Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

FreeView cannot open any images
by Greta Tuckute 01 Dec '22

01 Dec '22

Hello, I am attempting to use FreeView (have used it successfully for a few years, but suddenly it stopped working — cannot identify any cause. Have not updated operating system or similar). The problem is that nothing is loaded or shown. I cannot load e.g., an inflated LH surface from fsaverage. Running: ❯ freeview -f /Applications/freesurfer/subjects/fsaverage/surf/lh.inflated Only opens FreeView and shows the background. lh.inflated is shown under “Surfaces” in the upper left corner, but nothing is shown. Nothing changes with “Reset view”. I tried: - Updating FreeView (did not help) - Reinstalled FreeSurfer (did not help either) Any idea what is going on? No error message. Other FreeSurfer commands work fine. FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0.dmg (FreeView: freesurfer-darwin-macOS-dev-freeview.tar.gz from Operating system: macOS Catalina, version 10.15.7 (19H1824) Thanks so much, Greta External Email - Use Caution

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[Tracula] ERRORS when using trac-all -prep
by h21ms-utsumi＠jikei.ac.jp 01 Dec '22

01 Dec '22

External Email - Use Caution Dear Freesurfer experts I'm attempting to running TRACULA in a two subjects(one visit per subject and multiple deffusion scans per visit), as described on the TRACULA tutorial (https://secure-web.cisco.com/1YZplCc8ElxyKpvsfXb9OH_SNhToXmmPHixjCRlcZ51VHS…, https://secure-web.cisco.com/1nYtHW48eZdU7uUKv6TSjlFm9HP9CHGRmfSeoCOA7uunK3…, and https://secure-web.cisco.com/1i1x3WraESWH3k6zfmnPSieIq0qc66z7vq-nTTa6dKs81Q…) but for my subjects I get the following error when I run the trac-all - prep: cp dwi.nii.gz /media/sf_share\freesurfer\7.3.2/subjects/diffusion_ tutorial/trc/subject1/dmri/data.nii.gz cp: cannot stat 'dwi.nii.gz': No such file or directory. I checked the "dmri" directory and found that "data.nii.gz" was missing and "dwi.nii.gz " was there. I've searched the archive list and I found the following two things; the dwi.nii.gz file is the DWI after all corrections have been made and the data.nii.gz file is a symbolic link to the other, so they should be the exact same file. (https://secure-web.cisco.com/1qq_o3GFIoLx7Luv5Fgj2ZN5KBHCJCZzPPrZqzLzT3BdzI…) the data.nii.gz file is necessary for the process of "trac-all -bedp", not "trac-all -prep." (https://secure-web.cisco.com/1pjKE3HFIeU-FqIoHgU1xkoI3rom-BBboaeTQQ7MDiNVT7…) However, no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the dmrirc. tutorial, trac-all.log, pre-diffusion_tutorial_tree.text, and post- diffusion_tutorial_tree.text in case it's of any use. Best regards, Tomohiro Utsumi. ------------------------------------------------------------------------ -------- Tomohiro Utsumi, PhD Student. Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan. ------------------------------------------------------------------------ --------

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Re: [Freesurfer] Freesurfer Version
by fsbuild 30 Nov '22

30 Nov '22

External Email - Use Caution Hello Jacob, It looks like some digits at the end of "devel-2019128” are missing, but I read that to be a development build from December of 2019. If you look at the dates on the 7.X releases under https://secure-web.cisco.com/1UnwnrVRzttVZt3syMWUb0DaKV1piu03ood…, then a 2019 development build would pre-date the 7.X releases listed there, i.e.,7.1.1 in 7/20207..2.0 in 7/20217.3.2 in 8/2022 We don’t in general recommend use of development builds unless there is a feature or bug fix you need that is in a development build newer than the current release.  Release builds are preferable because they have gone through more testing compared to development builds. We also note the following on the page above when considering upgrading to a new release, Important Note: When processing a group of subjects for your study, it is essential to process all your subjects with the same version of FreeSurfer, on the same OS platform and vendor, and for safety, even the same version of the OS. While we continue to work to ensure that results match across platforms, there are none-the-less system-level libraries that are OS dependent. An exception to this rule is that you may view and edit files across any platform or version, and run some post-processing tools (outside the recon-all stream) if you check with us first (for instance you may run the longitudinal processing with newer versions). There is a link to the release notes on that page.  Since you have 7.3.1 you could try that, but I suspect recon-all results won’t be exactly the same.  Maybe first try it out on just 1 subject.  Hope this helps. - R. On Nov 30, 2022, at 19:23, Jacob Bunyamin <jacob.bunyamin(a)monash.edu> wrote:        External Email - Use Caution        Good afternoon, I have run recon-all for my subjects,  however I just realised I am using the ver devel-2019128, I wonder which version is this?Is it recommended to re-run the recon-all using the newer updates? (At present we have the option of Freesurfer 7.3.1, 7..2.0, and 7.1.0 in our HPC) Thank you, Kind regards, Jacob --Department of Neuroscience Central Clinical School, Monash University99 Commercial RoadMelbourne VIC 3004E: jacob.bunyamin@monash.edu _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer Version
by Jacob Bunyamin 30 Nov '22

