1.61 1.65 1.68 1.74 1.78 1.79 1.75 1.68 1.79 1.85 1.49 1.65 1.74 1.70 1.79 1.76 1.41 1.46 1.56 1.60 1.61 1.62 1.65 1.61 1.69 1.48 1.74 1.82 1.83 1.79 1.77 1.84 1.86 1.88 1.87 1.70 1.77 1.88 1.98 1.90 1.82 1.77 1.83 1.84 1.89 1.92 1.97 2.03 2.06 2.13 2.11 2.19 2.17 2.23 2.24 2.18 2.18 2.28 2.19 2.15 2.35 ++ Max displacement in automask = 2.35 (mm) at sub-brick 359 ++ Wrote dataset to disk in 002/tmp.mc-afni2.21157/outvol.nii.gz #@# -------------------------------- /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold mri_convert 002/tmp.mc-afni2.21157/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz mri_convert.bin 002/tmp.mc-afni2.21157/outvol.nii.gz 002/fmcpr.nii.gz --in_like 002/template.nii.gz reading info from 002/template.nii.gz... $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from 002/tmp.mc-afni2.21157/outvol.nii.gz... TR=2000.00, TE=0.00, TI=0.00, flip angle=0.00 INFO: frames are not the same i_ras = (-1, 0, 0) j_ras = (0, 0.946649, 0.322266) k_ras = (0, -0.322266, 0.946649) writing to 002/fmcpr.nii.gz... ... cleaning up .... Sun Feb 11 14:20:46 PST 2018 mc-afni2 done INFO: Making external regressor from mc params mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg Sun Feb 11 14:20:46 PST 2018 setenv SUBJECTS_DIR /opt/fmritools/freesurfer/subjects cd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold /opt/fmritools/freesurfer/fsfast/bin/mcdat2mcextreg --i 002/fmcpr.mcdat --o 002/mcprextreg freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux msm2 4.12.0-1-amd64 #1 SMP Debian 4.12.6-1 (2017-08-12) x86_64 GNU/Linux mri_glmfit --table /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat --glmdir /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm --osgm --y-out /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/y.out.nii --pca $Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $ cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold cmdline mri_glmfit.bin --table /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat --glmdir /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm --osgm --y-out /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/y.out.nii --pca sysname Linux hostname msm2 machine x86_64 user bensmith FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 1 y /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat logyflag 0 usedti 0 glmdir /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm Loading y from /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/table.dat Found 6 data colums Found 360 data rows Saving design matrix to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/glm/Xg.dat Computing normalized matrix Normalized matrix condition is 1 Matrix condition is 1 search space = 6.000000 DOF = 359 Starting fit and test Fit completed in 1.66667e-05 minutes Writing results osgm maxvox sig=-1e+10 F=676.016 at index 2 0 0 seed=1519356491 Measure:MC osgm Tx 10.001 Ty -16.531 Tz -10000000000.000 Rx -13.508 Ry -13.109 Rz 34.326 Computing PCA (360) mri_glmfit done ninputs = 1 Checking inputs nframestot = 360 Allocing output Done allocing nframes = 360 Computing PCA Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/tmpdir.mcdat2extreg.21416/pca.nii mcdat2mcextreg done Sun Feb 11 14:20:48 PST 2018 mc-sess completed SUCCESSFULLY sub106sess To Surface ----------------------------- rawfunc2surf-sess -fwhm 5 -s sub106sess -d /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed -fsd bold -trgsubject fsaverage -update -per-run instem fmcpr outstem fmcpr.sm5.fsaverage.hemi ------------------------------ 1/1 sub106sess 1/1 sub106sess 001 lh --------- Sun Feb 11 14:20:48 PST 2018 mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 1.00000 0.00076 -0.00217 -2.58076; 0.00226 -0.16210 0.98677 -9.17842; 0.00040 -0.98677 -0.16211 1.60844; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.white Done reading source surface Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 14848 Reading source surface registration /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.sphere.reg Done loading source registration surface Reading target registration /opt/fmritools/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (msm20171025T154741sub106 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (153634) Reverse Loop had 30979 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 120220, nSrcLost = 0, nSrcMulti = 33414, MnSrcMultiHits = 2.23263 nTrg121 = 140149, nTrgMulti = 23693, MnTrgMultiHits = 2.30752 Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname msm2 machine x86_64 user bensmith input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149949 values in range Counting number of voxels in first frame Found 149949 voxels in final mask Count: 149949 149949.000000 163842 91.520489 mri_binarize done 1/1 sub106sess 002 lh --------- Sun Feb 11 14:20:56 PST 2018 mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99805 -0.06220 -0.00581 -7.94137; -0.01829 -0.37984 0.92487 -14.76863; -0.05973 -0.92296 -0.38023 -8.59879; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.white Done reading source surface Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 14645 Reading source surface registration /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/lh.sphere.reg Done loading source registration surface Reading target registration /opt/fmritools/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (msm20171025T154741sub106 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (153634) Reverse Loop had 30979 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 120220, nSrcLost = 0, nSrcMulti = 33414, MnSrcMultiHits = 2.23263 nTrg121 = 140149, nTrgMulti = 23693, MnTrgMultiHits = 2.30752 Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/lh.cortex.label Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname msm2 machine x86_64 user bensmith input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149298 values in range Counting number of voxels in first frame Found 149298 voxels in final mask Count: 149298 149298.000000 163842 91.123155 mri_binarize done mri_concat --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz --mean /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.lh.pr.nii.gz /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.lh.pr.nii.gz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing mean across frames Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz sysname Linux hostname msm2 machine x86_64 user bensmith input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.lh.pr.nii.gz Binarizing based on threshold min 1e-09 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149949 values in range Counting number of voxels in first frame Found 149949 voxels in final mask Count: 149949 149949.000000 163842 91.520489 mri_binarize done 1/1 sub106sess 001 rh --------- Sun Feb 11 14:21:04 PST 2018 mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.nii.gz srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 1.00000 0.00076 -0.00217 -2.58076; 0.00226 -0.16210 0.98677 -9.17842; 0.00040 -0.98677 -0.16211 1.60844; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.white Done reading source surface Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 14509 Reading source surface registration /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.sphere.reg Done loading source registration surface Reading target registration /opt/fmritools/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (msm20171025T154741sub106 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (151643) Reverse Loop had 30576 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 117501, nSrcLost = 0, nSrcMulti = 34142, MnSrcMultiHits = 2.25286 nTrg121 = 140913, nTrgMulti = 22929, MnTrgMultiHits = 2.33351 Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz sysname Linux hostname msm2 machine x86_64 user bensmith input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149917 values in range Counting number of voxels in first frame Found 149917 voxels in final mask Count: 149917 149917.000000 163842 91.500958 mri_binarize done 1/1 sub106sess 002 rh --------- Sun Feb 11 14:21:12 PST 2018 mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi rh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.nii.gz srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Input reg is LTA -------- original matrix ----------- 0.99805 -0.06220 -0.00581 -7.94137; -0.01829 -0.37984 0.92487 -14.76863; -0.05973 -0.92296 -0.38023 -8.59879; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Loading label /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label Reading surface /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.white Done reading source surface Reading thickness /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 14335 Reading source surface registration /opt/fmritools/freesurfer/subjects/msm20171025T154741sub106/surf/rh.sphere.reg Done loading source registration surface Reading target registration /opt/fmritools/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (msm20171025T154741sub106 -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (151643) Reverse Loop had 30576 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 117501, nSrcLost = 0, nSrcMulti = 34142, MnSrcMultiHits = 2.25286 nTrg121 = 140913, nTrgMulti = 22929, MnTrgMultiHits = 2.33351 Masking with /opt/fmritools/freesurfer/subjects/fsaverage/label/rh.cortex.label Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz Dim: 163842 1 1 mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz --min .00001 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz sysname Linux hostname msm2 machine x86_64 user bensmith input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-05 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 148821 values in range Counting number of voxels in first frame Found 148821 voxels in final mask Count: 148821 148821.000000 163842 90.832021 mri_binarize done mri_concat --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz --mean /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/masks/brain.fsaverage.rh.pr.nii.gz /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/002/masks/brain.fsaverage.rh.pr.nii.gz ninputs = 2 Checking inputs nframestot = 2 Allocing output Done allocing nframes = 2 Computing mean across frames Writing to /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz mri_binarize --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed cmdline mri_binarize.bin --i /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz --min 10e-10 --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz sysname Linux hostname msm2 machine x86_64 user bensmith input /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz frame 0 nErode3d 0 nErode2d 0 output /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/masks/brain.fsaverage.rh.pr.nii.gz Binarizing based on threshold min 1e-09 max +infinity binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 149917 values in range Counting number of voxels in first frame Found 149917 voxels in final mask Count: 149917 149917.000000 163842 91.500958 mri_binarize done 1/1 sub106sess 001 lh --------- Sun Feb 11 14:21:20 PST 2018 mri_vol2surf --mov /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz --reg /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi lh --o /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.sm5.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg niiRead(): error reading from /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz srcvol = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz srcreg = /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/register.dof6.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilin float2int = round GetProjMax = 0 INFO: float2int code = 0 ERROR: Read 13, expected 64 ERROR: could not read /expdata/bensmith/joint-modeling/data/msm/freesurfer/functional_preprocessed/sub106sess/bold/001/fmcpr.nii.gz as type 24 _______________________ Ben Smith, MSc. Ph.D. Candidate University of Southern California https://bjsmith.github.io/ w | +1 213-740 7851 m | +1 323-385 9349 skype | ben.smith.nz

