Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30057 discussions

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

23 Apr '24

External Email - Use Caution Yes, it's all sourced correctly. The output after sourcing: bash:/opt/freesurfer/freesurfer-7.4.1$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-linux-ubuntu22_x86_64-7.4.1-20230614-7eb8460 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /opt/freesurfer/freesurfer-7.4.1 FSFAST_HOME /opt/freesurfer/freesurfer-7.4.1/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /opt/freesurfer/freesurfer-7.4.1/subjects MNI_DIR /opt/freesurfer/freesurfer-7.4.1/mni Is your Freesurfer Environment sourced correctly? Here is the wiki help https://secure-web.cisco.com/1ijMGNvsZHBy0jgsTYEFevQx_e5Y2oKLcFa7pDhxI5jfNg… Best, Yujing From: freesurfer-boun...(a)nmr.mgh.harvard.edu <freesurfer-boun...(a)nmr.mgh.harvard.edu> On Behalf Of Gregory Book Sent: Tuesday, April 23, 2024 9:21 AM To: freesurfer <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Problem running recon-all 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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/1csRj5QjHjBcNMSF5ZdSm_KFjj2CdCWqkNIeDVnTqmNRvC… <https://secure-web.cisco.com/1csRj5QjHjBcNMSF5ZdSm_KFjj2CdCWqkNIeDVnTqmNRvC…> . 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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Problem running recon-all
by Gregory Book 23 Apr '24

23 Apr '24

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?

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recon-all error
by Gregory Book 22 Apr '24

22 Apr '24

External Email - Use Caution I installed freesurfer 7.4.1 on Debian 12 (using the Ubuntu 22 .tar.gz). Some programs run fine, but some do not. 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 It does have execute permissions. What might be happening?

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