Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Intracranial electrode visualization in Freeview
by Kerezoudis, Panagiotis, M.D., M.S. 27 Mar '23

27 Mar '23

External Email - Use Caution Hi, I have completed the Freesurfer segmentation and parcellation in a patient that has intracranial electrodes. I also have the electrode locations in various file formats (tsv, nii and pom). Is there a way to visualize their location in Freeview and particularly in 3D? For example, for 2D I can easily do that with microGL. Thank you very much in advance! Best, Panos Kerezoudis

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mri_glmfit error - matrix ill-conditioned. no solution from archive.
by miracle ozzoude 27 Mar '23

27 Mar '23

External Email - Use Caution Hello, Any idea how to solve this problem? I have tried the suggested solutions on the archive, that's Demean and Rescale but to no avail. I have attached the necessary files in the email below. Many thanks, Miracle mri_glmfit command: mri_glmfit --y results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.thickness.10B.mgh --fsgd thickness_DHI_Emotional_edit.fsgd dods --C thickness_edit.mtx --surf fsaverage lh --cortex --glmdir results/wholebrain/lh.thickness_DHI_Emotional_edit.fsgd.glmdir

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cortical thickness and z-scores correlation
by Maria Czarnecka 27 Mar '23

27 Mar '23

External Email - Use Caution Dear Sisters and Brothers in neuroscience I am a huge fan but a very new user of the freesurfer, please treat me as such when answering this email. I have successfully performed anatomical and functional data analysis using fmriprep, freesurfer and fsfast. I have all the files needed, everything looks perfect. As a next step of my analysis I would like to perform a correlation of Cortical thickness and the functional activation in one of my contrasts (I would like to correlate the CT with the z-scores). I would like to do that separately for each subject and in ROIs (ideally, self-defined Rois, but if there is an easy way to do it in anatomical ones I will be very happy as well). What I need is for the program to take the z-score from each vertex in an ROI and the value of cortical thickness for each vertex and do the correlation on those values. I can also do the statistics in another tool (R), so simply extracting those values for vertices in an ROIs would be great. Do you have any suggestions how to do that? Best, Maria Czarnecka

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negative uptakes after GTM pvc correction
by Federica Di Antonio 27 Mar '23

27 Mar '23

External Email - Use Caution Dear experts, I report an answer you gave about some negative values avatar partial volume correction: "[...] Usually this only happens in small ROIs and/or low uptake regions. Why might the model not be perfect? It could be a number of things: 1. the MRI-PET registration is inaccurate 2. the MRI segmentation is inaccurate 3. the ideal segmentation is not reflected by the MRI segmentation (eg, one of the segmentations has a hot spot)" I wonder if it is possible for you to give me an hint about the reason why an inaccurate registration or segmentation can cause negative uptake values. At first sight it seemed intuitive to me, but on second thought that's not so obvious. I would be very grateful for any help! Federica Di Antonio

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mri_glmfit-sim error
by mariangela asimina 27 Mar '23

