Freesurfer April 2019

freesurfer@nmr.mgh.harvard.edu

99 participants
136 discussions

ERROR: flirt in bbr Matlab Execution
by Pfannmoeller, Joerg Peter 14 May '19

14 May '19

Hello, I have a problem with bbregister and the option --init-best. In the current dev version of freesurfer 6 the processing stops with the error message: terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) ERROR: flirt if I run bbr using Matlab and the Matlab command 'system', where Matlab was started from a terminal in which all FreeSurfer environment variables are set as described on your webpage. However, if I execute the same bbr command from the terminal in which I started Matlab it seemingly runs without any problems. The output files look okay. There is just one output in the log-file which I do not understand: (standard_in) 1: illegal character: K (standard_in) 1: syntax error I got two questions: 1.) Is the run started from the terminal okay? 2.) What do I need to do to get the run started from Matlab to work? The data used worked fine in the stable version for bbregister with fsl flirt initialization in Matlab. However, --init-best did not work in the stable version. In the example discussed here a single slice was registered to the brain anatomy. Here is some information on my operating system: lsb_release -a Distributor ID: CentOS Description: CentOS Linux release 7.6.1810 (Core) Release: 7.6.1810 Codename: Core Can you help me with this issue? Best Joerg

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ERROR! FOV=265.909 > 256
by Anik Dar 02 May '19

02 May '19

External Email - Use Caution Hello All, I am running recon-all highres on 10 7T MP2RAGE datasets that has been skull striped and in two subjects, I get the following error - I tried the suggested workaround ie I included the flag -cw256 but that didnt help and I got the error again. Can you suggest how to fix this ? Many thanks Ani P.S. The error below For more details, see the log file /Applications/freesurfer6/subjects/HighResT1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting \n**************************************** ERROR! FOV=265.909 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. ****************************************\n Darwin Kernel Version 15.6.0: Thu Jun 21 20:07:40 PDT 2018; root:xnu-3248.73.11~1/RELEASE_X86_64 x86_64 recon-all -s HighResT1 exited with ERRORS at Mon Apr 22 20:20:31 EDT 2019 For more details, see the log file /Applications/freesurfer6/subjects/HighResT1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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nu_correct crashing in FreeSurfer v6.0
by Jayasekera, Dinal 01 May '19

01 May '19

External Email - Use Caution Dear all, I have been running version 4 of the HCP Pipelines which now used FreeSurfer 6.0. I get the following error when running recon-all using their FreeSurferPipelineBatch script: nu_evaluate: crashed while running minc_modify_header (termination status=134) nu_correct: crashed while running nu_evaluate (termination status=65280) ERROR: nu_correct I didn't get this error previously when running FreeSurfer 5.3.0 on the same set of data. Are the MNI tools distributed through FreeSurfer 6.0 sensitive to the operating system and its version? Does anyone have a record of it working on an Ubuntu 14.04 OS? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0 2) Platform: Ubuntu 14.04 3) recon-all.log: see attached Kind regards, Dinal Jayasekera<https://dinaljay.weebly.com/> PhD Candidate | InSITE Fellow<https://www.insitefellows.org/> Ammar Hawasli Lab<https://hawaslilab.weebly.com/> Department of Biomedical Engineering<https://bme.wustl.edu/Pages/default.aspx> | Washington University in St. Louis<https://wustl.edu/>

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Hippocampal subfields segmentation template
by Dongsheng Wu 30 Apr '19

30 Apr '19

External Email - Use Caution Dear FS developers, I uesd the ''recon-all command'' to get the volumes of the hippocampal subfields, and we would like to perform further analysis with these subfields in MNI. Could you show us the templates which are used to perform hippocampal segmentation (CA1, CA3, HATA, etc.)? Best wishes, Wu

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Re: [Freesurfer] Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area not visible in visual QC
by Sally Grace 29 Apr '19

