Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

brain volumes normalization
by yunus soleymani 02 May '24

02 May '24

External Email - Use Caution Hello freesurfers, I have some questions about the output variables of Freesurfer: 1. In the case of brain volume normalization, do I need to normalize all the volumetric results to the eTIV or just the subcortical volumes? 2. Are there any formulas other than simple division in order to normalize the volumes? 3. How are the .ThckStd values (like FS_R_Insula_ThckStd) calculated? What does the "std" mean here? 4. I believe that the surface area outputs are also affected by brain size differences in the population. Are there any reference values in the Freesurfer outputs to which surface areas can be normalized? Thank you in advance for your help. Best regards,Yunus --------------------------------------------------------------------------------Yunus Soleymani Ph.D. Candidate of Neuroimaging Tehran University of Medical Sciences soleymani.yunus(a)yahoo.com+98 914 526 9298--------------------------------------------------------------------------------

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Figures for publication
by Asuka Toyofuku 02 May '24

02 May '24

External Email - Use Caution Dear Freesurfer experts, Thanks to all the help from this community, we're finally done with GLM analysis(mri_glimfit) and the cluster-wise correction (mri_glmfit_sim), and now I'm making figures for publication. My question is 1. Which output mgh files are commonly used for making figures for publication? Do people use, for example, cache.th40.abs.sig.cluster.mgh (cluster-wise corrected map: overlay) or cache.th40.abs.sig.masked.mgh (uncorrected sig values masked by the clusters that survive correction) or even uncorrected ones, such as sig.mgh file in the contrast directory before running the correction? From my impression, not many people use e.g., cache.th40.abs.sig.cluster.mgh (which shows no colour gradation inside the clusters)... 2. How do you select the colour-bar cut-off and max values? Most publications I saw use min cut-off value: -log10(p) = 2.00 and max: -log10(p) = 5.00, but some uses min: p=0.05 and max: p=0.01. Obviously, if you set the max value (with the configure section) very low (e.g., 2.0), the size of the cluster gets bigger and looks more significant. Are there any suggestions for setting the configure/threshold for the figures? Many thanks, Asuka

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[FreeSurfer] recon-all exited with error - watershed error
by Krystal Xiwing Yau 01 May '24

01 May '24

External Email - Use Caution Dear FS experts, I am encountering an error when running recon-all. I followed the FAQ <https://secure-web.cisco.com/1UCt6p3edZmVlY3vv2VBSKmRgX9p8Xmur_qX9QMrgPbk8p…> page to rerun the command but still not running through. Would you please kindly advise? The log file is attached to this email. Thank you. Regards, Krystal Tel.: +852 2255 5024 Fax: +852 2872 5828 Address: Room 304, 3/F, New Clinical Building, 102 Pokfulam Road, Hong Kong.

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Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 01 May '24

01 May '24

External Email - Use Caution Hello, I wanted to bump this post once more to see if I can get any guidance here. I believe I am close to solving this problem, but I have two lingering questions that are preventing me from moving forward. Thanks again. Dan

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Registration in PETSurfer
by Ruben Dörfel 01 May '24

01 May '24

External Email - Use Caution Hi FreeSurfer Team, I am currently using PETSurfer to analyze FDG data. Following the guide https://secure-web.cisco.com/11AP3L-fRQ1NyWLwYgy3qW-ObrGxWQsVDEGWJEidxYaLFl…, it is suggested that you use _mri_coreg_ to register PET and MRI images. However, I was wondering whether _bbregister_ might not be the more appropriate tool to use, especially in a case like FDG, where we have a lot of uptake in the brain. Best regards, -- Ruben Dörfel, MSc PhD Student Center for Psychiatry Research Karolinska Institutet Neurobiology Research Unit Copenhagen University Hospital, Rigshospitalet

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Error: Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!
by Pamela González Méndez 25 Apr '24

25 Apr '24

External Email - Use Caution Hi everyone, While running a FreeSurfer command, I encountered the following error message: "Label FG1.mpm.vpnl does not exist in SUBJECTS_DIR fsaverage!" This error seems to indicate that the specified label is missing in the fsaverage directory within the SUBJECTS_DIR. Any insights on resolving this issue would be appreciated. Thank you!

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Lingering questions for Longitudinal spatiotemporal LME analysis
by Dan Levitas 24 Apr '24