27 Mar '23

External Email - Use Caution Hello FreeSurfer developers and experts, I am trying to do cluster correction with mri_glmfit-sim after running mri_glmfit. The command I ran: mri_glmfit-sim --glmdir lh.volume.SCNStudyTest.10.glmdir --cache 3.0 abs --cwp 0.05 --2spaces produces the following error: ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 FreeSurfer version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b Operating System: Ubuntu 22.04.2 LTS Kernel: Linux 5.19.0-35-generic I have searched the archive and cannot find a similar error. I would appreciate your help. Mariangela Asimina I also ran the command with the --debug flag and I get the following output, but I'm afraid I can't interpret it: set echo = 1 ; breaksw breaksw end end while ( $#argv != 0 ) while ( 8 != 0 ) set flag = $argv[1] ; shift ; set flag = --glmdir shift switch ( $flag ) switch ( --glmdir ) if ( $#argv < 0 ) goto arg1err ; if ( 7 < 0 ) goto arg1err set glmdir = $argv[1] ; shift ; set glmdir = lh.volume.SCNStudyTest.10.glmdir shift breaksw breaksw end end while ( $#argv != 0 ) while ( 6 != 0 ) set flag = $argv[1] ; shift ; set flag = --cache shift switch ( $flag ) switch ( --cache ) if ( $#argv < 2 ) goto arg2err ; if ( 5 < 2 ) goto arg2err set thresh = $argv[1] ; shift ; set thresh = 3.0 shift set simsign = $argv[1] ; shift ; set simsign = abs shift set UseCache = 1 ; set UseCache = 1 set DoSim = 0 ; set DoSim = 0 set thresh = `echo $thresh | sed 's/,/./g'` set thresh = `echo $thresh | sed 's/,/./g'` sed s/,/./g echo 3.0 set thresh = `printf %2.1f $thresh` set thresh = `printf %2.1f $thresh` printf %2.1f 3.0 if ( $thresh != 1.3 && $thresh != 2.0 && $thresh != 2.3 && $thresh != 3.0 && $thresh != 3.3 && $thresh != 4.0 ) then if ( 3,0 != 1.3 && 3,0 != 2.0 && 3,0 != 2.3 && 3,0 != 3.0 && 3,0 != 3.3 && 3,0 != 4.0 ) then echo "ERROR: thresh = $thresh, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0" echo ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 ERROR: thresh = 3,0, must be 1.3, 2.0, 2.3, 3.0, 3.3, 4.0 exit 1 ; exit 1

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head in a bad position in scanner
by Aaron Tanenbaum 27 Mar '23

27 Mar '23

External Email - Use Caution We acquired some data this morning where the participant's head was in an unusual orientation. The participant has cervical dystonia. I have processed data like this before and freesurfer always fails. I am assuming Freesurfer is unable to register the image. I have not even run this image through freesurfer yet. Is there a way to deal with this without altering the image?

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longitudinal skullstrip issue
by KennethSPrice 27 Mar '23

27 Mar '23

External Email - Use Caution Hello all, I'm wondering if I can use brainmask or pial surface of timepoint1 as a reference for the skullstrip of timepoint2. TP2 is being problematic during skullstrip. I've tried -wsthresh and -gcut. Any option to use brainmask1 as a reference point for brainmask2? Sent with [Proton Mail](https://secure-web.cisco.com/1mDhhZToXGJnAuPW3XS4AmJXdzD8P3Gy61kty6fb… secure email.

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Unable to quantify FWHM, everything significant
by Yuri Yeshinsky 27 Mar '23

