Freesurfer April 2022

freesurfer@nmr.mgh.harvard.edu

97 participants
155 discussions

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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Re: [Freesurfer] Failed to load MRI error
by HYE JUNG YOUN 20 Apr '22

20 Apr '22

External Email - Use Caution Hi, Thanks for your email. I checked the space: And I also made an empty file as you advised. Is there any specific reason to create this new empty file? Should I move the previous recon-all files to this new folder to successfully view them via freeview? I’ll have to get into the previous subjects_dir to select specific MRI file to view unless I move them or re-do the recon-all process to the newly created empty folder, right? Thank you. H From: fsbuild <fsbuild(a)contbay.com <mailto:fsbuild@contbay.com> > Sent: Tuesday, April 19, 2022 12:40 PM To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Cc: hyejung7890(a)amc.seoul.kr <mailto:hyejung7890@amc.seoul.kr> Subject: Re: [Freesurfer] Failed to load MRI error You could try checking some things with these commands, $ cd /Applications/freesurfer/7.2.0 $ df -h . Under the column “Avail” it will list how much free disk space you have available. If you are running out of disk space then maybe deleting files you don’t need from your Downloads folder will free up some disk space. (It’s a good idea to keep at least 10G of free space available on your boot drive for MacOS and many people keep 20G - 30G free). See if you can create a new empty file under that location with, $ touch /Applications/freesurfer/7.2.0/subjects/211025/empty_file Without write permission that will fail, and you will probably need to preface the command with “sudo” for it to work and then authenticate with your password. Once your sudo privileges expire, you won’t be able to write files there until you sudo again. So some users create a new subdirectory for subjects in a location where they always have write permission, like their home subdirectory. For example, $ cd $HOME $ mkdir -p subjects/211025 … copy in whatever files you need to that new location and then … $ export SUBJECTS_DIR=$HOME/subjects/211025 You would need to always set that in your environment to override the default SUBEJCTS_DIR location of /Applications/freesurfer/7.2..0/subjects - R. On Apr 18, 2022, at 20:02, HYE JUNG YOUN <hyejung7890(a)amc.seoul.kr <mailto:hyejung7890@amc.seoul.kr> > wrote: External Email - Use Caution Hi Bruce, Do you mean that I should re-do the recon-all process? I tried to re run freeview but it did not work. And Yes I think the files have been overwritten at some point which I am trying to figure out to avoid making the same mistake in the future. However, the question is I have done the exact same process I always did to view mri files on freeview. I have set and used the same subject directory, used the same code, and etc. Here’s the code I used: <image004.png> Which gives me this: <image005.png> Then, when I check mri folder, notice the selected files have been overwritten (I think) and are shown as 0 byte in size. <image006.png> Can you see where I went wrong to overwrite those files? Thank you for your help. Best, H From: <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu < <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of Fischl, Bruce Sent: Monday, April 18, 2022 10:35 PM To: Freesurfer support list < <mailto:freesurfer@nmr.mgh.harvard.edu> freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Failed to load MRI error Is this for a subject that you can’t load the wm.mgz for? It doesn’t show any errors. Is the wm.mgz zero length? I don’t see how those things can both be true unless you overwrote it at some point. If you haven’t manually edited this subject maybe you should just rerun it? From: <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu < <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of HYE JUNG YOUN Sent: Monday, April 18, 2022 2:44 AM To: 'Freesurfer support list' < <mailto:freesurfer@nmr.mgh.harvard.edu> freesurfer@nmr.mgh..harvard.edu> Subject: Re: [Freesurfer] Failed to load MRI error External Email - Use Caution Hi Bruce, Please find the attached log file. Thanks. H _______________________________________________ Freesurfer mailing list <mailto:Freesurfer@nmr.mgh.harvard.edu> Freesurfer(a)nmr.mgh.harvard.edu <https://secure-web.cisco.com/1lbYaY5CGlZ9b-xDOPo18Ud8lnTXespGfJOrr-fPro1Abj…> https://secure-web.cisco.com/1lbYaY5CGlZ9b-xDOPo18Ud8lnTXespGfJOrr-fPro1Abj…

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Postdoctoral Research Associate at the Institute of Psychology, University of Muenster (WWU), Germany
by Falko Mecklenbrauck 20 Apr '22

20 Apr '22

External Email - Use Caution Dear all, the Department of Biological Psychology (Institute of Psychology) at the University of Muenster (WWU), Germany (https://secure-web.cisco.com/1RZ-xwuqqr0H1V5QPM6K90JjpfVOkoZ1LEvfjmBpM3Zdv6…) is looking for a *Postdoctoral Research Associate* (/Wissenschaftliche/r Mitarbeiter/in/) *(salary level TV-L E13, 100%)* in the field of Cognitive Neuroscience. The duration of this full-time position is three years, with the possibility of an extension. You are invited to join a collaborative research team working on predictive mechanisms in the human brain and behaviour. We are interested in the classification of different types of surprise, predictions, the statistical and declarative knowledge that supports predictions, and the adaptation and learning processes triggered by prediction errors. We use neuroimaging (fMRI) and electrophysiological (EEG, SCR) techniques on healthy subjects and impaired populations (e.g. Parkinson’s disease, stroke, schizophrenia, Asperger autism). The research group has an EEG laboratory with a shielded booth and systems for acquisition of heartbeat and skin conductance data, behavioural laboratories, a laboratory with neuro-navigated transcranial magnetic stimulation (TMS) and controlled access to a 3T research MRI scanner (Magnetom Prisma, Siemens). A 3D video data acquisition system for analysing body and eye movements of group of individuals is currently under construction. We maintain several active collaborations with neurological and psychiatric departments. *Your tasks:* You will develop and conduct your own research project in line with the methodology and research focus of the group. At the moment, we want to advance two topics in particular: the prediction horizon and the cost-benefit functions of prediction. We value your active involvement in the research projects of our doctoral students, supporting and advancing them through scientific exchange and sharing of methodological expertise. As a full-time employee, you will be required to teach four hours per week during the semester. *Our expectations:* Applicants should hold a graduate degree and a completed PhD in neuroscience/psychology/biology or related fields, have already demonstrated a strong motivation for cognitive neuroscience and/or computational neuroscience, and a promising publication list. We are particularly looking for candidates who have advanced skill using fMRI or EEG and a profound knowledge of statistics and programming. Experience with eye tracking and/or SCR would also be a plus. The University of Muenster is an equal opportunity employer and is committed to increasing the proportion of women academics. Consequently, we actively encourage applications by women. Female candidates with equivalent qualifications and academic achievements will be preferentially considered within the framework of the legal possibilities. The University of Muenster is committed to employing more staff with disabilities. Candidates with recognized severe disabilities who have equivalent qualifications are given preference in hiring decisions. Positions can generally be filled as part-time positions if there are no compelling work-related reasons against doing so. To apply, send your CV, a brief description of research interests, list of publications, and the names of two potential references to Prof. Dr. Ricarda Schubotz, rschubotz(a)uni-muenster.de. *Applications will be considered until 1 June 2022.*

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Freesurfer April 2022