Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Issues with transferring edits from v6.0dev into v7.1
by Melanie Ganz 06 Oct '20

06 Oct '20

External Email - Use Caution Dear FS list, as soon as samseg was available in FS v6dev we used it to process some of our data. The plan was always to wait for v7 to use a stable version, but edits were made already on v6FSdev, while we waited last spring for v7 to come out. Now I have been having issues with transferring edits from v6dev into v7.1, which I thought should be a straight forward thing to do. The way I did it, is I ran v7.1 on the raw data, then I copied the files where edits where made, e.g. brainmask.mgz, wm.mgz as well as control.dat. Finally, at this point I reran recon-all -all ( since I actually couldn't get recon-all with the -make flag to work). But I see my rerun fails with the error message: Saving brainmask.auto.mgz Command terminated by signal 11 @#@FSTIME 2020:10:06:14:45:45 mri_watershed N 10 e 20.81 S 1.93 U 22.55 P 117% M 893740 F 0 R 330549 W 0 c 83 w 1353 I 22344 O 2312 L 3.35 3.67 2.94 @#@FSLOADPOST 2020:10:06:14:46:06 mri_watershed N 10 3.10 3.59 2.93 Linux krogh 4.12.14-lp151.28.59-default #1 SMP Wed Aug 5 10:58:34 UTC 2020 (337e42e) x86_64 x86_64 x86_64 GNU/Linux recon-all -s g612_GD exited with ERRORS at Tue Oct 6 14:46:06 CEST 2020 and I don't understand why. The earlier FSrun with v7.1 ran fine and I also tried copying to a separate directory to check file permissions and the same error appears again. I have uploaded the subject to the ftp server at surfer.nmr.mgh.harvard.edu and it's called subject.tar.gz. Kind regards, Melanie -- Yours sincerely Melanie Ganz-Benjaminsen Forsker Direct: + 45 35 45 67 18 Mail: melanie.ganz(a)nru.dk Neurobiology Research Unit Rigshospitalet, building 6931 Juliane Maries Vej 28, 3rd floor DK-2100 Copenhagen, Denmark Phone: +45 3545 6712 Fax: +45 3545 6713 URL:http://nru.dk This e-mail and any attachment may contain confidential and privileged material intended for the addressee only. If you are not the addressee, you are notified that no part of the e-mail or any attachment may be disclosed, copied or distributed, and that any other action related to this e-mail or attachment is strictly prohibited, and may be unlawful. If you have received this e-mail by error, please notify the sender immediately by return e-mail, and delete this message.

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[WARNING: UNSCANNABLE EXTRACTION FAILED]Macaque brain segmentation
by Jie Zhao 06 Oct '20

06 Oct '20

External Email - Use Caution Hello Freesurfer Team I am trying to segment the macaque brain. After skull strip, control point adding and white matter editing, I try to inflate the brain surface. My command is :recon-all -s monkey2 -autorecon2-wm -noaseg -cc-crs 100 85 112 -pons-crs 99 105 80 The output error is: #@# WhitePreAparc lh 2020年 10月 05日星期一 13:23:44 CST cd /usr/local/freesurfer/subjects/monkey2/mri mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 7.1.0 7.1.0 cd /usr/local/freesurfer/subjects/monkey2/mri setenv SUBJECTS_DIR /usr/local/freesurfer/subjects mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --wm wm.mgz --invol brain.finalsurfs.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --white --nsmooth 5 Reading in input surface ../surf/lh.orig Smoothing surface with 5 iterations Area 230166 0.28728 0.06614 0.000899 0.5852 Corner 690498 60.00000 9.22592 3.263084 157.1301 Edge 345249 0.81774 0.11586 0.028436 1.5900 Hinge 345249 4.79409 6.13323 0.000002 153.5438 Not reading in aparc Reading in input volume brain.finalsurfs.mgz Reading in wm volume wm.mgz MRIclipBrightWM(): nthresh=30761, wmmin=5, clip=110 MRIfindBrightNonWM(): 6937 bright non-wm voxels segmented. Masking bright non-wm for white surface MRImask(): AllowDiffGeom = 1 MRImask(): AllowDiffGeom = 1 Ripping frozen voxels ERROR: need seg for ripping Command exited with non-zero status 1 @#@FSTIME 2020:10:05:13:23:44 mris_place_surface N 14 e 12.39 S 0.16 U 10.80 P 88% M 434260 F 25 R 126035 W 0 c 3134 w 27 I 5168 O 0 L 1.41 1.59 1.40 @#@FSLOADPOST 2020:10:05:13:23:56 mris_place_surface N 14 1.32 1.56 1.39 Linux zhao-VirtualBox 4.15.0-118-generic #119-Ubuntu SMP Tue Sep 8 12:30:01 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux Can you help me explain above error and how to solve this problem? I have attached the wm.mgz,but recon-all.log and brainmask.mgz are beyond the size limit . Thanks in advance! All best, Jie

