Freesurfer April 2024

freesurfer@nmr.mgh.harvard.edu

54 participants
64 discussions

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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MRInormFindControlPoints
by Shahar Ben Noun 21 Apr '24

21 Apr '24

External Email - Use Caution Dear Freesurfer team, I am attempting to use freesurfer using fmriprep but I get the following error message: error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed I've searched the archive but couldn't find a solution. Does anyone have any thoughts on how to trouble-shoot this one? I've contacted you before and was asked to look at the input to that step - It seems like the problem is indeed somewhere else in the process, if I understand correctly, at "autorecon1" [Node] Executing "fs_isrunning" <nipype.interfaces.utility.wrappers.Function> 240417-14:16:30,667 nipype.workflow INFO: [Node] Finished "fs_isrunning", elapsed time 0.004s. 240417-14:16:44,30 nipype.workflow INFO: [Node] Setting-up "fmriprep_23_2_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1" in "/ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_work/fmriprep_23_2_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon1". 240417-14:16:44,70 nipype.workflow INFO: [Node] Executing "autorecon1" <smriprep.interfaces.freesurfer.ReconAll> 240417-14:16:44,77 nipype.interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-01 -sd /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sourcedata/freesurfer -nomotioncor -notalairach -nonuintensitycor 240417-14:16:44,78 nipype.interface INFO: resume recon-all : recon-all -autorecon1 -noskullstrip -noT2pial -noFLAIRpial -openmp 8 -subjid sub-01 -sd /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sourcedata/freesurfer -nomotioncor -notalairach -nonuintensitycor 240417-14:16:52,329 nipype.workflow INFO: [Node] Finished "autorecon1", elapsed time 8.257549s. 240417-14:16:52,337 nipype.workflow WARNING: [Node] Error on "fmriprep_23_2_wf.sub_01_wf.anat_fit_wf.surface_recon_wf.autorecon1" (/ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_work/fmriprep_23_2_wf/sub_01_wf/anat_fit_wf/surface_recon_wf/autorecon1) 240417-14:16:52,558 nipype.workflow ERROR: Node autorecon1 failed to run on host benyakov-a.elsc.huji.ac.il. 240417-14:16:52,569 nipype.workflow ERROR: Saving crash info to /ems/elsc-labs/benyakov-a/Lab-Shared/fmriprep_output/sub-01/log/20240417-141555_c3b0815f-caf3-41ba-ab5a-fb57155be490/crash-20240417-141652-shahar.bennoun-autorecon1-682b0086-8863-4f60-9204-6d485fe4a790.txt Also, I've been asked to post "a couple of images of the processing (the orig.mgz, the T1.mgz, the brainmask.mgz, …)", what does that mean? How do I do it? 1) FreeSurfer version: freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275 2) Platform: Linux 3) PlatformVersion: 5.4.0-159-generic #176-Ubuntu SMP Mon Aug 14 12:04:20 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux Tue Apr 16 13:13:35 IDT 2024 4) recon-all.log 5) autorecon1 command Best regards, Shahar

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Template mapping seems inconsistent
by Dipterix Wang 19 Apr '24

19 Apr '24

External Email - Use Caution Dear FreeSurfer Devs, I'm following the fswiki ( https://secure-web.cisco.com/1W5RqZmGDk4DqrkitgyXA6TeSK5f9Nimf0vTibPbawbImA…) to map sEEG contacts to the template *cvs_avg35_inMNI152*. *I've got MNI305 coordinates for each contact, and I want to plot them on cvs_avg35_inMNI152.* According to the wiki, once I have MNI305 coordinates, I have two choices to calculate the transform from MNI305 to the scanner RAS for this template (instruction 2 and 8b, see below for comparisons). Normally I use instruction 2 since it seems to be more general and can be applied to any template. For MNI152-based templates, instruction 8b seems to be more straightforward. According to your Wiki, these two instructions would yield the identical mapping. *However, a recent case suggested a result of ~5mm difference between these two methods.* My questions are: * Is this error range expected/acceptable in the eyes of FreeSurfer? * Which image defines MNI305 RAS. (For example, MNI152 RAS usually aligns with the scanner RAS of one of ICBM 152 Nonlinear atlases version 2009) * If I need more accurate scanner->MNI305 mapping (instead of using talairach.xfm), what's your recommendations on FreeSurfer templates that are not sitting in MNI152a/b/c space? *Here's my case study:* Here is a screenshot of the native subject's brain. The two contacts (in red) are at the level of thalamus. [image: image.png] Choice 1: Following the instruction 2, > I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS" from tksurfer) and want to compute the MNI305 RAS that corresponds to this point: > MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]' This is the method that I usually use. I can calculate MNI305 RAS from scanner RAS via talairach.xfm (in mri/transforms/). This transform is 1.0540 0.0028 -0.0071 -0.0761 -0.0105 1.0914 0.0090 1.7791 0.0201 -0.0599 1.1014 *-5.4613* Result: the contacts are at the level of brainstem [image: image.png] Choice 2: instruction 8b However, since the template already aligns with MNI152, as an alternative, I can follow the instruction 8b, > I have an RAS from a voxel in MNI152 space which I want to convert to MNI305 space (fsaverage space). Create a vector of the MNI152 space point like v = [R A S 1]'. Multiply this vector by the matrix below (ie, M*v) 1.0022 0.0071 -0.0177 0.0528 -0.0146 0.9990 0.0027 -1.5519 0.0129 0.0094 1.0027 *-1.2012* *Notice the translation on Z axis is -1.2mm instead of -5.5mm* Result: This mapping seems better [image: image.png] Best, - Dipterix

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editing segmentations from recon-all-clinical
by Agata Wolna 19 Apr '24

19 Apr '24

External Email - Use Caution Hi! I have a question regarding the recon-all-clinical pipeline: is it possible to edit the outputs of the synthseg segmentation run as a part of the pipeline (synthseg.mgz) similarly to editing recons from the standard freesurfer pipeline, and getting updated segmentation estimates (the synthseg.vol.csv files) for these manually updated segmentation? Thanks for your help! Agata

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Freesurfer April 2024