27 Mar '23

External Email - Use Caution Dear FreeSurfer experts, I ran many analyses on a large sample and everything goes well. However, I encounter here a problem I've never encountered before about one of my analyses. I'm looking at the presence of a difference in slope between three groups while covarying for several variables and classes. My contrasts are: contrast1: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 0 0 contrast2: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 0 0 -0.5 -0.5 contrast3: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 6 classes (gender 2, disease 3), so first 6 for intercepts, next 30 for the covariates 1 to 5, and the last columns to test the slope difference between the three groups on the variable I have used these contrasts to test the differences in slopes of several variables and I found significant clusters. However, for one variable specifically, mri_glmfit seems to be unable to quantify the FWHM from the data and when running mri_glmfit-sim, the resulting output, for every contrast (positive direction), gives a significant cluster where the whole cortex is included; see for contrast2 (it's the same result for every contrast anyways): yuri@rodonor:/lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13$ cat cache.th40.pos.sig.cluster.summary # Cluster Growing Summary (mri_surfcluster) # 7.3.2 # 7.3.2 # CreationTime 2023/03/16-13:19:18-GMT # cmdline mri_surfcluster --in lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/sig.mgh --mask lh.Cogn.moca.egfr.thickness.15.glmdir/mask.mgh --cwsig lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.cluster.mgh --sum lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.cluster.summary --ocn lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.masked.mgh --no-fixmni --csd-out lh.Cogn.moca.egfr.thickness.15.glmdir/csd/all.cache.th40.pos-Cogn-egfr-g13.csd --csd lab/yuri/FreeSurfer/average/mult-comp-cor/fsaverage/lh/cortex/fwhm01/pos/th40/mc-z.csd --csdpdf lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.pdf.dat --vwsig lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.voxel.mgh --vwsigmax lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.voxel.max.dat --oannot lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/cache.th40.pos.sig.ocn.annot --bonferroni 2 --surf white # cwd /lab/yuri/egfrproject # sysname Linux # hostname rodonor.bri.upall.sv # machine x86_64 # FixVertexAreaFlag 1 # FixSurfClusterArea 1 # # Input lh.Cogn.moca.egfr.thickness.15.glmdir/Cogn-egfr-g13/sig.mgh # Frame Number 0 # srcsubj fsaverage # hemi lh # surface white # group_avg_surface_area 82220 # group_avg_vtxarea_loaded 1 # annot aparc # SUBJECTS_DIR /lab/yuri/egfrproject # SearchSpace_mm2 74258.8 # SearchSpace_vtx 144277 # Bonferroni 2 # Minimum Threshold 4 # Maximum Threshold infinity # Threshold Sign pos # AdjustThreshWhenOneTail 1 # CW PValue Threshold: 0.05 # Area Threshold 0 mm^2 # CSD thresh 4.000000 # CSD nreps 10000 # CSD simtype null-z # CSD contrast NA # CSD confint 90.000000 # Overall max 1e+10 at vertex 0 # Overall min 0 at vertex 8 # NClusters 1 # FixMNI = 0 # # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs WghtVtx Annot 1 10000000000.0000 0 74258.42 -36.8 -18.3 64.5 0.00020 0.00000 0.00040 144276 1442760045363200.00 precentral I feel that something is wrong in there, unless you think that it is possible that the slope difference manifests as a global effect for every contrast. It really seems to happen to happen specifically with this variable, as when replacing this variable by another, I can generate specific clusters that do not cover the whole cortex. Here is the terminal output from mri_glmfit when I run it on my "problematic" variable: yuri@rodonor:/lab/yuri/egfrproject$ mri_glmfit --y lh.Cogn.moca.egfr.thickness.15.mgh --fsgd analysis/egfr-Cogn-moca-egfr.fsgd dods --C analysis/Cogn-egfr-g12.mtx --C analysis/Cogn-egfr-g13.mtx --C analysis/Cogn-egfr-g23.mtx --surf fsaverage lh --cortex --glmdir lh.Cogn.moca.egfr.thickness.15.glmdir gdfRead(): reading analysis/egfr-Cogn-moca-egfr.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 60.1017 7.57085 1 Bmi 26.8664 4.97535 2 FRS 10.9088 9.29652 3 wm 1642.17 1761.49 4 educ 3.48198 0.959607 5 moca 27.2733 2.25488 Class Size and Means of each Continuous Variable 1 g1gender0 324 57.7939 25.8998 5.0538 1164.8920 3.4753 27.6883 2 g1gender1 309 58.2326 27.0854 14.3098 1722.7615 3.4822 26.9450 3 g2gender0 311 61.0777 26.8550 6.1809 1492.9781 3.4084 27.6785 4 g2gender1 345 62.4106 27.2979 16.8165 2059.6704 3.5391 26.8986 5 g3gender0 20 63.1610 27.9590 6.8020 1252.0200 3.4500 27.4000 6 g3gender1 23 67.2335 30.2713 26.5796 3377.0609 3.7391 25.8696 INFO: gd2mtx_method is dods Reading source surface /lab/yuri/FreeSurfer/fsaverage/surf/lh.white Number of vertices 163842 Number of faces 327680 Total area 65417.000000 AvgVtxArea 0.399269 AvgVtxDist 0.721953 StdVtxDist 0.195472 7.3.2 cwd /lab/yuri/egfrproject cmdline mri_glmfit --y lh.Cogn.moca.egfr.thickness.15.mgh --fsgd analysis/egfr-Cogn-moca-egfr.fsgd dods --C analysis/Cogn-egfr-g12.mtx --C analysis/Cogn-egfr-g13.mtx --C analysis/Cogn-egfr-g23.mtx --surf fsaverage lh --cortex --glmdir lh.Cogn.moca.egfr.thickness.15.glmdir sysname Linux hostname rodonor.bri.upall.sv machine x86_64 user yuri FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.mgh logyflag 0 usedti 0 FSGD analysis/egfr-Cogn-moca-egfr.fsgd labelmask /lab/yuri/FreeSurfer/fsaverage/label/lh.cortex.label maskinv 0 glmdir lh.Cogn.moca.egfr.thickness.15.glmdir IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory lh.Cogn.moca.egfr.thickness.15.glmdir Loading y from /lab/yuri/egfrproject/lh.Cogn.moca.egfr.thickness.15.mgh ... done reading. INFO: gd2mtx_method is dods Saving design matrix to lh.Cogn.moca.egfr.thickness.15.glmdir/Xg.dat Computing normalized matrix Normalized matrix condition is 6285.08 Matrix condition is 8.72285e+09 Found 149955 points in label. Pruning voxels by thr: 1.175494e-38 Found 144277 voxels in mask Saving mask to lh.Cogn.moca.egfr.thickness.15.glmdir/mask.mgh Reshaping mriglm->mask... search space = 71879.345725 DOF = 1290 Starting fit and test Fit completed in 28.4991 minutes Computing spatial AR1 on surface WARNING: ar1 = 0 <= 0. Setting fwhm to 0. Residual: ar1mn=0.000000, ar1std=0.000000, gstd=0.000000, fwhm=0.000000 Writing results Cogn-egfr-g12 maxvox sig=1e+10 F=0 at index 0 0 0 seed=1679933797 Computing efficiency Cogn-egfr-g13 maxvox sig=1e+10 F=0 at index 0 0 0 seed=1679933797 Computing efficiency Cogn-egfr-g23 maxvox sig=1e+10 F=0 at index 0 0 0 seed=1679933797 Computing efficiencymri_glmfit done Many thanks, Yuri