30 Nov '22

External Email - Use Caution Good afternoon, I have run recon-all for my subjects, however I just realised I am using the ver devel-2019128, I wonder which version is this? Is it recommended to re-run the recon-all using the newer updates? (At present we have the option of Freesurfer 7.3.1, 7.2.0, and 7.1.0 in our HPC) Thank you, Kind regards, Jacob -- *Department of Neuroscience* Central Clinical School, Monash University 99 Commercial Road Melbourne VIC 3004 *E:* jacob.bunyamin(a)monash.edu

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passcode
by Eckhart Schulz 30 Nov '22

30 Nov '22

Hello. I'm trying to expand the 7Zip archive for FreeSurfer on the VirtualBox. Please can I get the passcode for FS_7_2_0_ubuntu_18_04_06.ova.7z Sincerely, Eckhart Schulz Dipl.Ing.(FH) Eckhart Schulz Technische Universität Dresden Fakultät Psychologie External Email - Use Caution

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ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
by Vicente Ferrer 29 Nov '22

29 Nov '22

External Email - Use Caution Dear Freesurfer users, I was trying yo use mri_glmfit-sim after using mri_glmfit that run successfully and I encounter this error: 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 --C /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/tmp.mri_glmfit-sim-29440/contrast_moca_groups.mtx --sim perm 1000 1.5 /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_b br.FA_Avg.corr_g_glmdir/csd/perm.th15.abs.j001 --sim-sign abs --fwhm 0 --fsgd /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd dods --mask /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg 16_syn_bbr.FA_Avg.corr_g_glmdir/mask.mgh --y /bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/eres.mgh --perm-force --seed 1669778971 2. The terminal output of this program (ie, everything it prints to the screen) 3. The FSGD file (/bcbl/home/public/PD_ANALYSIS/FREESURFER_PPMI/stats/lh.atr.avg16_syn_bbr.FA_Avg.corr_g_glmdir/y.fsgd) 4. The design matrix (null)/Xg.dat Attempting to diagnose further SumSq: Min=1.455099 (col 24), Max=8.657582 (col 23) ... could not determine the cause of the problem --^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^---- Seems like there is a problem with the condition matrix, but I do not understand why. Could you help me with this problem? I attached the contrast and fsgd files Best, Vicente Ferrer Predoctoral Researcher BCBL http://secure-web.cisco.com/1kWZEOu8GTFhJvEwUHVoEpHYRwVtjwPjaW-68jFXGIsKvsc… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/1rEQgkEB6hY4LJfH-np0OE9PS23Pj1ILuIHA5pV4sVGy6iI…

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Creating or Using Alt Templates
by Olivier Brown 29 Nov '22

29 Nov '22

External Email - Use Caution Dear Freesurfer experts, I am using a pediatric sample for my study. I understand that the default template has been used with younger samples in the past. However, is there a command or flag to input an external template, such as the MNI? Otherwise, is there a method for creating my own template using the acquired imaged with Freesurfer? I cannot seem to find many resources online for selecting alternate templates in the preprocessing steps of recon-all. Warm regards, Olivier Brown

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time-series from Yeo's Network components
by stdp82＠virgilio.it 29 Nov '22

29 Nov '22

External Email - Use Caution Hi list, I would extract the rs-fMRI time-series from spitted components of Yeo's 7 Network Atlas (fsaverage5). To this aim, I'm planning to convert the "fmcpr.odd.sm0.fsaverage.lh.nii.gz" (obtained by preproc-sess) on fsaverage5. However, the fmcpr.odd.sm0.fsaverage.lh.nii.gz should still include some nuisance variables (CSF, the white matter, motion, first 4 time points). To address this issue, is it corrected to apply the command lines reported below? mkanalysis-sess -analysis fc.noseed.surf.lh -surface fsaverage lh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten mkanalysis-sess -analysis fc.noseed.surf.rh -surface fsaverage rh -fwhm 0 -notask -nuisreg vcsf.dat 5 -nuisreg wm.dat 5 -polyfit 5 -nskip 4 -mcextreg -fsd rest -TR 1.67 -per-run -hpf 0.01 -lpf 0.1 -nowhiten selxavg3-sess -s subj_folder_name -a fc.noseed.surf.lh -overwrite -no-con-ok selxavg3-sess -s subj_folder_name -a fc.noseed.surf.rh -overwrite -no-con-ok Thanks Stefano

