Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

Grey matter excluded from pial surface
by Borges Pereira Ines Isabel 14 Jan '19

14 Jan '19

External Email - Use Caution Dear FreeSurfer developers, I am trying to obtain adequate pial surface boundaries. Unfortunately, on a few subjects, some grey matter is being excluded from the pial surface, at the temporal pole. I have attempted to solve this problem by adding control points and adding voxels on the wm.gz volume, so as to have FreeSurfer first update the wm boundary and then hopefully the pial surface. As you can see on the attached images, the control points were only partially taken into account and the pial surface was not updated. It would be great to get your support in understanding why this is happening. I am using the following Freesurfer version on Centos: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thanks! Best regards, Inês Pereira [cid:3140210C-B81A-431D-92FC-E5BD9026A4CE@ethz.ch][cid:36204321-D704-4182-A1A8-B43F8CE27A4F@ethz.ch]

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DKT vs. DK Freesurfer atlases
by Gabor Perlaki 11 Jan '19

11 Jan '19

Dear all, I've found an article comparing DK and DKT atlas based automatic segmentations to manual labels (Klein and Tourville, Front Neurosci. 2012; 6:171, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3514540/) It seems that using DKT40 works better than DK in most of the cortical regions (based on Dice). Does anybody know that the DKTatlas related results created by Freesurfer (e.g. aparc.DKTatlas+aseg.mgz, lh.aparc.DKTatlas.stats) are based on the same DKT40 atlas used in the article and whether the DKT40 atlas related results were also created by Freesurfer in the article by Klein and Tourville? Are the Freesurfer created results in lh.aparc.DKTatlas.stats generally more reliable than the results in lh.aparc.stats? -- Gabor Perlaki research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-30-2084367 E-mail: petzinger.gabor(a)gmail.com

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LME
by Tefera, Getaneh B 07 Jan '19

07 Jan '19

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g0 : 0 1 0 0 0 0 The slope of g1: 0 1 0 1 0 0 The slope of g2: 0 1 0 0 0 1 The slope difference between g0 and g1: 0 0 0 1 0 0 The slope difference between g0 and g2: 0 0 0 0 0 1 The slope difference between g1 and g2: 0 0 0 -1 0 1 1) Is this contrast matrix correct to observe pairwise slope difference? In the tutorial the contrast matrix C = [zeros(3,3) [1 0 0 0 0; -1 0 1 0 0; 0 0 -1 0 1] zeros(3,6)] 2) Is it necessary to combine contrast matrix of the pair difference the same as the tutorial? If so, my contrast matrix can be C=[0 0 0 1 0 0; 0 0 0 -1 0 1] 3) How can we interpret the result for this contrast matrix? 4) How can I obtain B1, B2, ... ? [sz1,sz2] = lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,... dr,pw,alpha,gr_pr) 5) For sample size calculation how can I get Dhat ( Estimated random effects covariance matrix) and phisqhat (Estimated intra-subject variability)? With regards Getaneh

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[PETsurfer] Use of MGX and RBV partial volume correction
by Matthieu Vanhoutte 07 Jan '19

07 Jan '19

External Email - Use Caution Dear Freesurfer's experts, I tried to use PETSurfer to correct partial volume effect on my FDG PET images, testing both Muller-Gartner and RBV corrections. I ran the commands specified in PETSurfer website and used the two following commands for both MGX and RBV corrections respectively: mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o ./gtmpvc.output mri_gtmpvc --i PET.nii.gz --reg register.dof6.lta --psf-col 5.51 --psf-row 5.51 --psf-slice 5.9 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --rbv --o rbv.output.orig 1) However, I found that cortical output mgx.ctxgm.nii.gz of MGX correction encompass more than just GM and values at the boundaries of mgx.ctxgm.nii.gz seem to me very high or aberrant. 2) Concerning RBV correction, output rbv.nii.gz seems to me following more precisely the GM ribbon. However contrary to what is said in PETSurfer website, rbv.nii.gz seems to be in the anatomical space (not in native PET) at the resolution of gtmseg.mgz. How then map rbv.nii.gz to the anatomical space when mapping the volume to the surface ? 3) What are the advantages/inconveniences of RBV vs GMX ? 4) Would it be beneficial to upsample native PET to the anatomical resolution before launching gtmpvc in order to preserve the high resolution of the anatomical tissues during partial volume correction ? Could you have a look at and give me back your opinion on these questions ? I could send the associated files if needed. Thank you. Best, Matthieu

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Longitudinal stream : LME and limits of model
by Matthieu Vanhoutte 14 Dec '18