24 Apr '24

External Email - Use Caution After spending additional time working through this, here are the current steps I’ve taken for running a mass-univariate LME longitudinal analysis on both hemispheres: 1). mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi lh --meas thickness --out lh.thickness.mgh mris_preproc --qdec-long long.qdec.table.dat --target fsaverage --hemi rh --meas thickness --out rh.thickness.mgh 2). mri_surf2surf --hemi lh --s fsaverage --sval lh.thickness.mgh --tval lh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape mri_surf2surf --hemi rh --s fsaverage --sval rh.thickness.mgh --tval rh.thickness_sm10.mgh --fwhm-trg 10 --cortex --noreshape 3). [lh_Y, lh_mri] = fs_read_Y('lh.thickness_sm10.mgh’); [rh_Y, rh_mri] = fs_read_Y(‘rh.thickness_sm10.mgh’); 4). lhsphere = fs_read_surf(‘$FREESURFER_HOME/subjects/fsaverage/surf/lh.sphere'); lhcortex = fs_read_label('$FREESURFER_HOME/subjects/fsaverage/label/lh.cortex.label’); rhsphere = fs_read_surf(‘$FREESURFER_HOME/subjects/fsaverage/surf/rh.sphere'); rhcortex = fs_read_label('$FREESURFER_HOME/subjects/fsaverage/label/rh.cortex.label’); 5). Truncated/sample design matrix, where I have 2 time points (baseline, follow-up), two groups (Control=0, Clinical=1), and no covariates of interest for now: Intercept Time(months) Group Group*Time 1 0 1 0 1 5 1 5 1 0 0 0 1 4 0 0 Contrast for testing group x time interaction: CM.C = [0 0 0 1] 6). initial vertex-wise temporal covariance estimates computed [lhTh0, lhRe] = lme_mass_fit_EMinit(X, [1 2], lh_Y, lh_ni, lhcortex, 3, 8); [rhTh0, rhRe] = lme_mass_fit_EMinit(X, [1 2], rh_Y, rh_ni, rhcortex, 3, 8); 7). covariance estimates segmented into homogeneous regions [lhRgs, lhRgMeans] = lme_mass_RgGrow(lhsphere, lhRe, lhTh0, lhcortex, 2, 95); [rhRgs, rhRgMeans] = lme_mass_RgGrow(rhsphere, rhRe, rhTh0, rhcortex, 2, 95); 8). Model fit lhstats = lme_mass_fit_Rgw(X, [1 2], lh_Y, lh_ni, lhTh0, lhRgs, lhsphere, [], 'euc’, 'exp’, 8, 10^-1); rhstats = lme_mass_fit_Rgw(X, [1 2], rh_Y, rh_ni, rhTh0, rhRgs, rhsphere, [], 'euc’, 'exp’, 8, 10^-1); 9). Get significance maps F_lhstats = lme_mass_F(lhstats, CM, 8); fs_write_fstats(F_lhstats, lh_mri, ‘lh_sig.mgh’, 'sig’); F_rhstats = lme_mass_F(rhstats, CM, 8); fs_write_fstats(F_rhstats, rh_mri, ‘rh_sig.mgh’, 'sig’); 10). Multiple comparisons correction lh_mri1 = lh_mri; lh_mri1.volsz(4) = 1; [lh_detvtx, lh_sided_pval, lh_pth] = lme_mass_FDR2(F_lhstats.pval ,F_lhstats.sgn, lhcortex, 0.05, 0); fs_write_Y(lh_sided_pval, lh_mri1, ‘lh_spval.mgh'); rh_mri1 = rh_mri; rh_mri1.volsz(4) = 1; [rh_detvtx, rh_sided_pval, rh_pth] = lme_mass_FDR2(F_rhstats.pval ,F_rhstats.sgn, rhcortex, 0.05, 0); fs_write_Y(rh_sided_pval, rh_mri1, 'rh_spval.mgh'); 11). Compute single threshold for both hemispheres P = [ F_lhstats.pval(lhcortex) F_rhstats.pval(rhcortex) ]; G = [ F_lhstats.sgn(lhcortex) F_rhstats.sgn(rhcortex) ]; [detvtx, sided_pval, pth] = lme_mass_FDR2(P, G, [], 0.05, 0); pcor = -log10(pth) My remaining questions are: 1). Assuming the above steps are correct (steps 3 and 5 in particular), I’m unsure how to apply the single computed threshold across both hemispheres (pcor) into my freeview and mri_surfcluster commands. Since pcor is the -log10 transformed value, does that mean it should be included as a threshold value for the *sig.mgh files? 2). If the pcor threshold is to be used with the *sig.mgh, how then do I correct for multiple comparisons. From the LME tutorial, it appears that this correction is done and applied to the *spval.mgh files.

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Re: [Freesurfer] Problem running recon-all
by fsbuild 23 Apr '24

