Freesurfer December 2019

freesurfer@nmr.mgh.harvard.edu

85 participants
117 discussions

T2 in recon-all: command to correct pial surfaces errors
by Steve Petersen 05 Dec '19

05 Dec '19

External Email - Use Caution Dear Freesurfer experts, I used t2 image as input in subjects that have already been processed without them following the instructions of the website. Although pial surface segmentation has improved there is still some error. After edit the brainmask.mgz file in Freeview (recon edit option), what command should I use to correct the pial surfaces obtained after the -T2pial flag? I tried to use the -autorecon-pial command to correct the edits but I think that this command only takes into account the T1, is that right? Best regards,

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Re: [Freesurfer] Question on GLM - correlation
by Greve, Douglas N.,Ph.D. 05 Dec '19

05 Dec '19

That does not have the pvr in it. You can extract the pvr for that vertex and add it as a column to the X matrix with pvr = fast_vol2mat(MRIread('pvr.mgz')); pvrvtx = pvr(:,vertexno+1); ps. Please remember to post to the list On 12/3/2019 1:29 PM, Barletta, Valeria wrote: Ok done. This is the Xg.mat 1 29 1 44 1 38 1 47 1 34 1 25 1 30 1 22 1 52 1 31 1 37 1 42 1 28 1 39 1 44 1 44 1 32 1 32 1 36 1 47 1 52 And the cond(Xg'*Xg) is again: 3.0555e+04 Looks like there is no extra column for the pvr in the Xg.mat ________________________________ From: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> Sent: Tuesday, December 3, 2019 11:03 AM To: Barletta, Valeria <VBARLETTA(a)mgh.harvard.edu><mailto:VBARLETTA@mgh.harvard.edu>; Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question on GLM - correlation I'm not sure those condition numbers include the pvr. Try loading the Xg.mat into matlab and computing cond(Xg'*Xg) Make sure Xg has the extra column for the pvr On 12/3/2019 10:42 AM, Barletta, Valeria wrote: Ok it worked. So I tried with a non-zero vertex and I got: Normalized matrix condition is 81.1382 Matrix condition is 30558.5 Found 149926 points in label. Found 149926 voxels in mask Saving mask to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh Reshaping mriglm->mask... search space = 74490.928733 DOF = 18 Dumping voxel 1024 0 0 to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-1024-0-0 ...and with a zero vertex and got: Normalized matrix condition is 81.1382 Matrix condition is 30558.5 Found 149926 points in label. Found 149926 voxels in mask Saving mask to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/mask.mgh Reshaping mriglm->mask... search space = 74490.928733 DOF = 18 Dumping voxel 150252 0 0 to /autofs/space/lipari_001/users/valeria/NODDI/GLM//GLM_CME_ficvf_doug2/rh_contrast-MS_CME_all_FIS_ICA1/voxdump-150252-0-0 ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu><mailto:DGREVE@mgh.harvard.edu> Sent: Monday, December 2, 2019 2:56 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Question on GLM - correlation oh, sorry, did not see the pvr. It could very well be the pvr that is causing the patchiness. Unfortunately, you have to debug it vertex by vertex. I would choose a few vertices (one with signal, on without) and run mri_glmfit with --voxdump vertexno 0 0 This will create a subfolder with the GLM for that vertex. I'm not sure what to tell you to look for, but I would at least check the condition numbers in each vertex. What is the nature of ficvf? On 12/2/2019 1:22 PM, Barletta, Valeria wrote: My other continuous variable is --pvr ${hemi}.ficvf.mgh Not sure about --no-prune, I found it in my script as a default... Shall I remove it? ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu><mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Barletta, Valeria <VBARLETTA(a)mgh.harvard.edu><mailto:VBARLETTA@mgh.harvard.edu> Sent: Friday, November 29, 2019 3:08 PM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu><mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] Question on GLM - correlation Dear Freesurfers, I am running glmfit to assess for correlation between y and another continue variable across the cortex (ficvf), correcting for the effect of age, using the command: mri_glmfit \ --y {surfname_cme}.mgh \ --fsgd {contrast}.fsgd \ --C {contrast}.mat \ --pvr ${hemi}.ficvf.mgh" \ --surf fsaverage $hemi \ --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_cme} \ --no-prune This is my matrix: 1 0 0 And my fsgd file: Title CME Class MS Variable age Input MS069_R01_01 MS 29 Input MS070_R01_02_R1year MS 44 Input MS072_R01_04 MS 38 Input MS073_R01_05 MS 47 Input MS075_R01_07_R1year MS 34 Input MS076_R01_08 MS 25 Input MS077_R01_09 MS 30 Input MS078_R01_10 MS 22 Input MS080_R01_12 MS 52 Input MS081_R01_13 MS 31 Input MS082_R01_14 MS 37 Input MS084_R01_16 MS 42 Input MS086_R01_18 MS 28 Input MS087_R01_19_R1year MS 39 Input MS088_R01_20 MS 44 Input MS089_R01_29 MS 44 Input MS090_R01_21 MS 32 Input MS091_R01_22 MS 32 Input MS092_R01_23 MS 36 Input MS094_R01_25 MS 47 Input MS104_R01_36 MS 52 This is the result: [cid:part10.AAFB4919.2AE170D2@mgh.harvard.edu][cid:part11.F1A0EFEC.57C56985@mgh.harvard.edu] Am I proceeding correctly? Thank you, Valeria _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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about label to surface
by 于倩倩 05 Dec '19