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Re: [Freesurfer] VirtualBox Ubuntu Password Request
by fsbuild 06 Oct '20

06 Oct '20

External Email - Use Caution Hello TSUJI, I will send the password to your email directly. - R. On Oct 6, 2020, at 01:49, tsujisss(a)mattohp.com wrote:        External Email - Use Caution        Dear FreeSurfer Developers, My question is the same as that by Ms. XU Eileen Mon, 31 Aug 2020  I also cound not find the password for the "developer" account,please tell it to me. Sincerely, TSUJI Shiro               Dept. of Thyroidology(Neuclear Medicine)              Public Central Hospital of Matto Ishikawa              _______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr..mgh.harvard.edu/mailman/listinfo/freesurfer

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VirtualBox Ubuntu Password Request
by tsujisss＠mattohp.com 06 Oct '20

06 Oct '20

External Email - Use Caution Dear FreeSurfer Developers, My question is the same as that by Ms. XU Eileen Mon, 31 Aug 2020 I also cound not find the password for the "developer" account, please tell it to me. Sincerely, TSUJI Shiro Dept. of Thyroidology(Neuclear Medicine) Public Central Hospital of Matto Ishikawa

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Infant FreeSurfer - some questions re. inputs and outputs
by Fleur Warton 05 Oct '20

05 Oct '20

External Email - Use Caution Hi FreeSurfer experts, I have a few questions regarding the infant freesurfer tool, which I'm currently trying to get up and running on my neonatal data. Question 1: I've run the command infant_recon_all --s SUBJ --age 0, but I was wondering if there are specific additional flags that you would recommend. The main thing we're wanting to look at right now is total cortical gray and cerebral white matter volumes (L and R hemispheres separate). Should I be including --gmwm2 and --force (or any others)? Questions 2,3: After running that command (without the extra flags) I couldn't find any aseg.stats. I was wondering if there's something I've either done wrong, or should be including. Also, which of brainvol.stats, lh.aparc.stats and rh.aparc.stats should I use for the most accurate measure of cortical gray volume and cerebral white volume? Question 4: I saw on this mailing list a thread about quality-checking/ manual editing of the outputs, and that this is currently not available for the infant tool. Is that still the case, i.e. we can check the outputs visually but not make corrections. If so, would we then just run the infant_recon_all command and use those outputs as is? Sorry for the load of questions. I've attached the infant_recon_all log file in case that's needed. Thanks very much, -- Fleur Warton Postdoctoral Research Fellow Division of Biomedical Engineering Faculty of Health Sciences University of Cape Town

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postdoc opening with Thomas Yeo
by Fischl, Bruce 05 Oct '20

05 Oct '20

Thomas Yeo is looking for a postdoc with a PhD in neuroscience, psychology or related field. Start date is any time in 2021. Topics are quite flexible. More details can be found here: https://sites.google.com/view/yeolab/jobs Contact Thomas if you are interested. Cheers Bruce

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mri_vol2surf MRISread error
by KN Qiao 05 Oct '20

05 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, mri_vol2surf --mov $mask_dir/rest_brainmask.nii.gz --reg $reg_dir/rest2t1.dat --trgsubject fsaverage --interp trilin --projfrac 0.5 --hemi ${hemi} --o ${mask_dir}/mask.fsaverage.${hemi}.nii.gz --noreshape --cortex --surfreg sphere.reg Error: Loading label /Applications/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /Applications/freesurfer/subjects/freesurfer/surf/lh.white MRISread(/Applications/freesurfer/subjects/freesurfer/surf/lh.white): could not open file No such file or directory This problem happens again when I try to use this command on a server in my lab. I didn’t get why it attempted to get surface from /Applications/freesurfer/subjects/freesurfer Should it try /Applications/freesurfer/subjects/fsaverage as well? It can load label properly. Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Platform: Darwin-OSX and CentOS6_x86_64

