Freesurfer November 2022

freesurfer@nmr.mgh.harvard.edu

80 participants
119 discussions

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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PETsurfer: PVC without psf of the scanner
by Federica 29 Nov '22

29 Nov '22

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Passcode request for Freesurfer virtual machine
by Gillian Grennan 28 Nov '22

28 Nov '22

External Email - Use Caution Hi, I am a graduate student at the University of Washington. I am trying to download the FS_7_2_0_Ubuntu_18_04_06.ova.7z but was prompted for a password. Could I get access to this password? Best, Gillian

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Pass code request for Freesurfer virtual machine
by Eduardo Europa 28 Nov '22

28 Nov '22

External Email - Use Caution Hello, I would like to follow up on my request to receive the pass code for the Freesurfer virtual machine: FS_7_2_0_Ubuntu_18_04_06.ova.7z Thank you, *Eduardo Europa, PhD, CCC-SLP (he/him)* Assistant Professor, Communicative Disorders & Sciences San José State University eduardo.europa(a)sjsu.edu

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Re: [Freesurfer] VM password
by fsbuild 28 Nov '22

28 Nov '22

External Email - Use Caution Hello Eyesha, The password was (re)sent to your email about ~30 minutes ago - please check your spam filters. The password is for the VM itself and not tied to the machine hosting the VM. - R. On Nov 28, 2022, at 20:04, Eyesha Younus <eyeshayounas(a)gmail.com> wrote:        External Email - Use Caution        Hello,I need a password to install the VM. Is this password tied to an email address or to a machine?The reason I ask this is because I need to install the VM on two computers; one personal and one work. Thanks_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Permission denied error
by fsbuild 28 Nov '22

28 Nov '22

External Email - Use Caution Hello Adam, I hope you saw the previous email I sent you about changing SUBJECTS_DIR to be different from the default.   Just wondering if you did that for SUBJECTS_DIR before running the recon-all. - R. On Nov 23, 2022, at 23:13, Adam Tartaglia <aetartaglia(a)gmail.com> wrote:        External Email - Use Caution        Hello,Immediately after running recon-all, I get an error that says cannot create directory, permission denied. I am not sure as to why this is happening. My license is in the correct location.Thank you for your time,- Adam_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer November 2022