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Tracula multiple fatal errors: Eddy and MRI binarize (thalamic segmentation)
by Ward Deferm 29 Nov '22

29 Nov '22

External Email - Use Caution Dear Freesurfer developers, I am attempting to perform tracula on a single participant but i am running into multiple fatal errors during trac-all prep. The first fatal error is this one : eddy_openmp --imain=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi_orig_las.nii.gz --mask=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/lowb_topup_brain_mask.nii.gz --bvecs=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi_orig_las.bvecs --bvals=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi_orig_las.bvals --acqp=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/acqp.txt --index=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/index.txt --data_is_shelled --topup=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/topup --out=/Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/dwi eddy_openmp: Command not found. Darwin gbw-d-m0128.luna.kuleuven.be 21.6.0 Darwin Kernel Version 21.6.0: Thu Sep 29 20:12:57 PDT 2022; root:xnu-8020.240.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Nov 29 13:03:33 CET 2022 I checked my FSL installation and there seems to not be anything wrong here, although the command eddy_openmp is missing from the bin folder. If i change the config file to set doeddy = 1 to work with eddy correct this error disappears. But I would prefer to use eddy here instead is there any way to fix this. Further along i get another fatal error in the mri binarize part of the code which is related to a previous issue found in the mailing archives (https://secure-web.cisco.com/1eL0pyxEECqHmJx6yIaWdwio_XR8d47T_BB4CncFLEYAt8… Applying LTAtransformInterp (resample_type 0) writing to /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/diff/White-Matter++.bbr.nii.gz... mri_convert -at /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz mri_convert -at /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dmri/xfms/anatorig2diff.bbr.lta -rt nearest /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/diff/aparc+aseg+thalnuc.bbr.nii.gz reading from /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz... error: niiRead(): error opening file /Users/r0755008/Desktop/mri_data/TRACULA/NT001/dlabel/anatorig/aparc+aseg+thalnuc.nii.gz Darwin gbw-d-m0128.luna.kuleuven.be 21.6.0 Darwin Kernel Version 21.6.0: Thu Sep 29 20:12:57 PDT 2022; root:xnu-8020.240.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Nov 29 13:24:02 CET 2022 I wanted to try the proposed solution but i have no permission to edit the files as specified in the thread. Would there be another fix for this. In the attachment you can find the log and error files of both runs (1 is the eddy error, 2 the mri binarize) and the config file I used. I am using freesurfer 7.2.0 platform MacOS Monterey 12.6.1 Kind regards, Ward Deferm CDP KU Leuven

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new public dataset: one brain - 557 MRI images
by roland.opfer＠web.de 29 Nov '22

29 Nov '22

External Email - Use Caution There is a new public MRI dataset available: The dataset contains 557 MRI images of the brain of a single healthy male volunteer: . scans were acquired on 116 different MRI machines . For some scanners, the volunteer was scanned in several imaging sessions with different MRI protocol setting. . Altogether the dataset includes data from 157 imaging sessions with 3-5 repeated scans in each session The dataset can be downloaded at <https://secure-web.cisco.com/1fNCUqZ8ZA6D2TTutvPAZ0UA_4KaK4dkLDZl1tr7KT6lu1… tom-fthp-dataset> https://secure-web.cisco.com/1GC7pqwRfRZrvpuFL_zi3rWLSyKjw2G6obQ8drZdf8OtG_… om-fthp-dataset see also <https://secure-web.cisco.com/1FPdqeZeeS8wEr0-NFNDvjNbK_LWh4_OU2dc0hl-iQbvXa…> https://secure-web.cisco.com/1FPdqeZeeS8wEr0-NFNDvjNbK_LWh4_OU2dc0hl-iQbvXa… This dataset offers a unique possibility to study intra- and inter-scanner variabilities of brain quantification tool (see https://secure-web.cisco.com/1BRSlJ-rZ3iuvnBloZ8OJ5pAacHNn71RLP4OiXrD3aweVa… <https://secure-web.cisco.com/1n1PME6GkRb3RtwkBTnyZgNrS9Ad0D6JNYJze3E81Bk78h…> &t=13s)

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Freesurfer