23 Apr '24

External Email - Use Caution  If you use a shared drive that is formatted in a way that is not compatible with the linux (ext3, ext4) file system, e.g., a shared windows drive, then running the linux software is not expected to work.  A Windows file system does not support soft links, permissions etc. which means recon-all will fail when it tries to use soft links to point to files.  So SUBJECTS_DIR has to point to a directory you can write to (on a linux file system).   Similarly, the linux packaging tools (apt, dpkg, yum, rpm) expect to install Freesurfer on to a linux file system in order to set permissions, etc. - R. On Apr 23, 2024, at 11:50, Gregory Book <gregory.a.book(a)gmail.com> wrote:        External Email - Use Caution        I did not see that message, which is why I posted again. Sorry about that!I will try using the package installer. We're using the .tar.gz method because it is located on a shared drive, but maybe we'll just need to install it locally if that works.On Tue, Apr 23, 2024 at 11:23 AM fsbuild <fsbuild(a)contbay.com> wrote: Did you try the instructions  you were sent yesterday to run the actual installer and not use the tar file (which is not an installer) ?- R.I would try downloading and running the actual package installer,  MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1uViOtWTuZtLn_S-t5ZXgvMBVJDZpi3jEUIyVF… to the target system..  Then change directories to where you downloaded the package and try,$ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.debI cannot guarantee the installer will work as the Debian linux packaging tools may find requirements in the Ubuntu package they cannot resolve/satisfy on your Debian system.  We don’t test on debian linux.  But the installer should notify you if it fails and why that is.On 4/23/24 09:21, Gregory Book (gregory.a.book(a)gmail.com) wrote:        External Email - Use Caution        I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the following error:-bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file not foundPaths are all set, and all scripts and executables have execute permissions.What might be happening?_______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-JQYLUxMaRFGVYXQgiVBp3x6S8AOp7o-1GJmVB_WrdMAq… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1YSC_5-yK_syGsrpbV_FlchsehO6_LZWlIQjx7-t0KMR0z… <MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1_G0ZVPLNmtmKmt_wysLzFxsWKaGnqKJh6r9LMQNommXRw…; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Problem running recon-all
by fsbuild 23 Apr '24

23 Apr '24

External Email - Use Caution   Did you try the instructions  you were sent yesterday to run the actual installer and not use the tar file (which is not an installer) ? - R. I would try downloading and running the actual package installer,   https://secure-web.cisco.com/1mB3zzEt6hQJ2VvtNrO3nW8sgR7_P581WGaaGeCTSIwiN-Z-x8Mtw6Z5nF23uvW00XlyjmsjQtPTwUkHji_2-9LmsBV2L2NfcLNBFy1Gsw0HvQ045CqPAZjAVhMRFnyyvnfw4xOPMnU-gIj1bM4eLgNASRmckkz7PGd6j28HxgvfDZkF1VK3pZSwTcISKqhKHuNQatTZ9vZjaWbY5k7I5N6dvIOuntBKrq-p5rjI7Q9G73EQ-rCrhQLcAOOyFsAtGAF4BJS1Ph12Iri8OA0T7HkE4bJHEf8g0Rde3zzo82KH1VslH5icbSMuRfXtKveMgAUF6jySJNeW6klBJSbUdsw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.1%2Ffreesurfer_ubuntu22-7.4.1_amd64.deb on to the target system.  Then change directories to where you downloaded the package and try, $ sudo apt install ./freesurfer_ubuntu22-7.4.1_amd64.deb I cannot guarantee the installer will work as the Debian linux packaging tools may find requirements in the Ubuntu package they cannot resolve/satisfy on your Debian system.  We don’t test on debian linux.  But the installer should notify you if it fails and why that is. On 4/23/24 09:21, Gregory Book (gregory.a.book(a)gmail.com) wrote:         External Email - Use Caution         I recently installed freesurfer 7.4.1 on a Debian 12 system (using the Ubuntu 22 .tar.gz). When running recon-all, I get the following error: -bash: /opt/freesurfer/freesurfer-7.4.1/bin/recon-all: cannot execute: required file not found Paths are all set, and all scripts and executables have execute permissions.What might be happening? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://secure-web.cisco.com/1SqDEz4wELZL2ecp4LsUGnw8nhV4bVWQUj3TOG5K_ebNud… The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://secure-web.cisco.com/1b5TUTVtPusBNEm83E0MNUu7lAF2DA0LT4edaHsGpFUa1l… <https://secure-web.cisco.com/1IR6tisOvPBnZWeL5j2Jdqq3FZeK6PgOTurCPPEoSMSlbkJdxNf-ImiZAZa8C-lKt_LtGajcn7GwrMY1DmZZKf3KoCk0WaB5tsz6SML6Kiajxf80yMaz62Q3PefQqspJlIpFt2DpYuoBklRTrHVBfKku09E65ER_39Afv1rx0Xb18GRHKrVDu412tsFZvQFBXOMvldVFWnWpLt626uLD6CLZ3Fm3IkB3WkY00BdpaYCs9l1aXN5H2EG-CbbhSCgUUxvDfzUiBvk2wvAfxM7gRYGIJFMKxAu2j3v99uBlPpna2-nUbu0NvSOhAajQ2yqORnzcwtu5qCNBfB_Lexlc_FA/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline%26gt; . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.

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Re: [Freesurfer] Problem running recon-all
by Gregory Book 23 Apr '24

23 Apr '24

External Email - Use Caution I also see this error which is sent to stderr: /usr/bin/time: cannot run recon-all: No such file or directory It seems to be something related to the time command (or bash keyword) Is your Freesurfer Environment sourced correctly? Here is the wiki help https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNg… Best, Yujing

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