Freesurfer July 2022

freesurfer@nmr.mgh.harvard.edu

90 participants
122 discussions

How should I use fslreoient2std?
by Arman Avesta 17 Jul '22

17 Jul '22

External Email - Use Caution Hi gang, I want to use fslreorient2std to reorient my NIfTI files in the standard MNI format. I tried: fslreorient2std T1.mgzfslreorient2std -file T1.mgzfslreorient2std --file T1.mgz but none of them worked. And I cannot find any documentation online that explains how I can use this command. I would appreciate your help for telling me how I can use this command. Best,Arman

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Surface-based vertex-wise analysis of two imaging outcomes
by Silva Rudberg, Jason 17 Jul '22

17 Jul '22

External Email - Use Caution Hello Freesurfers, I am trying to conduct a vertex-wise comparison of diffusion MRI and PET data. I know how to do group vertex-wise comparisons for one imaging outcome (ie. vertex-wise comparison of a diffusion MRI outcome between two groups). Is this type of analysis comparing the vertex values of multiple imaging outcomes possible in Freesurfer? Thank you! Jason

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CC mask in ASEG calculations
by Ramtilak Gattu 17 Jul '22

17 Jul '22

External Email - Use Caution Hello all, We built a CC mask with 3 segments ( Genu, body and Splenium) and made it a part of the existing ASEG.mgz in "fsaverage" folder. Would like to incorporate this shown Corpus Callosum (CC) mask into aseg calculations replacing the existing inbuilt CC 5 segments. What is the best way to do it? We replaced the original aseg.mgz in fsaverage folder with our aseg.mgz that has whole CC with 3 segments and re-ran the recon-all but still we got the same old results. We even tried the mri_cc (mri_cc -aseg aseg.mgz -o aseg.auto_CCseg.mgz sub_01) where aseg.mgz is the aseg.mgz with new CC but still we got the same old results. Does this new aseg.mgz should be a part of labels file in "rb_xxx_xx.gca" ? If so can it be done by extracting the old "rb_xxx_xx.gca" file with mriconvert and add this aseg_CC and rebuild a new .gca file? Can mriconvert create a gca file? Please advice. Thanks Regards Tilak

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mri_vol2surf error
by Rachel Wagner 17 Jul '22

17 Jul '22

External Email - Use Caution Hello everyone, I am trying to display my lesion map I created in Matlab on a cortical surface, and am getting the following error: developer@developer-VirtualBox:~$ mri_vol2surf --mov rReslice_Combined_roi_meanRD.nii --mni152reg --trgsubject fsaverage --hemi lhrh --out lh_spm.mgh --projfrac-max 0 1 .1 srcvol = rReslice_Combined_roi_meanRD.nii srcreg = /usr/local/freesurfer/7.2.0/average/mni152.register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lhrh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat -------- original matrix ----------- 0.99753 -0.00732 0.01760 0.95709; -0.01296 -0.00926 0.99706 -17.81596; -0.01460 -1.00094 0.00244 -18.54964; 0.00000 0.00000 0.00000 1.00000; -------- original matrix ----------- Reading surface /usr/home//fsaverage/surf/lhrh.white error: No such file or directory error: MRISread(/usr/home//fsaverage/surf/lhrh.white): could not open file error: No such file or directory error: mri_vol2surf: could not read surface /usr/home//fsaverage/surf/lhrh.white Could anyone help me fix this? I am very new to this software and need to have this results ready for my supervisor if possible! Thank you, Rachel

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Re: [Freesurfer] FW: How to project SPM image
by Douglas N. Greve 17 Jul '22

