Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

recon.all strange run time
by Ottavio Morciano 03 Jul '18

03 Jul '18

External Email - Use Caution Hi!I have a macbook pro MY 2014 with a Intel Core i7(quad core,2.7 ghz) and 16 gb of ram with El Capitan.This Macbook to run recon-all it takes 47 hours with -openmp 8 flag. A Dell with Intel Core i7 3632Q,8 GB RAM DDR3 1600mhz with Linux takes 8 hours...The same Dell on windows with linux virtualizated takes 13 hours. Why recon-all on mac is so slow? is the OS?the type of compilator used for each platform?freesurfer not optimized for El Capitan? the architecture of the cpu? Some Advice? Morciano Ottavio MD Student Università Di Foggia.Italy

2 1

Proposed addition for Freesurfer - automated control points
by Chris Adamson 30 Jun '18

30 Jun '18

External Email - Use Caution Freesurfer devs, I presented an automated control point adding tool at HBM and a few freesurfer lab people came over and had a look. I was wondering if someone would like to review it for either inclusion or to perhaps reference from the wiki as a tool for people to use if they choose? Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email

2 2

TIV should be considered as a covariant for thickness, volume and area analyses
by Ting Li 29 Jun '18

29 Jun '18

External Email - Use Caution Hi FreeSurfer Experts, I would like to do the surface analysis among two groups, like the thickness, volume and area. When I run the GLM, do I have to consider the eTIV as a covariant or not? Thanks a lot! Best wishes, Ting

2 2

Eddy correct command not found
by Renew Andrade 29 Jun '18

29 Jun '18

External Email - Use Caution Dear community: I have a problem with trac-all processing with the tutorial data. sh-3.2# trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons INFO: Diffusion root is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423 Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c flirt: Command not found. INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /usr/local/freesurfer/dev trac-preproc -c /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local -log /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log -cmd /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Jun 29 21:19:12 CEST 2018 mri_convert --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm... Getting Series No INFO: Found 75 files in /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig INFO: Scanning for Series Number 11 Scanning Directory INFO: found 70 files in series INFO: loading series header info. RunNo = 10 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 1048.1801 1002.6923 -265.4914 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID unknown INFO: sorting. INFO: (128 128 60), nframes = 70, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5 Repetition Time = 10100, TR = 10100 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.99970 0.02376 -0.00570 -0.49480; -0.02443 0.97638 -0.21466 -40.55519; 0.00047 0.21474 0.97667 12.50291; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 131.1612 149.7402 -72.6670 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.5005 40.7699 13.4796 TransferSyntaxUID unknown UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 sagrev = 1, correv =1, trarev = 0 Vs = 0.0057 0.214665 0.976671 INFO: no Siemens slice order reversal detected (good!). TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999702, 0.0244268, 0.000465598) j_ras = (-0.023757, -0.976382, 0.21474) k_ras = (0.0057, 0.214665, 0.976671) writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz... mri_probedicom --i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dcminfo.dat cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/gradients.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/bvalues.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals orientLAS /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 mri_convert -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999701, 0.0244268, 0.000465598) -> (-0.999702, 0.0244268, 0.000465598) normalizing out_j_direction: (0.023757, 0.976382, -0.21474) -> (0.023757, 0.976382, -0.21474) normalizing out_k_direction: (0.0057, 0.214665, 0.976671) -> (0.0057, 0.214665, 0.976671) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz... TR=10100.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999701, 0.0244268, 0.000465598) j_ras = (-0.023757, -0.976382, 0.21474) k_ras = (0.0057, 0.214665, 0.976671) Reslicing using nearest writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz... INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals, copying INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LAS mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals eddy_correct /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz 0 eddy_correct: Command not found. Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Jun 29 21:20:22 CEST 2018 What should be the problem? Sincerely, Andrade.

1 0

mri_glmfit question
by Nillo, Ryan Michael R 29 Jun '18

29 Jun '18

External Email - Use Caution Hello FreeSurfer Users, I want to run an ROI-based analysis on mri_glmfit as opposed to vertex-based. I know that if I run mri_glmfit with the --table flag and give it the output of asegstats2table or aparcstats2table, it will run the analysis on the ROIs and output tables showing significance. In each contrast directory that was created from mri_glmfit, I see there is a pcc.mgh. Is there any way to display this on the surface or put it into a table format? Mahalo, Ryan M Nillo Staff Research Associate I UCSF Department of Radiology and Biomedical Imaging

2 1

Freeview not showing images
by Mark Wagshul 29 Jun '18

29 Jun '18

External Email - Use Caution Hi. I'm a newbie to Freeview, hoping that this is a simple problem. When I open it (specifying the lh.pial surface), I get this view: [cid:image001.jpg@01D40F16.EC48FB10] Anyone have an idea what's going on here, is it an issue with the screen resolution settings? Thanks, Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

2 4

3T Intensity Normalization (Re-Submission)
by David S Lee 29 Jun '18

29 Jun '18

External Email - Use Caution Hello Experts, I believe -3T Flag can be used with "recon-all" on scans collected by 3T scanners. I believe it performs intensity normalization to set white matter intensity threshold at 110. I am hoping to learn more about the flag option as it produces slightly better output for me. Would you be able to guide me to a documentation on this -3T flag? Thank you! -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

