Freesurfer October 2019

freesurfer@nmr.mgh.harvard.edu

111 participants
180 discussions

Re: [Freesurfer] Issues with segmentHA_T1.sh command
by Iglesias Gonzalez, Juan E. 10 Oct '19

10 Oct '19

Dear Ola, This looks like a very ugly error but someone experienced something similar in the past and it turned out to be a permissions problem. https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subj… Can you please double check this is not your case? 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 Olamide Abiose <oabiose(a)stanford.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, 10 October 2019 at 14:29 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Issues with segmentHA_T1.sh command External Email - Use Caution Hello, I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated! Thank you very much. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019 /usr/bin/time -o /dev/stdout @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01 run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67) Error in deployrc (line 9) Error in matlabrc (line 238) Command exited with non-zero status 255 @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01 @#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90 Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019

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Re: [Freesurfer] Contents of Freesurfer digest...
by David Kamson 10 Oct '19

10 Oct '19

External Email - Use Caution Martin, thank you for these comments. These are extremely valuable! Although my patients had tumors, these are cured (this is why I have so few of them…) and have no residual mass effect/deformity beyond biopsy tracks / small resection cavities. Thus far, I was able to get pretty accurate looking segmentations of deep nuclei on aseg. Segmentation issues were associated with the surface structures (e.g. dura/falx being misclassified as gray or brain tissue adjacent to resection cavities are correctly classified as brain but GM/WM often misclassified). I’m OK restricting the analysis to ventricular and deep GM volume, since what I’m trying to measure is marked atrophy of these structure after chemotherapy which I guess is in the range of 1-5%/year. The changes are mostly marked enough to enable a visual qualitative analysis, however, quantitative data would be clinically more helpful to clarify when, and how much change to expect after treatment. Do you think increasing the number of time points analyzed (I have 4-6 scans per year for each patient) could eliminate the noise from head positioning/slicing as long as the volumetric trends remain consistent? Again, the data would be normalized per individual and I would not use absolute volume for any comparative analysis. Thank you again. This message board is of incredible value! Best regards, David ---------------------------------------------------------------------- Message: 1 Date: Wed, 09 Oct 2019 10:48:48 +0200 From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu<mailto:mreuter@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Questions re slice thickness, aseg and longitudinal analysis To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <7a4d059cb5cb42f390e03f523677a3362d17cb81.camel(a)nmr.mgh.harvard.edu<mailto:7a4d059cb5cb42f390e03f523677a3362d17cb81.camel@nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="UTF-8" Hi David, I am not very optimistic: 5mm is too thick for FreeSurfer (recommendation is 1 up to 1.5). You will certainly get something, but it can be very unreliable and completely wrong. Especially longitudinally these thick slices will induce large variance due to different head positioning (and different slice angulations) in the scanner. Furthermore, FreeSurfer does not take Gad-Enhanced images. Also it will not work if tumor lesions are present. About your questions: 1. Surfaces update the aseg, but if you are only interested in the volumes, you can skip this expensive step (potentially at the cost of slightly higher noise levels in your measurements). 2. I think not (see above). 5mm is too low. 3. Theoretically yes, but I have never tested if the scripts will do it. You could run up to the aseg in the cross, then create base (up to aseg) and then run the longs up to aseg. Not even sure you really need the base aseg. You might be able to just run the initial base registration step, obtain the transformations and median norm.mgz image, could be sufficient for the long runs. 4. No. Gad images won't work. Best, Martin External Email - Use Caution Freesurfers, First of all, I'd like to express my gratitude to the community for the support that keeps researchers like myself afloat! I have a unique set of oncology patients that I want to evaluate for brain atrophy in a retrospective longitudinal analysis. I was thinking about using Aseg.auto results to assess longitudinal volume changes, but before I invest all the time I wanted to check with the community whether this makes any sense at all: The dataset that looks like this: - 22 patients (no control dataset [yet]) - 10-25 MRIs per patient acquired over 2-8 years in relatively uniform intervals - Patients had most of their scans on the same scanner, but scanners differed widely between patients - All patients have axial T1 post gadolinium scans of 1x1x5mm resolution (3D acquisition available in <10%) - About 80% of scans have an axial pre-contrast T1 sequence - All scans are skullstripped (third party algorithm) I'm looking for crude changes, no subtleties; volumes of interest are: - Whole brain volume - White matter volume - Ventricular volume (mainly lateral ventricle) - Subcortical gray matter volume (whole thalamus most importantly) I ran a few test analyses and to my surprise I was able to generate pretty acceptable surfaces, however, topology fixing took about 24H per scan, and I feel aseg.auto contained all the volumetric data I was really interested in. My concrete questions are: 1) Does the full autorecon pipeline affect Aseg.auto? If there is no benefit, I could reduce the per scan analysis time from 28 hours to 1-2 h. 2) Would this low-resolution dataset be accepted by reviewers if used for Aseg? Should I do any quantitative validation beyond a visual quality analysis of Aseg? 3) Can I perform a longitudinal analysis only for the Aseg results? 4) Is it OK to use T1-gad images for the analysis? I'd appreciate any input! Best regards, David O. Kamson, MD PhD Neuro-oncology fellow Johns Hopkins Hospital & National Institutes of Health _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Issues with segmentHA_T1.sh command
by Olamide Abiose 10 Oct '19