05 Dec '19

External Email - Use Caution Dear Freesurfer Expert: First, I got the lh.parsorbitalis.label according to the command:mri_annotation2label --subject fsaverage --hemi lh --outdir /Users/qianqianyu/Desktop/fsl_bold/label_fsaverageNow, I want to make the lh.parsorbitalis.label to fsaverage surface file (nii.gz). How? I did the conversion myself using the following method, but an error occurred. The structure of lh.parsorbitalis.label is as follows： I think the first column is coordinate information. So, I use the following commands to convert in Matlab. a=[116,255,256,735,...3806,...];%All values in the first column are assigned to the matrix, a. n=1:163842; %cause the vol matrix of fsaverage lh is1*163842 t=zeros(1,length(n)); t(1,a)=1;%value of lh.parsorbitalis area were 1 MRIread('/Users/qianqianyu/Desktop/Project/Sess06/bold/my-syn.sm04.lh/sem-v-fj/sig.nii');%read a fsaverage image ans.vol=t; err = MRIwrite(ans,'lh.parsorbitalis.mask.nii.gz') But, when I check the lh.parsorbitalis.mask.nii.gz in Freeview, I find it is not consistent with the lh.parsorbitalis.label I am now very very anxious to know how to get the right lh.parsorbitalis.mask.nii.gz！Looking forward to your reply！ Best wishes! Qianqian Yu

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DWI to T1 registration accuracy with bbregister
by VictorM - Gmail 05 Dec '19