17 Jul '22

First, what is rReslice_Combined_roi_meanRD.nii? How was it created? If that is you lesion map, then it is not the right input to BBR. I can't remember, but if the AAL is in the MNI152 space, then it will be easier to just run recon-all on the MNI152 ( or whatever the atnatomical reference is for the AAL). You can then just run mri_vol2surf using --regheader and skip BBR. You may have to play with some of the options (eg, projection fraction) On 7/5/2022 2:08 PM, Rachel Wagner wrote: > > External Email - Use Caution > > Hello Dr. Greve, > > I hope this finds you well! I am currently working on displaying my > SPM overlay on a 3D brain volume in FreeSurfer (email below). Dr. > Fischl mentioned you may know the command line to do so – I hope this > isn’t a bother, I know you must be quite busy – totally understood if > you don’t have the time. > > So far, I have the following: > > bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated > -overlay --s fsaverage \ --init-rr --lta register.lta > > I am hoping to smooth out the surface and change the coloring to > ultimately export a heatmap image from FreeSurfer that looks something > like this. > <https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXS…> > > Would you have any suggestions for how I should alter my code? > > Thank you very much in advance – no problem again if you don’t have > the time! > > > Kind Regards, > > Rachel Wagner > > *From: *Fischl, Bruce <mailto:BFISCHL@mgh.harvard.edu> > *Sent: *July 5, 2022 9:34 AM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > Hi Rachel > > I’ll leave bbreg command lines to others (Doug?), but in general you > don’t want to base the registration on the inflated since it doesn’t > have a meaningful location within the volume. I would use the standard > bbreg command, then use mri_vol2surf to paint what you want onto the > surface. Once it is on any surface for a subject you should be able to > display it on any other surface for that same subject (and same > hemisphere). > > Cheers > > Bruce > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Tuesday, July 5, 2022 12:17 AM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thank you, that would work very well! I’m trying this code without > success, am I missing a component to display on an inflated surface? > > bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated > -overlay --s fsaverage \ --init-rr --lta register.lta > > *From: *Fischl, Bruce <mailto:BFISCHL@MGH.HARVARD.EDU> > *Sent: *July 4, 2022 3:45 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > Well you can display it on inflated surfaces instead of white ones, > which will remove most of the folds. Then you can smooth the surface > overlay however you like (the colors on the surface) in freeview > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Monday, July 4, 2022 3:27 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thank you, noted! > > I think I am on the right track, but I’d like to smooth the surface > out (particularly the coloring and the sulci, which are quite deep) > considerably – is there any way for me to do that? > > *From: *Fischl, Bruce <mailto:BFISCHL@mgh.harvard.edu> > *Sent: *July 3, 2022 7:44 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > I see, and what’s wrong with the screen shot you have? (and “Bruce” is > fine). > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Sunday, July 3, 2022 7:41 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Hi Dr. Fischl, > > My apologies, I don’t have much of a background in software generally! > > For the SPM image, I used the AAL atlas to label lesioned brain > regions and colored by frequency to generate the heatmap. Image > dimensions: 1x1x1, Image Size [91 109 91], Pixel Dimensions [2 2 2], > Bits Per Pixel: 32. I will map onto fsaverage! > > I’m hoping to display it as a heatmap on an average surface, to look > something like this: *MailScanner has detected a possible fraud > attempt from "secure-web.cisco.com" claiming to be* | Decreased > functional connectivity from Wernicke's area homologue in... | > Download Scientific Diagram (researchgate.net) > <https://secure-web.cisco.com/1oOMXS4Xcve-ZJ8PxylSUuZevRGR5aotHueMxgJxcMGkXS…> > > This is a screenshot of what I currently have within FreeSurfer: > *MailScanner has detected a possible fraud attempt from > "secure-web.cisco.com" claiming to be* > https://drive.google.com/file/d/150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD/view?usp=… > <https://secure-web.cisco.com/117ePUqDOWTzA8pswn-Mibsr2qBEZIMKV-Yd9P886w1Gz_…> > > Thank you very much again for your help! > > Rachel > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Fischl, Bruce > <BFISCHL(a)mgh.harvard.edu> > *Sent:* Sunday, July 3, 2022 6:37:42 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > Can you give us more details? How did you create the > rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are > you trying to display it? On an average surface? Why are you mapping > it to bert and not fsaverage? > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Sunday, July 3, 2022 6:26 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Hello Dr. Fischl, thank you for your reply, it is much appreciated. > > I am trying to cortically project my spm lesion location/frequency > map, according to instructions linked here: > AnalyzingData/MNE_SPM2Freesurfer - Meg Wiki (cam.ac.uk) > <https://secure-web.cisco.com/1Qq-eLDAcZvkiA1oj8V5IkWowioqEfn5og-amJx-SY4k1i…> > > I have used the following code: bbregister --mov > rReslice_Combined_roi_meanRD.nii --bold \ --s bert \ --init-rr --lta > register.lta > > However, my results still look very grainy. Is there a better way to > do this? > > Thank you again, > > Rachel Wagner > > *From: *Fischl, Bruce <mailto:BFISCHL@mgh.harvard.edu> > *Sent: *June 30, 2022 9:09 PM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > Can you summarize what you are trying to do? What kind of overlay are > you trying to visualize and what exactly do you mean by a “3D image”? > > *From:*freesurfer-bounces@nmr.mgh.harvard.edu > <freesurfer-bounces(a)nmr.mgh.harvard.edu> *On Behalf Of *Rachel Wagner > *Sent:* Thursday, June 30, 2022 2:48 PM > *To:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > *Subject:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thank you so much for your response – I’m a master’s student and am > really struggling - I’ve been stuck trying to do this for about 2 > weeks now, so the help is so appreciated! > > My results look very grainy in mricron so my supervisor wants me to > keep trying in FreeSurfer unfortunately for me. > > I uploaded a the brain.mgz volume in freeview, but I’m not sure how to > add an overlay and project as a 3D image. Would you happen to have any > ideas? > > Thank you so, so much again, > > Rachel Wagner > > *From: *niels.foit(a)gmx.de > *Sent: *June 30, 2022 2:35 PM > *To: *'Freesurfer support list' <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > > > > You don't often get email from niels.foit(a)gmx.de > <mailto:niels.foit@gmx.de>. Learn why this is important > <https://secure-web.cisco.com/1IGyjHfcGxatghbnnU4QrmkjiCFhtGpKgDShLha5LYdEXD…> > > > > Sure is, through freeview, however if you already have spm format > files, it is much easier to use mricron > > *Von:*freesurfer-bounces@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>> *Im Auftrag von > *Rachel Wagner > *Gesendet:* Donnerstag, 30. Juni 2022 18:18 > *An:* Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > *Betreff:* Re: [Freesurfer] How to project SPM image > > * External Email - Use Caution * > > Thanks very much, I will absolutely do so! Just so I know – is there > not any way of generating such figures in Freesurfer? > > *From: *niels.foit(a)gmx.de > *Sent: *June 30, 2022 4:47 AM > *To: *Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu> > *Subject: *Re: [Freesurfer] How to project SPM image > > > > > You don't often get email from niels.foit(a)gmx.de > <mailto:niels.foit@gmx.de>. Learn why this is important > <https://secure-web.cisco.com/1i1UJeVjwlumrCAM-yAFlTcIKRz-AyoK3nEvXbthMrwntc…> > > > > * External Email - Use Caution * > > Rachel, these figures were likely created with a software called > mricron, not freesurfer. Check it out :) > > Holen Sie sich Outlook für Android > <https://secure-web.cisco.com/1XvY3sA4-dRCvGWfgKiNWJHfOTGrrzAnDZB_-8JrFkF7ZC…> >

