Freesurfer November 2018

freesurfer@nmr.mgh.harvard.edu

121 participants
189 discussions

回复： ?????? Recon-all run error
by 1013364183 16 Nov '18

16 Nov '18

External Email - Use Caution Dear BrucenFischl, Our high resolution data has been running for a few weeks, but the computer did not react. It runs too slowly. We give our run commands and expert files as well as log files in the attachment. Please help us check if there is an error? If there are no errors, then can I use multithread in recon-all to speed up? Please give us some guidance. In addition, Could you help us run these data? We will send you 3 sets of data. We will give 9 download links because of these data is too large. If you can help us run our high resolution data, we will be very grateful. And can we write your name in the acknowledgments section? Our tutor is now at Boston Children's Hospital (BCH). If possible, she would like to consult you in person. The download link is: https://drive.google.com/file/d/1d8QMcSXjCq46HkqKFU-krpGTJO41eYbe/view?usp=… https://drive.google.com/file/d/1JHDmrVAHmzSO7NTZ0DsKmMwKh3HtDeyZ/view?usp=… https://drive.google.com/file/d/1ipC4svGbud_gvYEt9qF4oy3IGwmZhUuW/view?usp=… https://drive.google.com/file/d/1mKzYM2uNJEZv06nlP65sbBxa7S1gAwYh/view?usp=… https://drive.google.com/file/d/108y0FsujcaqDvQO7sYXcCTy9-gCoTzsD/view?usp=… https://drive.google.com/file/d/1NikZZDY0TPGXLjDdzgYayuOVh4BUl43g/view?usp=… https://drive.google.com/file/d/15da1mixza-1oH9uB1DXPKw5FluiuOmVe/view?usp=… https://drive.google.com/file/d/15W2MSnk5WUiToQBWRJS6VyCyMcQBFuK/view?usp=d… https://drive.google.com/file/d/1gVYV_UynTXKaWaAbYvreoY1O9574zU8s/view?usp=… Looking forward to your reply. Thanks in advance ------------------ 原始邮件 ------------------ 发件人: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; 发送时间: 2018年11月7日(星期三) 凌晨2:42 收件人: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; 主题: Re: [Freesurfer] ?????? Recon-all run error does it occur if you run it outside of recon-all? Do you have enough free ram? If so, you can filedrop us the dataset and we can try to replicate and fit ix. On Tue, 6 Nov 2018, 1013364183 wrote: > > External Email - Use Caution > > Dear Bruce, > I found the error location in the recon-all.log folder. Here is the place where it went wrong??I > don't think it's the reason for insufficient memory.. > ''mri_convert.bin: putget.c:322: fill_NC_var: Assertion `chunksz % 4 == 0' failed.'' > This data is ok when we run with versions prior to freesurfer 6.0. But after we run the 6.0 > version and set the expert file, this error will occur.Do I need to step through the instructions to > see the problem? How should this error be solved? > > Thanks in advance > > yours yujunjie > > ------------------ ???????? ------------------ > ??????: "Bruce Fischl"<fischl(a)nmr.mgh.harvard.edu>; > ????????: 2018??11??6??(??????) ????9:40 > ??????: "Freesurfer support list"<freesurfer(a)nmr.mgh.harvard.edu>; > ????: Re: [Freesurfer] Recon-all run error > > that certainly looks like something is running out of ram. Can you run > the command that failed directly on the command line and see if it works? > Was anything else running on the machine at the time? We do report total > and free memory at the start of the recon in the recon-all.log file > > cheers > Bruce > On Tue, > 6 Nov 2018, 1013364183 wrote: > > > > > External Email - Use Caution > > > > Dear FS, > > When we run ??recon-all?? with a 5GB high-resolution image, core dumped appears when the > mri_convert > > command is executed. The specific errors are as follows: > > /opt/el7/pkgs/freesurfer/freesurfer_6.0/bin/mri_convert: line 3: 29235 Aborted (core dumped) > > mri_convert.bin "$@" > > ERROR: converting to minc > > We want to know if our high resolution image is too large for freesurfer to handle, or our > computer > > memory (64GB running memory) is limited. > > > > Thanks a lot in advance! > > yours sincerely, > > yu junjie > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mri_glmfit-sim error
by C.P.E. Rollins 16 Nov '18