2 1

Funded PhD at Cardiff University in collaboration with UCL and University of Wisconsin-Madison on Brain Complexity and Consciousness
by Chen Song 11 Feb '18

11 Feb '18

*PhD Project: Brain Complexity and Consciousness* *Application Deadline: Feb 23, 2018* Applications are invited for a PhD studentship to work with Dr. Chen Song <https://www.braincomplexity.com/> and Prof. Derek Jones <http://psych.cf.ac.uk/contactsandpeople/jonesd27.php> at Cardiff University Brain Research Imaging Centre (CUBRIC), one of Europe’s largest brain research centres, in collaboration with Prof. Geraint Rees <https://en.wikipedia.org/wiki/Geraint_Rees> at University College London and Prof. Giulio Tononi <https://en.wikipedia.org/wiki/Giulio_Tononi> at University of Wisconsin-Madison. This PhD studentship offers an excellent opportunity for candidates interested in the broad area of brain imaging, neuroscience, and/or consciousness research, to conduct research on the following topics: - *Brain complexity* - how different brain regions differ structurally, how their structural differences underpin their functional differences, whether the empirically-observed function of a brain region is what the structure of this brain region is theoretically optimal for; - *Mapping between brain complexity and consciousness* - how different individuals differ in their brain structure, how the inter-individual differences in brain structure affect brain function, and lead to inter-individual differences in perception and cognition; - *Brain plasticity* - how learning and sleep interact to change brain structure and function, whether different mechanisms of brain plasticity may be at play during wake versus sleep, and whether the contrast between the two may hold key to our intelligence and consciousness. See some of our recent work on these topics at: Schwarzkopf et al. Nature Neuroscience 2010 <https://www.nature.com/articles/nn.2706>; Song et al. Journal of Neuroscience 2011 <http://www.jneurosci.org/content/31/26/9472.long>; Song et al. Journal of Neuroscience 2013 <http://www.jneurosci.org/content/33/48/18781.long>; Song et al. Nature Communications 2013 <https://www.nature.com/articles/ncomms3201>; Tononi et al. Neuron 2014 <http://www.cell.com/neuron/fulltext/S0896-6273(13)01186-0>; Song et al. Neuron 2015 <http://www.cell.com/neuron/fulltext/S0896-6273(14)01150-7>; Tononi et al. Nature Reviews Neuroscience 2016 <https://www.nature.com/articles/nrn.2016.44>; Song et al. Journal of Neuroscience 2017 <http://www.jneurosci.org/content/37/37/8929.long>; or a summary at: http://www.braincomplexity.com/research. The successful applicant will be able to use the *£44M cutting-edge brain imaging facilities at CUBRIC* to acquire multi-modal brain measures (structural, metabolic, electrical, chemical), and link the empirical data to theories on brain complexity and consciousness (integrated information theory), sleep and cognition (synaptic homeostasis hypothesis). As one of Europe’s largest brain research centres, CUBRIC hosts: - one of the only three Connectom MRI scanners in the world, specially designed for measuring brain microstructure and connectomics; - one 7T MRI scanner, two 3T MRI scanners, one MEG scanner, three EEG labs, five TMS labs; - six sleep study bedrooms built to clinical standard. The studentship is open to UK/EU/international students; it covers the full tuition fee (at UK/EU level) and an annual stipend of £14,553. Please contact Dr. Chen Song at SongC5(a)cardiff.ac.uk for any enquiries, or see application details at http://psych.cf.ac.uk/degre eprogrammes/postgraduate/research/docs/school_song.pdf.