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Help with FreeSurfer Tutorial FsFast Group Level
by Tchir, Sophia Mae 17 Jul '22

17 Jul '22

Hello, I've been trying to go through the FreeSurfer tutorials from the FreeSurfer wiki website (FsFastTutorialV6.0/FsFastGroupLevelPerm - Free Surfer Wiki (harvard.edu)<https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV6.0/FsFastGroupLev…>, but I've run into a roadblock with the FsFast Group Level tutorial. I have this version of FreeSurfer: /FreeSurfer/6.0.1-centos6_x86_64 and I'm trying to run it remotely through NoMachine on this system: My issue is with step 3.2: Correcting for Multiple Comparisons. [cid:8a8a9d8a-afaf-420d-8092-2525282e7e16] When I try to run "mri_glmfit-sim" I keep getting told that the included tag "--perm" is unrecognized. [cid:e82f076f-dc27-4767-90c9-8c4fc2603831] Running the help flag for "mri_glmfit" has not been helpful, as I do not see the flag in the information provided. Perm is mentioned here, but i'm not sure how to use this information. Do you have any recommendations for what to do? Is it an issue with my version of freesurfer? Thank you, Sophia Sophia Tchir Clinical Research Coordinator | MGH IASLab | Northeastern University

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Ubuntu 18.04.06 archive pass code
by Bevan Roberts 17 Jul '22

17 Jul '22

External Email - Use Caution Request for the pass code for FS_7_2_0_Ubuntu_18_04_06.ova.7z

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Expand Zip file
by David Bjanes 17 Jul '22

17 Jul '22

External Email - Use Caution Hi all, Trying to get open the *.zip file to install a Windows VM to run FreeSurfer. I need a passcode to extract the contents of the Ubuntu VM. Anyone know what that is? Thanks! David ****************************** David Bjånes, Ph.D. Neilsen Foundation Fellow Andersen Lab Caltech