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Structural covariance contrasts
by mariangela asimina 27 Mar '23

27 Mar '23

External Email - Use Caution Dear experts, I am looking into the covariance of the volume of subcortical structures with cortical vertex-wise volume, comparing between two groups, correcting for the effects of gender, age and eTIV. My approach was to extract the volume of a subcortical region from the aseg.stats file and add it as a covariate into the FSGD and Contrasts files. My FSGD therefore is in the form Class HCm Class HCf Class SZm Class SZf variables age eTIV L-ThaVol I have normalized all continuous variables, and have 12 different FSGD files, one for each subcortical area of interest My Contrasts matrix, to test for differences in volume covariance between HC and SZ in either slope or intercept, is the following (16 regressors): 0.5 0.5 -0.5 -0.5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5 Is this the right approach, and if yes is the contrast matrix correct? Or is there a way to do test for structural covariance through FreeSurfer commands? I would appreciate any help! Mariangela

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Pass code
by Santiago Gómez 26 Mar '23

26 Mar '23

External Email - Use Caution Dear professors, I have downloaded the FreeSurfer Vitrual VM images for my research project and a pass code is needed for this 7z archieve. Would you please send me the pass code for FS_7_2_0_ubuntu_18_04_06.ova.7z<https://secure-web.cisco.com/1MlcuMSSiFoTx0GjyrQW1D_iGKohpLuJFfWKiIEF3BcSo-…> ? I really appreciate it. Greetings, Santiago Gómez Castro, MD Neurosurgeon Universidad Nacional de Colombia Cel. +57 316 623 69 00 -- *Aviso legal:* El contenido de este mensaje y los archivos adjuntos son confidenciales y de uso exclusivo de la Universidad Nacional de Colombia. Se encuentran dirigidos sólo para el uso del destinatario al cual van enviados. La reproducción, lectura y/o copia se encuentran prohibidas a cualquier persona diferente a este y puede ser ilegal. Si usted lo ha recibido por error, infórmenos y elimínelo de su correo. Los Datos Personales serán tratados conforme a la Ley 1581 de 2012 y a nuestra Política de Datos Personales que podrá consultar en la página web http://secure-web.cisco.com/1GYOl7UuM7xf4ZhF71VSWMCVhFZCYuelWuXbjcGXGyzHOiT… <http://secure-web.cisco.com/1cYNL9a6ejl6w7JEp3F7zG0n1PylzIv5VwhJqbX6n3ZCuIX…>.* *Las opiniones, informaciones, conclusiones y cualquier otro tipo de dato contenido en este correo electrónico, no relacionados con la actividad de la Universidad Nacional de Colombia, se entenderá como personales y de ninguna manera son avaladas por la Universidad.

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