29 Apr '19

External Email - Use Caution Dear Eugenio and experts, I have performed a visual quality check of 1271 subjects that have been processed using Freesurfers latest hippocampal/amygdala subfield segmentation algorithm (on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR]) 16 subjects failed the visual QC as we were not able to visually detect a mask of the anterior amygdoid area (AAA) within FreeView using the following command: freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut -v rh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut However, in the output, there is a volumetric value for the AAA (within rh/lh.amygNucVolumes-T1.v21.txt). Have you come across this error before? Can we trust the volumetric value for the AAA if we cannot visually see it within the .mgz image files? Thanks in advance, Sally. --- Sally Grace, PhD Researcher, Cognition and Emotion Research Centre School of Behavioural & Health Sciences Australian Catholic University ________________________________ From: Sally Grace Sent: Tuesday, April 30, 2019 12:12 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area not visible in visual QC Dear Eugenio and experts, I have performed a visual quality check of 1271 subjects that have been processed using Freesurfers latest hippocampal/amygdala subfield segmentation algorithm (on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR]) 16 subjects failed the visual QC as we were not able to visually detect a mask of the anterior amygdoid area (AAA) within FreeView using the following command: freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut -v rh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut However, in the output, there is a volumetric value for the AAA (within rh/lh.amygNucVolumes-T1.v21.txt). Have you come across this error before? Can we trust the volumetric value for the AAA if we cannot visually see it within the .mgz image files? Thanks in advance, Sally. --- Sally Grace, PhD Researcher, Cognition and Emotion Research Centre School of Behavioural & Health Sciences Australian Catholic University ________________________________ From: Sally Grace Sent: Thursday, April 18, 2019 2:16 PM To: freesurfer(a)nmr.mgh.harvard.edu Cc: Valentina Lorenzetti Subject: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area not visible in visual QC Dear Eugenio and experts, I have performed a visual quality check of 1271 subjects that have been processed using Freesurfers latest hippocampal/amygdala subfield segmentation algorithm (on T1's preprocessed in -reconall in FS 5.3 using FS devel-20180612 using the command segmentHA_T1.sh bert [SUBJECTS_DIR]) 16 subjects failed the visual QC as we were not able to visually detect a mask of the anterior amygdoid area (AAA) within FreeView using the following command: freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut -v rh.hippoAmygLabels-T1.v21.FS60.mgz:colormap=lut However, in the output, there is a volumetric value for the AAA (within rh/lh.amygNucVolumes-T1.v21.txt). Have you come across this error before? Can we trust the volumetric value for the AAA if we cannot visually see it within the .mgz image files? Thanks in advance, Sally. --- Sally Grace, PhD Researcher, Cognition and Emotion Research Centre School of Behavioural & Health Sciences Australian Catholic University

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Re: [Freesurfer] recon-all error
by 1013364183 26 Apr '19

