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30132 discussions

Postdoctoral Researcher in Neuroimaging at Karolinska Institute
by Joana Braga Pereira 06 Dec '19

06 Dec '19

External Email - Use Caution Dear all, We are looking for a Postdoc to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Assistant Professor Joana B. Pereira and it will involve analyzing cross-sectional and longitudinal imaging data, combining clinical measures and cerebrospinal fluid biomarkers, as well as writing manuscripts and presenting results in international conferences. The fellow is expected to be independent, develop his or her own projects, supervise students and show an interest in approaches based on graph theory. In addition, he/she will have the opportunity to develop new skills, analyze large datasets, apply for grants and develop a wide network of collaborations. The ideal candidate should have the following qualities: - A PhD in neuroimaging, computational science, neuropsychology, physics, statistics or a related field; - Experience in statistical techniques, programming, or scripting; - Experience with structural MRI, DTI, fMRI or PET imaging analyses; - Clinical or research experience with aging and/or neurodegenerative disorders. - Excellent record of scientific publications. The Postdoctoral studies will be performed for 1 year, with possible extension for an additional year. There are also possibilities for a longer appointment after this 2-year period. To apply please go to: https://ki.varbi.com/what:job/jobID:305265/ For further information or general inquires, please contact Joana B. Pereira (joana.pereira(a)ki.se) Best wishes, Joana

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topological defect error
by Laurel Quinlan 05 Dec '19

05 Dec '19

External Email - Use Caution Hi Freesurfer Support, One of my colleagues receives the following error after running a recon: exited with errors: "excessive topologic defect encountered: could not allocate 289309485 edges for retessellation" I checked the inflated view and there does appear to be significant portions of the brain missing (however I cannot see this in 2D). I've attached a screenshot of the inflated view. How would I go about fixing the error? Thank you! Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Reporting Results in a three group analysis
by cody samth 05 Dec '19

05 Dec '19

External Email - Use Caution Hi, I have a statistical question about how to approach reporting results from FreeSurfer analyses containing three groups. I ran a group effect (F-test) and then post-hoc tests looking at pair-wise comparisons between the three groups. My question is why is that we run separate vertex-wise analyses for the post-hocs rather than extracting the values from significant clusters and running post-hocs in a statistical software for just the regions where a significance difference was found (ie the clusters)? As a post-hoc vertex wide analysis can lead to different results. For example in my group effect contrasts I found a cluster in the parietal lobe. Whereas in my post hoc-vertex wide analyses one of them found two clusters 1) within the parietal 2) within the frontal lobe. If I choose to run these post-hoc analyses via freesurfer (ie vertex-wise) rather than extracting the results to analyze in a statistical program, is it standard to report the second cluster? Even though it didn't come up in the group model? If so is there a paper that people reference that uses this approach? Thanks, Cody

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surfaceholes in aseg.stats
by Laurel Quinlan 05 Dec '19

05 Dec '19

External Email - Use Caution Hi Freesurfer Support, I'm wondering how ?h.surfaceholes prior to fixing and "Total number of defect holes in surfaces prior to fixing" are calculated in the aseg.stats file for each brain. I compared aseg.stats files for the same brain edited by two different people, and I noticed that there were different numbers of holes listed for each person, despite the brain being the same. For example: lhSurfaceHoles 130 vs 61 rhSurfaceHoles 102 vs 80 Total number of defect holes 232 vs 141 Why would those numbers be so different? Thanks, Laurel Quinlan Associate Research Specialist Center for Healthy Minds University of Wisconsin-Madison

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Multiple comparison using Monte Carlo
by Ting Li 05 Dec '19

05 Dec '19

External Email - Use Caution Dear Freesurfer Expert: I have used the simulation code as show below: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --cache 4 neg \ --cwp 0.05\ --2spaces My question is how many iterations are done during this simulation? I didn’t specify the iteration number. Why I didn’t have the csd file? Thanks a lot for your response! Best regards, Ting

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negative SUVr using PETsurfer
by miracle ozzoude 05 Dec '19

05 Dec '19

External Email - Use Caution Hello Experts, I ran the PETsurfer pipeline using AV45 pet and performed pvc using pons as reference point. When i looked at the gtm.stats.dat file for one of my subjects, the SUVr for right and left nucleus-accumbens areas were in the negative (left = -0.361; right = -0.046). This is strange because SUVR shouldn't be negative. How do i go about fixing this error? Below, is my pvc command. mri_gtmpvc --i pet.nii --reg register.lta --psf 6 --seg gtmseg.mgz --default--seg-merge --auto-mask PSF .01 --mgx .01 --o subject_gtmpvc --rescale 174 Thanks. Best, Paul

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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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