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mri_robust_template - MyMatrix::RotationMean Error
by Andrew Beaudin 16 Jul '22

16 Jul '22

External Email - Use Caution Hello Freesurfer Experts, I am trying to use mri_robust_template (with its default 6 DOF registration) outside of the Freesurfer longitudinal pipeline to generate within-participant T1 templates from 2 time points. Unfortunately, I am coming up against a 'MyMatrix::RotationMean input(s) not rotation' error on images acquired on our GE 3T Discovery 750 system, but not our colleagues' Seimens 3T Prisma images. I have pasted the output from the --debug flag below (3rd row from bottom is the MyMatrix::RotationMean message). Briefly: - the images I am using are skull-stripped niftis. - I am running Freesurfer 6.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) on a WSL2 Ubuntu 18.04 installation. - the call is: mri_robust_template --mov 2001A_T1o_brain.nii.gz 2001B_T1o_brain.nii.mgz --lta 2001A2template.lta 2001B2template.lta --average 1 --template 2001_template.nii.gz --satit - I have tried the following with no success: 1) using the --iscale flag - same result as shown below. 2) using --inittp 0 - results in a 'Segmentation fault' 3) using --average 0 - same result as shown below 4) using Freesurfer v7.2 - same result as below 5) running mri_robust_template call on Catalina and Big Sur systems with FS v6.0 - same result as below. Currently, the only way to get mri_robust_template to work with our GE images is to run it with the --affine flag. I would prefer to use the rigid body registration but am at a loss for why these images are failing using the rigid body registration is failing. Any help/insights/recommendations are greatly appreciated. Thank you very much. Andrew ---- Andrew Beaudin, PhD | Postdoctoral Scholar University of Calgary | Cumming School of Medicine Department of Clinical Neurosciences HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1 Phone: (403) 210-6273 DEBUG REPORT: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ --mov: Using 2001A_T1o_brain.nii.gz as movable/source volume. --mov: Using 2001B_T1o_brain.nii.gz as movable/source volume. Total: 2 input volumes --lta: Will output LTA transforms --average: Using method 1 for template computation. --template: Using 2001_template.nii.gz as template output volume. --satit: Will estimate SAT iteratively! --debug: Will output debug info and files! reading source '2001A_T1o_brain.nii.gz'... converting source '2001A_T1o_brain.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '2001B_T1o_brain.nii.gz'... converting source '2001B_T1o_brain.nii.gz' to bspline ... MRItoBSpline degree 3 Will use TP 2 as random initial target (seed 108242 ). MultiRegistration::initializing Xforms (init 2 , maxres 0 , iterate 5 , epsit 0.01 ) : MultiRegistration Parameters Outdir: ./ TransOnly: false Rigid: true Robust: true Satit: true Iscale: false IscaleOnly: false NoMulti: false SubsampleSize: -1 HighIt: -1 FixVoxel: false KeepType: true Average: 1 DoublePrec: false BackupWeights: false SampleType: 5 CRASCenter: false Debug: 1 [init] ========================= TP 1 to TP 2 ============================== Register TP 1 ( 2001A_T1o_brain.nii.gz ) to TP 2 ( 2001B_T1o_brain.nii.gz ) Registration::setSourceAndTarget(MRI s, MRI t, keeptype = TRUE ) Type Source : 3 Type Target : 3 keeping type Mov: (1, 1, 1)mm and dim (176, 256, 256) Dst: (1, 1, 1)mm and dim (176, 256, 256) Asserting both images: 1mm isotropic - no Mov reslice necessary - no Dst reslice necessary Registration::findSaturation - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 3 ) - Build Gaussian Pyramid ( Limits min steps: 0 max steps: 3 ) - Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter: -- Iteration: 1 trying sat: 16 min sat: 16 ( 0.729941 ), max sat: 0 ( -1 ), sat diff: -16, (wlimit=0.16) -- Iteration: 2 trying sat: 32 min sat: 32 ( 0.713406 ), max sat: 0 ( -1 ), sat diff: -32, (wlimit=0.16) -- Iteration: 3 trying sat: 64 min sat: 64 ( 0.692689 ), max sat: 0 ( -1 ), sat diff: -64, (wlimit=0.16) -- Iteration: 4 trying sat: 128 min sat: 128 ( 0.666858 ), max sat: 0 ( -1 ), sat diff: -128, (wlimit=0.16) -- Iteration: 5 trying sat: 256 min sat: 256 ( 0.637119 ), max sat: 0 ( -1 ), sat diff: -256, (wlimit=0.16) -- Iteration: 6 trying sat: 512 min sat: 512 ( 0.591624 ), max sat: 0 ( -1 ), sat diff: -512, (wlimit=0.16) -- Iteration: 7 trying sat: 1024 min sat: 1024 ( 0.550606 ), max sat: 0 ( -1 ), sat diff: -1024, (wlimit=0.16) -- Iteration: 8 trying sat: 2048 min sat: 2048 ( 0.485668 ), max sat: 0 ( -1 ), sat diff: -2048, (wlimit=0.16) -- Iteration: 9 trying sat: 4096 min sat: 4096 ( 0.370434 ), max sat: 0 ( -1 ), sat diff: -4096, (wlimit=0.16) -- Iteration: 10 trying sat: 8192 min sat: 8192 ( 0.19981 ), max sat: 0 ( -1 ), sat diff: -8192, (wlimit=0.16) -- Iteration: 11 trying sat: 16384 min sat: 8192 ( 0.19981 ), max sat: 16384 ( 0.0606314 ), sat diff: 8192, (wlimit=0.16) -- Iteration: 12 trying sat: 12288 min sat: 8192 ( 0.19981 ), max sat: 12288 ( 0.103499 ), sat diff: 4096, (wlimit=0.16) -- Iteration: 13 trying sat: 10240 min sat: 8192 ( 0.19981 ), max sat: 10240 ( 0.142423 ), sat diff: 2048, (wlimit=0.16) -- Iteration: 14 trying sat: 9216 min sat: 9216 ( 0.16727 ), max sat: 10240 ( 0.142423 ), sat diff: 1024, (wlimit=0.16) -- Iteration: 15 trying sat: 9728 min sat: 9216 ( 0.16727 ), max sat: 9728 ( 0.155264 ), sat diff: 512, (wlimit=0.16) -- Iteration: 16 trying sat: 9472 min sat: 9472 ( 0.160488 ), max sat: 9728 ( 0.155264 ), sat diff: 256, (wlimit=0.16) -- Iteration: 17 trying sat: 9600 min sat: 9472 ( 0.160488 ), max sat: 9600 ( 0.157199 ), sat diff: 128, (wlimit=0.16) -- Iteration: 18 trying sat: 9536 min sat: 9472 ( 0.160488 ), max sat: 9536 ( 0.159131 ), sat diff: 64, (wlimit=0.16) -- Iteration: 19 trying sat: 9504 min sat: 9472 ( 0.160488 ), max sat: 9504 ( 0.159604 ), sat diff: 32, (wlimit=0.16) -- Iteration: 20 trying sat: 9488 min sat: 9472 ( 0.160488 ), max sat: 9488 ( 0.159903 ), sat diff: 16, (wlimit=0.16) -- Iteration: 21 trying sat: 9480 min sat: 9480 ( 0.160034 ), max sat: 9488 ( 0.159903 ), sat diff: 8, (wlimit=0.16) -- Iteration: 22 trying sat: 9484 min sat: 9484 ( 0.160123 ), max sat: 9488 ( 0.159903 ), sat diff: 4, (wlimit=0.16) -- Iteration: 23 trying sat: 9486 min sat: 9484 ( 0.160123 ), max sat: 9486 ( 0.159831 ), sat diff: 2, (wlimit=0.16) -- Iteration: 24 trying sat: 9485 min sat: 9484 ( 0.160123 ), max sat: 9485 ( 0.159908 ), sat diff: 1, (wlimit=0.16) -- Iteration: 25 trying sat: 9484.5 - final SAT: 9485 ( it: 25 , weight check 0.159908 <= 0.16 ) Registration::computeMultiresRegistration - computing centroids - computing initial transform -- using translation info - Get Gaussian Pyramid Limits ( min size: 16 max size: -1 ) - initial transform: Ti = [ ... 1.0000000000000 0 0 -2.0251428914711 0 1.0000000000000 0 6.0311902437196 0 0 1.0000000000000 2.8105113695639 0 0 0 1.0000000000000 ] - initial iscale: Ii =1 Resolution: 3 S( 22 32 32 ) T( 22 32 32 ) Iteration(f): 1 -- diff. to prev. transform: 2.97694 Iteration(f): 2 -- diff. to prev. transform: 0.0903233 Iteration(f): 3 -- diff. to prev. transform: 0.0191757 Iteration(f): 4 -- diff. to prev. transform: 0.0116139 Iteration(f): 5 -- diff. to prev. transform: 0.00140989 <= 0.01 :-) Resolution: 2 S( 44 64 64 ) T( 44 64 64 ) Iteration(f): 1 -- diff. to prev. transform: 1.81202 Iteration(f): 2 -- diff. to prev. transform: 0.199033 Iteration(f): 3 -- diff. to prev. transform: 0.00925469 <= 0.01 :-) Resolution: 1 S( 88 128 128 ) T( 88 128 128 ) Iteration(f): 1 -- diff. to prev. transform: 1.02247 Iteration(f): 2 -- diff. to prev. transform: 0.0229168 Iteration(f): 3 -- diff. to prev. transform: 0.000719712 <= 0.01 :-) Resolution: 0 S( 176 256 256 ) T( 176 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.664624 Iteration(f): 2 -- diff. to prev. transform: 0.0108463 Iteration(f): 3 -- diff. to prev. transform: 0.000585613 <= 0.01 :-) - final transform: Tf = [ ... 0.9994709868827 -0.0113151175724 -0.0304912199489 4.8530791096303 0.0126622658755 0.9989355014916 0.0443568583483 2.1370162587100 0.0299568590234 -0.0447194809223 0.9985503265352 5.4716006804225 0 0 0 1.0000000000000 ] - final iscale: If = 1 CentroidT = [ 86.5860705940972 104.6067830299094 138.6676688710562 1.0000000000000 ] CentroidSinT = [ 88.1595712077722 107.7558909090270 139.3780739549505 1.0000000000000 ] Centroid = [ 87.3728209009347 106.1813369694682 139.0228714130033 1.0000000000000 ] MyMatrix::RotationMean input(s) not rotation meant = [ -1.2248131651588 1.2892456671960 3.1420193014715 ] Input rotation's max deviation from rotation is: 0.000393411 Andrew ---- Andrew Beaudin, PhD | Postdoctoral Scholar University of Calgary | Cumming School of Medicine Department of Clinical Neurosciences HSC Rm 2935J, 3330 Hospital Drive N.W. | Calgary, AB | T2N 4N1 Phone: (403) 210-6273