16 Nov '18

External Email - Use Caution Dear Freesurfer Developers, I'm trying to run mri_glmfit-sim to correct for multiple comparisons but am receiving the following error: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt SURFACE: fsaverage lh log file is lh.5.lgi_MAN_new.glmdir/cache.mri_glmfit-sim.log cd /home/cper2/BeneMin/Freesurfer /applications/freesurfer/freesurfer_6.0.0/bin/mri_glmfit-sim --glmdir lh.5.lgi_MAN_new.glmdir --cache 2 neg --cwp 0.05 --2spaces $Id: mri_glmfit-sim,v 1.66 2016/11/16 20:52:22 greve Exp $ Fri Nov 16 09:38:40 GMT 2018 Linux wbic-gate-2 3.16.0-6-amd64 #1 SMP Debian 3.16.57-2 (2018-07-14) x86_64 GNU/Linux cper2 setenv SUBJECTS_DIR /home/cper2/BeneMin/Freesurfer FREESURFER_HOME /applications/freesurfer/freesurfer_6.0.0 Original mri_glmfit command line: cmdline mri_glmfit.bin --y lh.5.lgi_MAN_new.mgh --fsgd FSGD_MAN_new.txt dods --glmdir lh.5.lgi_MAN_new.glmdir --surf fsaverage lh --C contrast_dods.txt DoSim = 0 UseCache = 1 DoPoll = 0 DoPBSubmit = 0 DoBackground = 0 DiagCluster = 0 gd2mtx = dods fwhm = 26.134985 CSD /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd mri_surfcluster --in lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh --mask lh.5.lgi_MAN_new.glmdir/mask.mgh --cwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.mgh --sum lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary --ocn lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh --annot aparc --cwpvalthresh 0.05 --o lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh --no-fixmni --csd /applications/freesurfer/freesurfer_6.0.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm26/neg/th20/mc-z.csd --csdpdf lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.pdf.dat --vwsig lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.mgh --vwsigmax lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.voxel.max.dat --oannot lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.annot --bonferroni 2 --surf white Creating CDFs from CSD files csd->threshsign = -1 thsign = neg, id = -1 version $Id: mri_surfcluster.c,v 1.60 2016/11/01 19:49:22 greve Exp $ hemi = lh srcid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/sig.mgh srcsubjid = fsaverage srcsurf = white srcframe = 0 thsign = neg thmin = 2 thmax = -1 fdr = -1 minarea = 0 Bonferroni = 2 xfmfile = talairach.xfm nth = -1 outid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.masked.mgh MGH ocnid = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.ocn.mgh MGH sumfile = lh.5.lgi_MAN_new.glmdir/contrast_dods.txt/cache.th20.neg.sig.cluster.summary subjectsdir = /home/cper2/BeneMin/Freesurfer FixMNI = 0 Found 149955 vertices in mask Found 149955 vertices in mask Found 149955 points in clabel. ------------- XFM matrix (RAS2RAS) --------------- /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; MRISread(?????): could not open file No such file or directory ---------------------------------------------------- Reading source surface /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white mri_surfcluster.bin: could not read surface /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white No such file or directory However, the files /home/cper2/BeneMin/Freesurfer/fsaverage/mri/transforms/talairach.xfm and /home/cper2/BeneMin/Freesurfer/fsaverage/surf/lh.white both exist and I can read them looking at the permissions. I was wondering if you might have any advice for this. Many thanks, Colleen

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Problems with skull stripping
by Rosalia Dacosta Aguayo 15 Nov '18

15 Nov '18

External Email - Use Caution Dear Free Surfer team, Sorry for double posting but I would like to explain well so it will be easier to understand what I am looking for. 1. I have run recon-all -all in a participant 2. The skull stripped image has skull and dura behind. 3. I can manual edit or I can do -autorecon1 and then supply the brainmask.nii.gz generated from my betted image. 4. Questions: a) If I run -autorecon1 and make the substitution of the brainmask: I am afraid this is not going to improve the grey matter and white matter segmentation. So, if this first step is not well solved, I think that then, no matter if I change my brainmask for a better one, that I will have the same problems with -autorecon2 and -autorecon3, is that correct? b) If I do manual edition, then I will have to run -autorecon1 again...not sure if this would be the best solution. As I am new to this, I would greatly appreciate your experience. Best wishes, Rosalia

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SUIT FS-FAST
by stdp82＠virgilio.it 15 Nov '18

15 Nov '18

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Posting a Message to Freesurfer List Members {Disarmed}
by Salerno, Joanna M. 15 Nov '18

15 Nov '18

External Email - Use Caution Hello, My name is Joanna Salerno and I am the lab manager of the Clinical Neuroscience Lab at The Ohio State University. I would like to send a message to all Freesurfer list members advertising for a few job postings in my lab. I have attached informational flyers to this email, and have included the message below: Posted on behalf of Dr. Ruchika Prakash: I am recruiting two post-docs for my lab with research interests in clinical neuroscience/neuropsychology. I am attaching the ads here and would appreciate if you can distribute it to any graduating students in your labs or programs. The first post-doc is 100% research and the student can either be from neuroscience or any subfield of psychology as far as their interests are aligned with the research going on in the lab. The second post-doc is 50% clinical and 50% research, and I am looking for someone with a clinical psychology doctoral degree. Additionally, I am looking for a research associate, with either a master’s or a doctoral degree, but who is primarily interested in helping manage the various studies going on in the lab and helping with graduate students and research staff. If you have anyone in mind for that, please send them my way. Here is the lab website for additional info: https://www.clinicalneurolab.<https://www.clinicalneurolab.org/>org<https://www.clinicalneurolab.org/>. <https://www.clinicalneurolab.org/><https://www.clinicalneurolab.org/>Please let me know if you need any more information from me for this. Thank you, Joanna Salerno