05 Dec '19

External Email - Use Caution Hi Freesurfer experts, I have been trying to run a registration between my DWi data and the T1. I am struggling to obtain a good cortical matching, despite I have previously run it withour problems in other datasets. The mincost for most of the individuals is >0.8, which is pretty bad. My guess is that there is a problem with the initialization (mri_coreg not converging correctly?). I have tried different approaches to improve the results with no success: 1) Typical bbregister command: >> bbregister --s XX --mov XX_b0_brain.nii.gz --reg dwi2anat.reg.lta --dti 2) Initialize with fsl (using --init-fsl and using flirt independently with mutual information cost) 3) Playing around with mri_coreg different parameters (dof, non-mask, different smooth of target/mov, etc). 4) Use bbregister with the pial surface (since the contrast CSF/GM is higher than GM/WM) with the command: >> bbregister --s XX --mov 'XX_b0_brain.nii.gz' --reg reg.csf.gm.contrast.dat --surf pial --o dwi2anat.nii.gz --t1 --gm-proj-abs 1 --wm-proj-abs 1 Any insight on how to improve the results? Victor Montal PS: Please, see below the output of mri_coreg when initializing the bbregister with default parameters (method1): $Id: bbregister,v 1.75 2016/05/10 20:02:28 greve Exp $ Linux testPC 4.15.0-64-generic #73~16.04.1-Ubuntu SMP Fri Sep 13 09:56:18 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux FREESURFER_HOME /usr/local/freesurfer mri_convert XX_b0_brain.nii.gz ./tmp.bbregister.28271/template.nii mri_convert.bin XX_b0_brain.nii.gz ./tmp.bbregister.28271/template.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from XX_b0_brain.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998604, 0.0523657, -0.00685515) j_ras = (0.0495749, 0.974205, 0.220152) k_ras = (-0.0182067, -0.219505, 0.975442) writing to ./tmp.bbregister.28271/template.nii... mri_coreg --s XX --mov ./tmp.bbregister.28271/template.nii --regdat ./tmp.bbregister.28271/reg.init.dat --reg ./tmp.bbregister.28271/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 $Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $ cwd /home/testPC/Desktop/tmp/todel_max/test_subject/DTI/XX cmdline mri_coreg --s XX --mov ./tmp.bbregister.28271/template.nii --regdat ./tmp.bbregister.28271/reg.init.dat --reg ./tmp.bbregister.28271/mri_coreg.lta --nthreads 1 --dof 6 --sep 4 --ftol .0001 --linmintol .01 sysname Linux hostname testPC machine x86_64 user testPC dof 6 nsep 1 cras0 1 ftol 0.000100 linmintol 0.010000 bf 1 bflim 30.000000 bfnsamp 30 SmoothRef 0 SatPct 99.990000 MovOOB 0 optschema 1 Reading in mov ./tmp.bbregister.28271/template.nii Reading in ref /home/testPC/Desktop/tmp/todel_max/test_subject/FS/XX/mri/brainmask.mgz Reading in and applying refmask /home/testPC/Desktop/tmp/todel_max/test_subject/FS/XX/mri/aparc+aseg.mgz Setting cras translation parameters to align centers Creating random numbers for coordinate dithering Performing intensity dithering Initial parameters -0.1963 -2.6892 11.5267 0.0000 0.0000 0.0000 1.0000 1.0000 1.0000 0.0000 0.0000 0.0000 Separation list (1): 4 min = 4 DoSmoothing 1 DoCoordDither 1 DoIntensityDither 1 nitersmax 4 ftol 1.000e-04 linmintol 1.000e-02 SatPct 99.990000 Hist FWHM 7.000000 7.000000 nthreads 1 movsat = 1692.0000 mov gstd 1.6917 1.6917 1.6917 Smoothing mov refsat = 116.0000 ref gstd 1.8914 1.8914 1.8914 Smoothing ref COREGpreproc() done Testing if mov and target overlap Init cost -1.0432535803 nhits = 124061 out of 16777216, Percent Overlap: 47.3 Initial RefRAS-to-MovRAS 1.00000 0.00000 0.00000 -0.19633; 0.00000 1.00000 0.00000 -2.68918; 0.00000 0.00000 1.00000 11.52671; 0.00000 0.00000 0.00000 1.00000; Initial RefVox-to-MovVox 0.49930 0.00343 0.02618 -3.93636; -0.02479 -0.11008 0.48710 18.58949; 0.00910 -0.48772 -0.10975 106.51717; 0.00000 0.00000 0.00000 1.00000; sep = 4 ----------------------------------- COREGoptBruteForce() 30 1 30 Turning on MovOOB for BruteForce Search #BF# sep= 4 iter=0 lim=30.0 delta=2.00 -2.19633 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0498706 Turning MovOOB back off after brute force search --------------------------------- Init Powel Params dof = 6 Starting OpenPowel2(), sep = 4 InitialCost -1.0708609819 #@# 4 188 -2.19633 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0708610 fs_powell::minimize nparams 6 maxfev 4 ftol 0.000100 linmin_xtol_ 0.010000 powell nthiter 0: fret = -1.070861 #@# 4 190 -1.19633 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0711184 #@# 4 195 -1.38650 7.31082 -4.47329 2.00000 0.00000 4.00000 -1.0711316 #@# 4 201 -1.38650 5.69279 -4.47329 2.00000 0.00000 4.00000 -1.0721272 #@# 4 202 -1.38650 4.18476 -4.47329 2.00000 0.00000 4.00000 -1.0723432 #@# 4 203 -1.38650 4.46454 -4.47329 2.00000 0.00000 4.00000 -1.0723693 #@# 4 206 -1.38650 4.64374 -4.47329 2.00000 0.00000 4.00000 -1.0723741 #@# 4 207 -1.38650 4.62484 -4.47329 2.00000 0.00000 4.00000 -1.0723747 #@# 4 216 -1.38650 4.62484 -4.34018 2.00000 0.00000 4.00000 -1.0723816 #@# 4 225 -1.38650 4.62484 -4.34018 1.38197 0.00000 4.00000 -1.0724094 #@# 4 237 -1.38650 4.62484 -4.34018 1.38197 -0.28207 4.00000 -1.0724264 #@# 4 238 -1.38650 4.62484 -4.34018 1.38197 -0.29894 4.00000 -1.0724277 #@# 4 251 -1.38650 4.62484 -4.34018 1.38197 -0.29894 3.98803 -1.0724281 powell nthiter 1: fret = -1.072428 #@# 4 283 -1.38650 4.62484 -4.37900 1.38197 -0.29894 3.98803 -1.0724293 #@# 4 292 -1.38650 4.62484 -4.39237 1.46777 -0.29894 3.98803 -1.0724353 #@# 4 303 -1.38650 4.62484 -4.39237 1.46777 -0.35779 3.98803 -1.0724378 Powell done niters total = 1 OptTimeSec 11.2 sec OptTimeMin 0.19 min nEvals 319 Final parameters -1.38650012 4.62484455 -4.39237213 1.46777403 -0.35779098 4.00846672 Final cost -1.072437818483776 --------------------------------- mri_coreg utimesec 72.570349 mri_coreg stimesec 0.163951 mri_coreg ru_maxrss 432564 mri_coreg ru_ixrss 0 mri_coreg ru_idrss 0 mri_coreg ru_isrss 0 mri_coreg ru_minflt 128483 mri_coreg ru_majflt 31 mri_coreg ru_nswap 0 mri_coreg ru_inblock 11360 mri_coreg ru_oublock 16 mri_coreg ru_msgsnd 0 mri_coreg ru_msgrcv 0 mri_coreg ru_nsignals 0 mri_coreg ru_nvcsw 35 mri_coreg ru_nivcsw 3612 Final RefRAS-to-MovRAS 0.99753 0.06990 -0.00624 -1.38650; -0.06972 0.99724 0.02561 4.62484; 0.00802 -0.02512 0.99965 -4.39237; 0.00000 0.00000 0.00000 1.00000; Final RefVox-to-MovVox 0.49992 -0.00036 -0.00871 1.07589; 0.00835 -0.12236 0.48473 17.73093; -0.00248 -0.48480 -0.12233 100.50899; 0.00000 0.00000 0.00000 1.00000; Final parameters -1.3865 4.6248 -4.3924 1.4678 -0.3578 4.0085 nhits = 123915 out of 16777216, Percent Overlap: 47.3 mri_coreg RunTimeSec 72.8 sec