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Re: [Freesurfer] Right-side bias in thalamic segmentation pipeline?
by Iglesias Gonzalez, Juan E. 05 Oct '20

05 Oct '20

Dear Evan, The atlas is designed to be symmetric. Is it possible that the asymmetry is in your data? Another FS user (Chris Vriend, CCed) reported a similar effect (you can find his massage in the archive). Doug: any further ideas? Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Gallagher, Evan (NGG)" <Evan.Gallagher2(a)pennmedicine.upenn.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Wednesday, September 30, 2020 at 14:18 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Right-side bias in thalamic segmentation pipeline? External Email - Use Caution Hi all, I’ve been working on a project that involves the thalamic segmentation pipeline published by Iglesias et al. in 2018 in NeuroImage (“segmentThalamicNueclei.sh”). While the pipeline itself works great, we have noticed that the right hemisphere VOIs tend to have slightly larger volumes than the left hemisphere VOIs. This has been true in two separate datasets (n=24 and n=25), neither of which has an obvious physiological trait that would lead us to expect these sorts of hemisphere differences. This is my first time posting a question on this list, so I’m not sure if images are OK. If yes, there are a couple posted at the bottom of this message that should visualize what I’m talking about. If not, I can say that the volume differences are most pronounced in the largest VOIs (PuM, VPL, VLp, etc); in these regions, the right side is ~200-300 cmm larger than the left side. Additionally, the average volumes on both sides are reasonable based on Figure 8 of Iglesias et al (in the sense that our average volumes are well within the violin plots in that figure). I’m wondering if anyone has encountered this trend before, and/or if there’s a correction I might implement to equalize the volumes. We want to be understand—to the extent possible—the extent to which these differences are driven by biology vs image processing. Thanks so much, Evan Images follow: [cid:image001.png@01D69736.EDCFE020] [cid:image002.png@01D69736.EDCFE020] [cid:image003.png@01D69736.EDCFE020]

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Error in selxavg3-sess and Xtmp.mat file
by Erica Israel 05 Oct '20

05 Oct '20

External Email - Use Caution Hi there, I am having trouble running the selxavg3-sess command, in which I am receiving the error: Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 35) s = svd(A); Error in fast_selxavg3b (line 394) XCond = cond(XtX); I assume it has something to do with my paradigm file, but was not able to figure out the main issue as I keep getting the same error after changing possible problems in the file (extra characters, changing to plain txt etc.) Looking into the Xtmp.mat file, I saw that only the 7th and 8th rows and columns consisted of NaN but am not sure how to interpret this. Below is what my paradigm file looks like and my Xtmp file is attached. 0.0000 0 20.00 1.0 rest 20.000 1 20.00 1.0 thumbab 40.000 0 20.00 1.0 rest 60.000 2 20.00 1.0 thumbflex 80.0000 0 20.00 1.0 rest 100.000 3 20.00 1.0 thumbrot 120.000 0 20.00 1.0 rest 140.000 4 20.00 1.0 index 160.000 0 20.00 1.0 rest 180.000 5 20.00 1.0 digits 200.000 0 20.00 1.0 rest 220.000 6 20.00 1.0 wristProSup 240.000 0 20.00 1.0 rest 260.000 7 20.00 1.0 elbowFlex 280.000 0 20.00 1.0 rest 300.000 8 20.00 1.0 wristFlex Additionally, here is an example of what I ran to make one of the analysis sessions: mkanalysis-sess -fsd left -stc up -surface self lh -fwhm 5 -event-related -paradigm ParadigmFile -nconditions 8 -spmhrf 0 -TR 1.08 -refeventdur 20 -nskip 4 -polyfit 2 -analysis left_arm.lh -per-session -force Thank you for the help! -- Erica Israel Senior Research Support Associate MIT Media Lab - Biomechatronics Group

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Extraction of subject-wise values after permutation test !
by Martin Juneja 05 Oct '20

05 Oct '20

External Email - Use Caution Hello everyone, I have significant group differences in volume (controls > patients) for one of the clusters (say C1) - calculated after permutation test using PALM, which gives me following outputs: *_clustere_tstat_fwep.mgz (this is significant at p < 0.05, number of voxels = 1105) *_clustere_tstat.mgz *_dpv_tstat_fwep.mgz *_dpv_tstat_uncp.mgz *_dpv_tstat.mgz I was wondering if there is a way to calculate volume values of C1 for each subject (i.e., controls and patients). Thanks.

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Freesurfer October 2020