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Brodmann areas annotation files
by Alon Baram 15 Nov '18

15 Nov '18

External Email - Use Caution Hi, I'm quite new to Freesurfer so sorry if this is a basic question. I'm trying to overlay my results (which are in fsaverage space) over some anatomical annotation files. To do that I loaded the ?h.PALS_B12_Brodmann.annot file from the $SuBJECTS_DIR/fsaverage/label folder . It seems to me there are many inaccuracies in this file, and I'm wondering if I'm using it wrongly. I'm attaching a screenshot to show some examples. This issue is in contrast to (for example) the ?h.PALS_B12_Brodmann.OrbitoFrontal.annot file which seems to be very accurate. Examples: - BA 22 includes both the middle and the superior temporal gyrus (instead of just the latter - the brighter, most dorsal green bit in the temoral lobe. Unless I'm mistaken, the middle temporal gyrus should by BA 21? - The angular gyrus seems to be divided between BAs 40,7 and 39 instead of just the later. [image: image.png] [image: image.png]

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myelin group difference and pvr of thickness
by Damien MARIE 15 Nov '18

15 Nov '18

External Email - Use Caution Hi, I would like to replicate an analysis I did with qdec but regressing out thickness at the vertex level. It’s a myelin group difference with age and left average myelin as nuisance factors. Q1/ should I use smoothed thickness maps or unsmoothed? I used the mri_glmfit command line generated during that qdec analysis and added the pvr flag but I got that error message: ERROR: dimension mismatch between X and contrast /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat X has 7 cols, C has 6 cols I understood I had to change the contrast.mat and added a 0 at the end for the pvr: +1.00000 -1.00000 +0.00000 +0.00000 +0.00000 +0.00000 +0.00000 Q2/ Can you please tell me if it is correct??? Many thanks, Damien fsgd: GroupDescriptorFile 1 Title 10nov MeasurementName R1projfrac0.5 Class group1 Class group2 Variables LH_mR1 Age Input suj1 group1 0.080687 1.644444 … glm: mri_glmfit --y /home/damien/bin/freesurfer6/subjects/qdec/10nov/y.mgh —fsgd /home/damien/bin/freesurfer6/subjects/qdec/10nov/qdec.fsgd dods --glmdir /home/damien/bin/freesurfer6/subjects/qdec/10nov --surf fsaverage lh —label /home/damien/bin/freesurfer6/subjects/fsaverage/label/lh.aparc.label --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Avg-Intercept-R1projfrac0.5.mat --C /home/damien/bin/freesurfer6/subjects/qdec/10nov/contrasts/lh-Diff-ct-dys-Intercept-R1projfrac0.5.mat --pvr lh.thicknessall.fsaverage.mgh

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Re: [Freesurfer] Surface failure in centos7 dev freesurfer
by fsbuild 14 Nov '18

14 Nov '18

External Email - Use Caution Hello Baxter, The daily/nightly builds happen at around midnight, so any changes made today won't get built until midnight.  There should be a new build tomorrow unless something fails the build. Baxter P. Rogers November 13, 2018 at 19:42         External Email - Use Caution         Ah - looking deeper, I think not. I'm not building it locally -  I downloaded today's available compiled version (commit 8abd50c judging by the build stamp) and it looks like the relevant fix was later, in commit 2720b25. Is there a way to tell what commit is available at the dev download URL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/ ? Anyway, I will try again in a day or two assuming the dev binaries update, and let you know how it goes. Thanks much, Baxter Greve, Douglas N.,Ph.D. wrote: _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Greve, Douglas N.,Ph.D. November 13, 2018 at 19:28 did it include the update to mri_tessellate? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Baxter P. Rogers November 13, 2018 at 18:33 External Email - Use Caution I am still getting the same error with today's build of freesurfer-linux-centos7_x86_64-dev.tar.gz SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c Thanks, Baxter _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Greve, Douglas N.,Ph.D. November 13, 2018 at 10:49 I just fixed it _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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What is "...S_central" in Destrieux atlas?
by Colin Birkenbihl 14 Nov '18

14 Nov '18

External Email - Use Caution Dear all, I am currently working with MRI features calculated with the Destrieux atlas. As an output I have features named like: Vol_Right_S_Central Vol_Left_G_precentral or Vol_Left_S_orbital-H_Shaped I wanted to ask you, what these features stand for and if there is some mapping of those feature names to brain region names which are clearly interpretable. If not, it would be great if you could tell me what the above mentioned features refer to. It would be great if you could help me. Best wishes, Colin

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Freeview volume measurements on newly created VOIs
by Kim, Jisoo,M.D. 14 Nov '18

14 Nov '18

Hello Freesurfer developers, I am trying to get volume measurements (mm^3) on VOIs (volume of interest) that I created on Freeview. All I can do is to export the VOI as an .mgz file. Do you know of an easy way to get the stats in .txt or any other formats? 1) Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c 2) OS: MacOS Sierra Thank you very much. Best, Jisoo

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Freesurfer November 2018