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Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch
by ZORO 04 Dec '19

04 Dec '19

External Email - Use Caution Thank you so much! It works.

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TRACULA QUESTION:CONFIGURATION FILE ISSUE
by Benxamin varela lópez 04 Dec '19

04 Dec '19

External Email - Use Caution Dear Freesurfers experts, I'm a beginner in the diffusion imaging preprocessing. I was following the freesurfer/dti tutorial with my own data when i get stuck in the trac-all step. I have created the configuration files trying to follow the tutorial instructions and when I tried to run the trac-all command I get the following error: pcpb3846:4220 lab1-rmn$ trac-all -prep -c $TUTORIAL_DATA/outputs/dmrirc.tutorial set: Variable name must contain alphanumeric characters. ERROR: must specify either one number of control points ERROR: or as many numbers as pathways You can find my configuration file in attached. Any help would be very appreciated. Thank in advance. Best regards,

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hippocampal subfields as masks for mri_segstats
by Marcel Heers 04 Dec '19

04 Dec '19

External Email - Use Caution Dear all, (dear Eugenio), I would like to use hippocampal subfields as masks for mri_segstats to retrieve intensity values. I am having problems loading the subfields file although it works fine with aseg.mgz. Does anyone know the cause? Thank you in advance! Best regards Marcel mri_segstats --seg $SUBJECTS_DIR/test/mri/aseg.mgz --ctab-default --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz mri_segstats --seg $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz --sum output.txt --in $SUBJECTS_DIR/test/mri/T1.mgz ERROR: loading $SUBJECTS_DIR/test/mri/lh.hippoAymgLabels-T1.v21.HBT.mgz

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MRI label 2 label issue
by Rellick, Stephanie 04 Dec '19