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Freesurfer MC simulations with fsaverage5
by Zhukovsky, Peter 16 Jul '22

16 Jul '22

Dear Freesurfer team, I have a more general question about how best to approach multiple comparison correction for a large dataset where permutations are not viable and where fsaverage resolution is too high. I've fitted a GLM with mri_fitglm in the fsaverage5 space, which results in smaller files and quicker compute times. Next, I've attempted to create MC simulations for fsaverage5 (following https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo) but am running into errors from mri_mcsim: Segmentation Fault (core dumped) mri_mcsim works fine on subject bert, however. I am aware that others also had this problem with fsaverage5: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg70327.html Could you please advise on the best way to run MC correction with large-scale data (30k+ subjects)? Thank you for your help, Best wishes, Peter PS Please find the full mri_mcsim output here: mri_mcsim --o ./mult-comp-cor/fsaverage5/lh/cortex --base mc-z --surface fsaverage5 lh --nreps 5000 --fwhm 10 7.1.1 cwd /<path>/fsaverage5/surf cmdline mri_mcsim --o ./mult-comp-cor/fsaverage5/lh/cortex --base mc-z --surface fsaverage5 lh --nreps 5000 --fwhm 10 sysname Linux hostname dev01.camhres.ca machine x86_64 user pzhukovsky OutTop ./mult-comp-cor/fsaverage5/lh/cortex CSDBase mc-z nreps 5000 fwhmmax 30 subject fsaverage5 hemi lh surfname white FixVertexAreaFlag 1 UseAvgVtxArea 0 SaveFile ./mult-comp-cor/fsaverage5/lh/cortex/mri_mcsim.save StopFile ./mult-comp-cor/fsaverage5/lh/cortex/mri_mcsim.stop UFSS (null) Creating ./mult-comp-cor/fsaverage5/lh/cortex Loading /<path>/data/fsaverage5/surf/lh.white group_avg_surface_area 84969.3 group_avg_vtxarea_loaded 1 Loading label file cortex Loading /<path>/data/fsaverage5/label/lh.cortex.label Segmentation fault (core dumped)

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Freesurfer July 2022