26 Apr '19

External Email - Use Caution Dear Bruce I have used FileDrop to upload the file to your email address (fischl(a)nmr.mgh.harvard.edu) I hope that you can take the time to help us solve the problem. Thank you in advance. cheers yu junjie ------------------ Original ------------------ From: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; Date: Wed, Apr 24, 2019 09:52 PM To: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; Subject: Re: [Freesurfer] recon-all error hmmm, how long did you let it run? I've never seen this before. Can you upload your subject to our ftp site? cheers Bruce On Wed, 24 Apr 2019, 1013364183 wrote: > > External Email - Use Caution > > Dear freesurfer > We run the recon-all command of freesurfer, but when it runs to the randomSeed 0 step below, it > will not run anymore, that is, the running terminal has been stuck in the following statement for > more than 10 days.We want to ask why this happens? How should we solve this problem? > The running statement is as follows: > only generating white matter surface > using aseg volume ../mri/aseg.presurf to prevent surfaces crossing the midline > not using aparc to prevent surfaces crossing the midline > INFO: assuming MGZ format for volumes. > using brain.finalsurfs as T1 volume... > $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ > $Id: mrisurf.c,v 1.781.2.6 2016/12/27 16:47:14 zkaufman Exp $ > reading volume > /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/filled.mgz... > reading volume/fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/brain.finalsur > fs.mgz... > reading volume/fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/../mri/aseg.pr > esurf.mgz... > reading volume > /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/mri/wm.mgz... > 1792 bright wm thresholded. > 583658 bright non-wm voxels segmented. > reading original surface position from > /fileserver/projects/Nian/EDSR_20181118_1/result/freesurfer/neck-stripping187547/surf/lh.orig... > computing class statistics... > border white: 318655 voxels (1.90%) > border gray 363634 voxels (2.17%) > WM (109.0): 109.3 +- 4.5 [70.0 --> 110.0] > GM (109.0) : 101.3 +- 17.8 [30.0 --> 110.0] > setting MIN_GRAY_AT_WHITE_BORDER to 92.2 (was 70) > setting MAX_BORDER_WHITE to 114.5 (was 105) > setting MIN_BORDER_WHITE to 110.0 (was 85) > setting MAX_CSF to 35.0 (was 40) > setting MAX_GRAY to 105.5 (was 95) > setting MAX_GRAY_AT_CSF_BORDER to 60.0 (was 75) > setting MIN_GRAY_AT_CSF_BORDER to 56.6 (was 40) > repositioning cortical surface to gray/white boundary > smoothing T1 volume with sigma = 2.000 > vertex spacing 0.26 +- 0.11 (0.00-->2.25) (max @ vno 28887 --> 31618) > face area > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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pvc error
by Donatienne Van Weehaeghe 26 Apr '19

26 Apr '19

External Email - Use Caution Dear freesurfer experts, I am running the rbv pvc correction on a mac system and encountered the following error. mghRead(/Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/unknown/mri/orig.mgz, -1): could not open file The subjects directory is Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair, the orig files are located in Volumes/DATA_PETMR/data_donatienne/Boston_final_analysis/Donatienne/Analyses_freesurfer/recon_flair/$subjectname Thank you! Kind regards Donatienne

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How to get Euler number from amygdala or hippocampus segmentation?
by Reetta-Liina Armio 26 Apr '19

26 Apr '19

External Email - Use Caution Dear Freesurfer experts! I have run the hippocampus segmentation with FS 6 (stable version) and the amygdala segmentation with FS development version. I would like to use the Euler number as a quantitative quality measure of my reconstructed data as Rosen et al. (2017) recommend in their recently published paper. Is it possible to get the Euler number from these specific segmentations or is the Euler number available only from subcortical segmentation? Thank you for the answer! Best, Reetta-Liina Armio

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Questions about multiple test correction and quality assurance
by Zhi Li 26 Apr '19

26 Apr '19

External Email - Use Caution Dear FreeSurfer experts, I am reading your work 'False positive rates in surface-based anatomical analysis' and having several questions about multiple test correction in mri_glmfit-sim: 1. The permutation is permuting the design matrix, but how to permute it in a one-sample t-test? According to my understanding, all the subjects are listed as one group in the design matrix. 2. What's the difference between clustering-forming thresholds (CFT) and cluster-wise p value (CWP)? Whether the clustering-forming thresholds is set to the p map from the permutation test? Then how the CWP is calculated? 3. In the paper ''False positive rates in surface-based anatomical analysis, you suggested ''For surface area, one would need CFT 0.001 and FWHM>10 mm". Whether I could understand this as "the bigger smooth kernel the better"? The default smooth kernel in FSFAST is 5mm, which one should I use? 4. For the quality assurance in 'tkregister-sess', if I can use the QA value as a exclude criteria during analysis? If so is there any reference I can cite? Looking forward to your kind suggestions. Best regards, Lizhi

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mri_convert : Error while loading library libGLdispatch.so.0
by Dev vasu 25 Apr '19

25 Apr '19

External Email - Use Caution Dear all, I am trying to convert .mgz file to nii.gz using mri_convert command mri_convert filename.mgz filename.nii.gz but i am getting an error "mri_convert: error while loading shared libraries: libGLdispatch.so.0: cannot open shared object file: No such file or directory " Thanks Vasudev

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Freesurfer April 2019