Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30080 discussions

rerunning on 7.2 with edited brainmask using hi-res
by Alexopoulos, Dimitrios 21 Apr '22

21 Apr '22

External Email - Use Caution We are running some hi-res 0.8mm3 isotropic data through FS 7.2 using the following command. recon-all -s subj -all -hires We are adding back brain which has been removed by the masking process by cloning the T1/brainmask images in freeview and adding back voxels. A revised brainmask.mgz is saved. Can/should the same command be used to rerun using hi-res data? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Recon process for skull-stripted data
by Muhammed Görünen 21 Apr '22

21 Apr '22

External Email - Use Caution Hi, How can I run a recon process if I have just skull stripted data? I need surface and annot files. Does the process need the volume files produced before the skull-stripting process? Thanks in advance. Best, --Muhammed

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Rerunning freesurfer with manual edits and T2 or FLAIR pial refinement
by VINCENT KOPPELMANS 21 Apr '22

21 Apr '22

External Email - Use Caution I have made manual edits to a subject that was initially run with the -FLAIR <input> and -FLAIRpial input flags. When I want to rerun freesurfer to implement these edits should I add these flags again, or is it sufficient to run recon-all -all?

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Multiple comparison correction
by David 21 Apr '22

21 Apr '22

External Email - Use Caution Hi Freesurfer experts, I'm very sorry to bother you, but I am very confused with the following questions: My experimental design includes two discrete factors: with three levels (d,m,h); gender (f, m), and two Nvariables So I can get 6 classes: df, dm,mf, mm,hf,hm. I want to perform the difference between any of the classes leves analysis with regressing out the effect of gender and two Nvariables, but I don't know the rules for setting the contrasts for the F-test. The contrast matrix I used is: 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 0 0 0 My orders are as follows： mris_preproc --fsgd glmteach.fsgd --target fsaverage --hemi lh --meas area --out lh_teach.mgh mris_preproc --fsgd glmteach.fsgd --target fsaverage --hemi rh --meas area --out rh_teach.mgh mri_glmdir --y lh_teach.mgh --fsgd glmteach.fsgd --C glmteach.mtx --glmdir group.area_sm.lh --fwhm 10 --surface fsaverage lh --eres-save mri_glmdir --y rh_teach.mgh --fsgd glmteach.fsgd --C glmteach.mtx --glmdir group.area_sm.rh --fwhm 10 --surface fsaverage rh --eres-save mri_glmdir-sim --glmdir group.area_sm.lh --2spaces --cwp 0.05 --perm 100 1.3 abs mri_glmdir-sim --glmdir group.area_sm.rh --2spaces --cwp 0.05 --perm 100 1.3 abs But there is no region of interest after running， Can I change the correction method or did I use it wrong Any help will be very appreciated. Best wishes,

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How to make surfaces below the GM-WM boundary?
by Lee Subin Kristine 21 Apr '22

21 Apr '22

External Email - Use Caution Dear FreeSurfers, I am interested in sampling values in the superficial white matter (SWM) region, which is an area of about 0.5mm below the GM/WM boundary. To extract values of each vertex in that region, I have successfully used the mri_vol2surf function with the projfrac option, such as below: mri_vol2surf --src <src_img> --out <output mgh file> --out_type mgh --hemi lh --projfrac -0.5 --regheader <recon-all output> --surf white --interp trilinear However, I would also like to get surface type files (like lh.pial, lh.white, etc) that I could overlay on Freeview for visualization purposes. I see papers with figures that have a visualization of surfaces below the GM/WM boundary, but I am not sure how I can obtain this. I would really appreciate if anyone could give me any hints or suggestions on how I could do the same. Thanks in advance! Best regards, Kristine Windows용 메일<https://secure-web.cisco.com/1ZrULsI2ejEjzxKmbYlrcXS6OQOs4N61qvt3YmnuwI2Lib…>에서 발송된 메일입니다.

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[Freeview] View Flatmap
by Morgenroth Elenor 21 Apr '22

21 Apr '22

External Email - Use Caution Dear Freesurfer Experts, I have been using https://secure-web.cisco.com/1LCTowYlrDekgf_ZV9MiK3GGkTFCmyhf35--SPPkPv8MWu… to create flatmaps of individual subjects. This ran without any errors and I have a 'rh.full.flat.patch.3d’ file now. I can’t figure out how to visualise it to check it (in freeview). I have also tried to use pycortex to visualise this as I’m eventually aiming to plot data onto my flatmap, but that isn’t working either (I get a different error (ExpatError) using my flatmap as I get with the example flatmap, but I also can’t visualise the example flatmap in freeview). Thank you for your help! Ellie

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Beta values (resubmitting)
by Laura Willers de Souza 21 Apr '22