2 1

Poor occipital signal and low contrast
by Chawla, Megha 28 Jun '18

28 Jun '18

External Email - Use Caution Hi, I have scans for ~60 participants, and for some reason the scans are of visibly poor quality when I convert them to .mgz (blurry, very low contrast). The white boundary also seems to exclude considerable white matter in the occipital in about half of the scans. Because of the extremely low contrast, I am unable to manually add control points as I cannot visibly tell the difference between wm and gm. I am attaching orig.mgz for one participant here. Acquisition parameters for these scans were: High-resolution T1-weighted anatomical images (1 × 1 × 1 mm3) were acquired with an MPRAGE pulse sequence (TI=900 ms, sagittal slices, 256 × 256 matrix) using a Siemens Allegra 3T head-only scanner. I tried running more iterations of during the nu_correct (as suggested here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-November/008985…) using the following command: mc2835% recon-all -autorecon1 -nuintensitycor -nuiterations 10 -subjid 30026_FS but got the following error: ERROR: Flag -nuiterations unrecognized. -autorecon1 -nuiterations 10 -subjid 30026_FS Darwin Ifats-Mac-Pro.med.yale.internal 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 recon-all -s exited with ERRORS at Tue Jun 19 14:56:04 EDT 2018 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Is there any way to salvage this data for analysis? Any help will be really appreciated. Thank you! Megha

2 2

Errors in scans
by Nasiriavanaki, Zahra 28 Jun '18

28 Jun '18

Hi Freesufer developers We are getting some errors in our resting state and ASL scans. Everything goes fine while we are scaning the subjects, but when we look at the data in BORGET, some of them come out with errors. I copied one of the scaninfo files, so you can see the errors. Is there anyway to not get errors? Or shall we just unpack the ok data and go on? Thanks 1 localizer_64ch ok 512 512 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716282052566788535 2 AAHead_Scout ok 160 160 128 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716283612565588717 3 AAHead_Scout ok 162 162 5 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031754889708 4 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031832189712 5 AAHead_Scout ok 162 162 3 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716284031887889715 6 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836176490274 7 MEMPRAGE ok 256 256 176 4 MR.1.3.12.2.1107.5.2.43.67026.2018062716353836150890273 8 MEMPRAGE ok 256 256 176 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716353850258890299 9 fMRI_DistortionMap_PA ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716372672952394688 10 fMRI_DistortionMap_AP ok 92 92 57 1 MR.1.3.12.2.1107.5.2.43.67026.2018062716380680499794923 11 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716403982376595295 12 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716480447089626419 13 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062716552453255257555 14 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717024484181988697 15 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717100568938419838 16 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717172417291250987 17 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717244528886782134 18 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.2018062717320619207913274 19 ep2d_bold_SMS3_PAT2_2p5iso ok 92 92 57 180 MR.1.3.12.2.1107.5.2.43.67026.201806271739232204744422 20 tgse_pcasl_optBS_M0_PLD2000 ok 96 96 1 22 MR.1.3.12.2.1107.5.2.43.67026.2018062717460555193775829 21 tgse_pcasl_optBS_M0_PLD2000 err 96 96 1 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717461445002086101 22 HCP_CMRR_SpinEchoFieldMap_AP ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461591061986321 23 HCP_CMRR_SpinEchoFieldMap_PA ok 104 104 72 3 MR.1.3.12.2.1107.5.2.43.67026.2018062717461993800986977 24 HCP_CMRR_fMRI_rest_AP err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.201806271747377337919554 25 HCP_CMRR_fMRI_rest_AP err 104 104 72 216 MR.1.3.12.2.1107.5.2.43.67026.2018062717473793126919992 26 HCP_CMRR_fMRI_rest_PA err 104 104 72 1 MR.1.3.12.2.1107.5.2.43.67026.2018062717540945183412846 27 HCP_CMRR_fMRI_rest_PA ok 104 104 72 488 MR.1.3.12.2.1107.5.2.43.67026.2018062717541118019513248 Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

2 2

Moderation analysis in Freesurfer
by Mark Wagshul 28 Jun '18

28 Jun '18

External Email - Use Caution Dear Freesurfer experts, We are interested in looking at the moderating effect of grey matter thickness on a non-imaging outcome measure. Thus, the model would be: Outcome measure = Condition + GM thickness + Condition * GM thickness + covariates. where Condition is a categorical variable (1/2, for two conditions of the non-imaging measures). The Freesurfer GLM usually solves for the thickness as a function of some contrast, but is really just determining the voxel-wise statistical significant of a GLM, so should be doable even with the imaging variable on the RHS. Ideally, we would like to run this as a linear mixed model with subject as a random effect, and the condition as a repeated measure. Is this possible to do with the current Freesurfer software, and if so, how would I implement it? Thanks for any advice you can provide. Mark ____________________ Mark Wagshul, PhD Associate Professor Gruss Magnetic Resonance Research Center Albert Einstein College of Medicine Bronx, NY 10461 Ph: 718-430-4011 FAX: 718-430-3399 Email: mark.wagshul(a)einstein.yu.edu<mailto:mark.wagshul@einstein.yu.edu> [einstein-logo-rgb] This email message and any accompanying attachments may contain privileged information intended only for the named recipient(s). If you are not the intended recipient(s), you are hereby notified that the dissemination, distribution, and or copying of this message is strictly prohibited. If you receive this message in error, or are not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately.

2 1

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Freesurfer June 2018