04 Dec '19

External Email - Use Caution Hello, I am having an issue with the mri_label2label command. What I did was mri merge of the BA4 a and p labels for each hemisphere from the fsaverage files, ending up with a lh.BA4.label and a rh.BA4.label. I am wanting to now map the fsaverage lh.BA4.label and rh.BA4.label onto the individual subjects into my study, and was told that to do this, I needed to create those same labels using the BA4 a & p labels in the individual subject label file, and then run the command mri_label2label. This is the command that I am running: mri_label2label --srcsubject fsaverage --srclabel lh.BA4.label --trgsubject SRMC01_1.long.SRMC01 --trglabel lh.BA4.label --regmethod surface --hemi lh And it keeps giving me this error message: srclabel = lh.BA4.label srcsubject = fsaverage trgsubject = SRMC01_1.long.SRMC01 trglabel = lh.BA4.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR ./ FREESURFER_HOME /Applications/freesurfer Loading source label. Found 7403 points in source label. Starting surface-based mapping Reading source registration .//fsaverage/surf/lh.sphere.reg Rescaling ... original radius = 100 Reading target surface .//SRMC01_1.long.SRMC01/surf/lh.white MRISread(.//SRMC01_1.long.SRMC01/surf/lh.white): could not open file No such file or directory ERROR: could not read .//SRMC01_1.long.SRMC01/surf/lh.white The lh.white file is definitely in the surface folder under that subject so I'm not sure why is says there is no such file or directory. Any help would be greatly appreciated!! Stephanie

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3 positions at Barcelonabeta Brain Research Center
by Juan Domingo Gispert López 04 Dec '19

04 Dec '19

External Email - Use Caution The Neuroimaging Research Group of the Alzheimer's Prevention Program of the Barcelonabeta Brain Research center is seeking a Post-Doctoral researcher (open to Ph.D. students), a Neuroimaging Data Analyst and a Scientific Project Manager. For further information on the positions and instructions on how to apply, please visit the following links: Post-Doctoral or PhD position: https://www.barcelonabeta.org/sites/default/files/2019-11/Predoc_postdoc_AM… Neuroimaging Data Analyst: https://www.barcelonabeta.org/sites/default/files/2019-11/MRI%20Analyst-AD%… Scientific Project Manager: https://www.barcelonabeta.org/sites/default/files/2019-11/1906%20Scientific… -- *Juan Domingo Gispert*Group Leader - Neuroimaging *BarcelonaBeta* * Brain Research Center (BBRC) *jdgispert(a)barcelonabeta.org T. (+34) 93 326 31 67 C/ Wellington, 30 <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> 08005 Barcelona <https://maps.google.com/?q=C/+Wellington,+30+08005+Barcelona&entry=gmail&so…> www.barcelonabeta.org www.fpmaragall.org ------------------------------ Confidencialitat correu electrònic BBRC <https://www.barcelonabeta.org/ca/politica-privacitat-web>. Confidencialidad correo electrónico BBRC <https://www.barcelonabeta.org/es/politica-privacidad-web>. E-mail confidentiality BBRC <https://www.barcelonabeta.org/en/privacy-policy-web>. Gràcies per estalviar paper. *Gracias por ahorrar papel. *Thanks for saving paper.

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Trouble running Freeview from Mac Terminal
by Stockmann, Jason 04 Dec '19

04 Dec '19

Hi, I have been having trouble running freeview from the Mac OS terminal via XQuartz on my laptop. I have seen the problem with both Mac OS 10.15.1 (Catalina) and the previous version of Mac OS. I get the error copied below. I am however able to run other GUIs such as fslview. The problem seems to be unique to freeview as best I can tell. Has anyone else ever experienced this error? --- Jason > [deepbrain:~] (nmr-stable60-env) freeview > X Error: BadValue (integer parameter out of range for operation) 2 > Extension: 149 (Uknown extension) > Minor opcode: 3 (Unknown request) > Resource id: 0x0 > Abort (core dumped) > [deepbrain:~] (nmr-stable60-env) > ---- Jason Stockmann Assistant Professor in Radiology A. A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown, MA 02129 jstockmann(a)mgh.harvard.edu<mailto:jstockmann@mgh.harvard.edu> +1 315 450 3309

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Freesurfer December 2019