14 Dec '18

Dear Freesurfer’s experts, I would have some questions regarding the LME model to be used in longitudinal stream: 1) Which are the ratio limits or % of missing timepoints accepted ? (according time, I have less and less subjects time points) 2) Is it possible to include patients that would miss the first timepoint but got the others ? 3) Considering a group in longitudinal study, which is the number of subjects minimal of this group accepted for LME modeling ? 4) Finally, concerning quality control and among a big number of total time points, which essential controls are necessary ? (Control of norm.mgz of the base, alignment of longitudinal timepoints on base,… ?) Best regards, Matthieu

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Longitudinal Stream - LONG step
by Figueiro Longo, Maria Gabriela 14 Dec '18

14 Dec '18

Hello FreeSurfer Developers, I'm attempting to run the longitudinal stream, but in the [LONG] step of one time-point of on of my subjects, I have the following error: MRInormInit(): INFO: Modifying talairach volume c_(r,a,s) based on average_305 MRInormalize(): MRIsplineNormalize(): npeaks = 11 Starting OpenSpline(): npoints = 11 MRInormFindControlPoints: could not find enough control points building Voronoi diagram... performing soap bubble smoothing, sigma = 8... Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 No such file or directory MRInormFindControlPoints failed No such file or directory The segmentation of the this time-point for this subject ([CROSS] step) looks good and I couldn't find any error. I didn't find any similar error in the email list. Does anyone have any thoughts on how to trouble-shoot this one? I attached the recon-all.log. FS version: freesurfer-linux-centos7_x86_64-dev-20181130-24625d8 Thanks, Gabriela

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longitudinal analyses after lesion segmentation
by kathleen Gerbino 14 Dec '18

14 Dec '18

External Email - Use Caution Hi FreeSurfer experts: I hope you are well. I need to segment quite a few longitudinal T1 scans from patients with multiple sclerosis. A colleague has applied an automated lesion segmentation algorithm to segment and fill the lesions. During this process, the follow-up scans were registered to the baseline scan. My question is whether I could still apply the Freesurfer longitudinal pipeline to these images or whether your had any recommendations on the appropriate steps to take if this is not appropriate. Kind regards, Kathleen

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segmentHA_T1 error DYLD_LIBRARY_PATH
by Jaime Gomez 13 Dec '18

13 Dec '18

External Email - Use Caution Hi, I have this error when I try to run segmentHA_T1.sh It seems that it sets up the wrong DYLD_LIBRARY_PATH, the one I have in my bash_profile is /Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64:/Applications/MATLAB_R2016a.app/bin/maci64:/Applications/MATLAB_R2016a.app/sys/os/maci64: [~/val...V/003_SAG_3D_IR] $ segmentHA_T1.sh sujeto_uno #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Tue Oct 30 12:04:16 CET 2018 ------------------------------------------ Setting up environment variables --- DYLD_LIBRARY_PATH is .:/Applications/freesurfer/MCRv84//runtime/maci64:/Applications/freesurfer/MCRv84//bin/maci64:/Applications/freesurfer/MCRv84//sys/os/maci64: dyld: Library not loaded: @loader_path/libmwmclmcrrt.8.0.dylib Referenced from: /Applications/freesurfer/bin/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML Reason: image not found /Applications/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 38: 7887 Abort trap: 6 "${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML.app/Contents/MacOS/segmentSubjectT1_autoEstimateAlveusML $args #-------------------------------------------- --

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Overall maxima is high and still no significant cluster
by Martin Juneja 06 Dec '18

06 Dec '18

External Email - Use Caution Hi FS experts, I am estimating the group-behavioral thickness interaction using contrast 2 FSGD file: https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf2G2V at CFT < 0.01 and CWT < 0.05 at FWHM of 12 mm. I do not find any significant clusters and my output summary text file looks like the following. This file shows that overall maxima is 4.58212 (which corresponds to p < 0.0001 because -log (0.0001) = 4, so I am just wondering despite the fact that maxima is > 4, why I do not see this cluster in the summary/output *.mgh file? I would really appreciate any clarification and tips to modify my input thresholds so that I do not miss any significant findings here. Thanks. ----------------------------- # SearchSpace_mm2 76467.1 # SearchSpace_vtx 149953 # Bonferroni 2 # Minimum Threshold 2 # Maximum Threshold infinity # Threshold Sign abs # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 2.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 4.58212 at vertex 10608 # Overall min -2.84277 at vertex 75476 # NClusters 0 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot

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Surface based paired t test
by john Anderson 06 Dec '18

06 Dec '18

External Email - Use Caution Dear Freesurfer experts, I would like to run surface based paired t test of PET data on surface. For every subject I have visit pre treatment and post treatment. I tried to follow the instructions here https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis but the toturial seems to be for cortical thickness data. How can i modify the command mris_preproc to do paired test of PEt data on brain surface mris_preproc --target fsaverage --hemi lh \ --meas thickness --out lh.paired-diff.thickness.mgh \ --fsgd pairs.fsgd --paired-diff thanks for any suggestion John

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Freesurfer November 2018