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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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fsaverage error with recon-all
by chen 25 Apr '19

25 Apr '19

External Email - Use Caution Dear All, I ran recon-all using single MPRAGE data set. Processing exited with an error pasted below indicating there is not fsaverage/surf/lh.sphere.reg. According to the fsaverage-recon-all.log, it completed without error. I was able to run a subject before without any error not sure why all the subjects I ran now over the weekend ended up with same error. I have attached an attachment about the recon-all.log.Secondly, i have studied the multi-site reliability of young traveling subjects which scanned in multi-site with the same scanner and protocol across 12 month. I ran these data with cross-pipeline. But, our results showed that the amygdala volumes have significantly lower reproducibility in inter-site than hippocampus and entorhinal cortex (ICC scores less than 0.5) with FreeSurfer rather than manual tracing. So, i want to assure that recon-all -all is the optimal process pipeline. If not, can you give me some advice? Should i use the longitudinal pipeline in multi-site study with traveling subjects? Thanks. ------------------ Capital Medical University

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CORRECTING DEFECT 1 problem
by Abby tang 25 Apr '19

25 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to recon_all my subjects which is .nii file. But I usually meet this error. CORRECTING DEFECT 0 (vertices=67, convex hull=73, v0=950) After retessellation of defect 0 (v0=950), euler #=20 (87340,255044,167724) : difference with theory (-32) = -52 CORRECTING DEFECT 1 (vertices=46367, convex hull=8524, v0=962) Segmentation fault (core dumped) Linux abby-virtual-machine 4.15.0-47-generic #50-Ubuntu SMP Wed Mar 13 10:44:52 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 2851A_T1_w4 exited with ERRORS at Thu Apr 18 20:25:16 CST 2019 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I check files in blow command and attached picture. freeview -v 2851A_T1_w4/mri/norm.mgz -f 2851A_T1_w4/surf/lh.orig.nofix 2851A_T1_w4/surf/lh.inflated.nofix almost all of subjects go wrong. I need your help. please give some advises with program statements in detail. I really appreciate your help 1) FreeSurfer version: freesurfer-linux-centos7_x86_64-dev.tar.gz 2) Platform: ubuntu 18 3) recon-all.log:see attached

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recon-all stops in CORRECTING DEFECT
by Marina Fernández 25 Apr '19

25 Apr '19

External Email - Use Caution Dear freesurfer experts, We run recon-all in a specific subject and we can see in the terminal every commands until the following line: *CORRECTING DEFECT 21 (vertices=36576, convex hull=4845, v0=64547)* When the procedure is in this line it takes a lot of time (days) and it doesn't advance. When we open the lh.inflated and [l/r]h.orig.nofix files we can see that this subject has several errors *(see attached images)* but we don't know how we can repair it to finish the initial recon-all. Does anyone know how to solve this situation? What can we do? We will appreciate any help. Thank you very much in advance. Best regards, Marina Fernández Álvarez, PhD-student. Laboratory of Functional Neuroscience Pablo de Olavide University

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calculation of the volume in mm3
by Schranzer René 25 Apr '19

25 Apr '19

External Email - Use Caution Hello FreeSurfer Developers, I was wondering about the volume calculation of the structures in the aseg.stats file. VoxelVolume_mm3 0.512 NVoxels 8616 Volume_mm3 4312.4 StructName Right-Hippocampus After my calculation of NVoxels * VoxelVolume I get a slightly different value. 0.512*8616 = 4411.4 Where does the difference come from? Thanks, René

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