21 Apr '22

External Email - Use Caution Hey! I'm resending this email because I think it got lost on the list. Hello FreeSurfer Developers, I'm extracting beta values from some analyzes and I would like to know if I'm extracting and interpreting these values correctly. To extract the beta values I used this command: mri_segstats --seg lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh --i lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf lh.cortisol_CSF.beta.clusters.dat The model consists of 1 group and 1 covariate. I used the contrasts for intercept and slope. The fsgd file looks like this: GroupDescriptorFile 1 Title cortisol_CSF Class Main Variables cortisol_CSF Input 011_S_0003_S9128 Main 2.397895273 Input 022_S_0004_S9233 Main 2.772588722 Input 011_S_0005_S9137 Main 3.044522438 Input 011_S_0008_S9196 Main 2.397895273 Input 011_S_0010_S8800 Main 2.151762203 ... (n=300) The beta values extraction file contains 2 lines (image below). [cid:69d5a8c2-68b8-43ac-85f3-0448f1e3a0b5] * Would the first line be the beta value for the intercept and the second line for the slope? * Thus the glm equation for the 1st cluster would be: cortical thickness = 2.57 - 0.12X + n Is this correct? Thank you very much in advance. Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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parallel make_average_subject
by Marina Fernández 21 Apr '22

21 Apr '22

External Email - Use Caution Dear experts, I would like to create an average subject from a very large population. I am going to compute it on a computer with a lot of threads and I would like to know if it is possible to parallelize the make_average_subject function to try to shorten the computation time. I have tried to add the -openmp flag but I get the error that the flag is unrecognized. How can I solve this? Thank you in advance. Best regards, Marina

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mri_glmfit error
by David 21 Apr '22

21 Apr '22

External Email - Use Caution Hello FreeSurfer Developers, my fsgd is this： GroupDescriptorFile 1 Title post compane Class d Class m Class h RescaleFlag 1 DemeanFlag 1 Variables gender Age Edu Input bd1 d 0 15 8 Input bd2 d 1 19 13 Input bd7 d 0 17 11 Input bd8 d 1 19 13 Input bd6 m 1 22 12 Input bd9 m 1 26 7 Input bd10 m 0 53 15 Input bd11 m 1 56 4 Input hc3 h 0 45 7 Input hc4 h 1 18 13 Input hc1 h 0 52 7 Input hc2 h 1 24 10 When I run Three Groups (One Factor/Three Levels), three Covariates,my MTX is 1 -1 0 0 0 0 0 0 0 0 0 0 1 0 -1 0 0 0 0 0 0 0 0 0 It’s wrong,What should I do -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- -------- ERROR: READ THIS ----------------- --vvvvvvvvvvvvvvvvvvvvvvvvvvvvvv----- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --y rh_teach66.mgh --fsgd glmteach66.fsgd --C glmteach66.mtx --glmdir group66.area_66sm.rh --fwhm 10 --surface fsaverage rh --eres-save 2. The terminal output of this program (ie, everything it prints to the screen) 3. The FSGD file (glmteach66.fsgd) 4. The design matrix group66.area_66sm.rh/Xg.dat Attempting to diagnose further WARNING: Class d has 4 members. With 3 variables and using DODS, This is the bare minimum which may cause problems with the design matrix. WARNING: Class m has 4 members. With 3 variables and using DODS, This is the bare minimum which may cause problems with the design matrix. WARNING: Class h has 4 members. With 3 variables and using DODS, This is the bare minimum which may cause problems with the design matrix. SumSq: Min=1.491914 (col 10), Max=2.676059 (col 11) ... could not determine the cause of the problem --^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^---- ERROR: cannot find residual group66.area_66sm.lh/eres needed with --perm-resid when running mri_glmfit, make sure to include --eres-save ERROR: cannot find residual group66.area_66sm.rh/eres needed with --perm-resid when running mri_glmfit, make sure to include --eres-save glm66.sh: line 14: --perm-resid: command not found -----------------------

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Failed to open FS 7.2 on Virtual Machine
by krystaly 20 Apr '22

20 Apr '22

External Email - Use Caution Dear Freesurfer experts, I would like to ask for your advise on how to fix the issue – failed to open VM. Please see below message for your reference: Failed to open a session for the virtual machine FS_7_2_0_ubuntu_18_04_06. Could not open the medium 'C:\Users\chauc\VirtualBox VMs\FS_7_2_0_ubuntu_18_04_06\Snapshots/{d9705495-47cf-4772-8e41-9473c3807781}.vdi'. VD: error VERR_FILE_NOT_FOUND opening image file 'C:\Users\chauc\VirtualBox VMs\FS_7_2_0_ubuntu_18_04_06\Snapshots/{d9705495-47cf-4772-8e41-9473c3807781}.vdi' (VERR_FILE_NOT_FOUND). Result Code: E_FAIL (0x80004005) Component: MediumWrap Interface: IMedium {ad47ad09-787b-44ab-b343-a082a3f2dfb1} I am currently using Windows 10. Would you please kindly advise? Thanks. Best regards, Krystal

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