1 0

Two versions of FreeSurfer in the same computer
by Vania de Aguiar 09 Feb '18

09 Feb '18

Dear, I will be attending the workshop in April and I started taking the tutorials online to get prepared. My laptop is running an older of freesurfer (5.0.0), because I have data to add to other data analysed by a previous lab member. I am aware that I shouldn't mix versions, but for tutorials and the workshop I think it would be best to work on the newest version. Can I have both versions running in my computer, to use one for that project and the other one for current tutorials and the workshop? ?Best, Vânia de Aguiar, PhD Postdoctoral research fellow Johns Hopkins Medical Institute Department of Neurology 600 N. Wolfe street, Phipps 477 Baltimore, MD, 21287 Phone: +1 (410) 955 8210

2 1

no white matter is labelled when using mri_aparc2aseg
by Sims, Sara A 09 Feb '18

09 Feb '18

Doug, I am sorry that I wasn’t clear before, here is all the info about it all in one place. I am trying to transfer a cortical label to label wm by using the following commands: subjects=/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon; unset SUBJECTS_DIR SUBJECTS_DIR=$subjects export SUBJECTS_DIR patient=211215 #Label 8 conversion mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s $patient --h lh --l $subjects/$patient/label/8_LH_V1.label --a 8V1 mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s $patient --h rh --l $subjects/$patient/label/8_RH_V1.label --a 8V1 mri_aparc2aseg --s $patient --annot 8V1 --labelwm mri_binarize --i $subjects/$patient/mri/8V1+aseg.mgz --o $subjects/$patient/mri/8V1_bin.mgz --match 4001 3001 mri_convert $subjects/$patient/mri/8V1_bin.mgz $subjects/$patient/mri/8V1_bin.nii mri_vol2vol --mov /data/project/vislab/raw/HCP_900sub/HCP_diff_data/$patient/data.nii.gz --targ $subjects/$patient/mri/8V1_bin.nii --reg /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/$patient/register_edit.dat --o $subjects/$patient/mri/8V1_diffROI.nii --inv --nearest This makes a 8V1+aseg.mgz file there are just no 4001 and 3001's in the file so when I binarize there is nothing there. So my question is why is it not identifying the wm next to my label? This is happening in multiple subjects on varying labels. I have attached a picture of what the error looks like. As you can see all the values in the volume are all zero (blue) and there is nothing next to the cortical label (red). I have tried changing the -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I could find but it won’t budge even though doing other labels in the same person works fine. The original cortical label is also correctly placed in the cortical ribbon. Here is the output from running the above commands: Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab Number of ctab entries 2 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/user/snolin/Scripts/Labelmaker cmdline mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s 211215 --h lh --l /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_LH_V1.label --a 8V1 sysname Linux hostname c0039 machine x86_64 user snolin subject 211215 hemi lh SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon ColorTable /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab AnnotName 8V1 nlables 1 LabelThresh 0 0.000000 ERROR: /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot already exists Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab Number of ctab entries 2 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/user/snolin/Scripts/Labelmaker cmdline mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s 211215 --h rh --l /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_RH_V1.label --a 8V1 sysname Linux hostname c0039 machine x86_64 user snolin subject 211215 hemi rh SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon ColorTable /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab AnnotName 8V1 nlables 1 LabelThresh 0 0.000000 ERROR: /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot already exists SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon subject 211215 outvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz useribbon 0 baseoffset 0 labeling wm dmaxctx 5.000000 RipUnknown 0 Reading lh white surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.white Reading lh pial surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.pial Loading lh annotations from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot Reading rh white surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.white Reading rh pial surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.pial Loading rh annotations from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot Loading ribbon segmentation from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1124316 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /data/user/snolin/Scripts/Labelmaker cmdline mri_binarize.bin --i /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz --o /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz --match 4001 3001 sysname Linux hostname c0039 machine x86_64 user snolin input /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz Binarizing based on matching values nMatch 2 0 4001 1 3001 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done mri_convert.bin /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii... Matrix from regfile: 1.00000 -0.00055 0.00091 -0.38465; -0.00091 0.00095 1.00000 0.38039; -0.00055 -1.00000 0.00095 -0.14575; 0.00000 0.00000 0.00000 1.00000; movvol /data/project/vislab/raw/HCP_900sub/HCP_diff_data/211215/data.nii.gz targvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii outvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_diffROI.nii regfile /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/211215/register_edit.dat invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1518108582 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 1.00000 -0.00091 -0.00055 0.38491; -0.00055 0.00095 -1.00000 -0.14632; 0.00091 1.00000 0.00095 -0.37990; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.25000 -0.00069 0.00114 36.96743; 0.00114 0.00118 -1.25000 218.81943; 0.00069 1.25000 0.00118 18.96824; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin(a)uab.edu

1 0

shift to account for hemodynamic response
by Ashley Cole 09 Feb '18

09 Feb '18

Dear experts, I just have switched from SPM to Freesurfer. I am wondering if in FSFAST analysis, we require to shift the regressors in time to account for the delay in hemodynamic response? Thanks

3 2

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