10 Oct '19

External Email - Use Caution Hello, I'm having great difficulty running the segmentHA_T1.sh command. I'm using the latest development version of Freesurfer and have downloaded Matlab R2014b. I get the following message when I try to run the command. Any advice/suggestions you can offer would be greatly appreciated! Thank you very much. #-------------------------------------------- #@# Hippocampal Subfields processing (T1) left Wed Oct 9 17:49:49 PDT 2019 /usr/bin/time -o /dev/stdout @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e %e S %S U %U P %P M %M F %F R %R W %W c %c w %w I %I O %O L 41.67 41.74 45.01 run_segmentSubjectT1_autoEstimateAlveusML.sh /opt/freesurfer-dev/MCRv84/ PI004 /mnt/barry/projects/Mormino_TauPET/PI2620/Analysis/Ola_Practice 0.333333333333333333333333333333333333 /opt/freesurfer-dev/average/HippoSF/atlas/AtlasMesh.gz /opt/freesurfer-dev/average/HippoSF/atlas/AtlasDump.mgz /opt/freesurfer-dev/average/HippoSF/atlas/compressionLookupTable.txt 0.05 left L-BFGS v21 /opt/freesurfer-dev/bin/ 0 ------------------------------------------ Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/lib/x86_64-linux-gnu:/opt/freesurfer-dev/MCRv84//runtime/glnxa64:/opt/freesurfer-dev/MCRv84//bin/glnxa64:/opt/freesurfer-dev/MCRv84//sys/os/glnxa64:/native_threads:/server:/client:: Error using checkRequiredMCRProducts (line 25) Java exception occurred: java.lang.NullPointerException at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:56) at com.mathworks.install.InstalledProductFactory$1.execute(InstalledProductFactory.java:49) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.executeTask(InstalledProductFactory.java:193) at com.mathworks.install.InstalledProductFactory$InstallerWorkSpace.access$200(InstalledProductFactory.java:108) at com.mathworks.install.InstalledProductFactory.getInstalledProducts(InstalledProductFactory.java:67) Error in deployrc (line 9) Error in matlabrc (line 238) Command exited with non-zero status 255 @#@FSTIME 2019:10:09:17:49:49 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 e 26.55 S 0.33 U 5.00 P 20% M 235704 F 0 R 45707 W 0 c 211 w 2331 I 0 O 84096 L 41.67 41.74 45.01 @#@FSLOADPOST 2019:10:09:17:50:15 run_segmentSubjectT1_autoEstimateAlveusML.sh N 13 41.42 41.68 44.90 Linux gene 4.4.0-154-generic #181-Ubuntu SMP Tue Jun 25 05:29:03 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux T1 hippocampal subfields exited with ERRORS at Wed Oct 9 17:50:15 PDT 2019

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TRACULA error - MRISread could not open file
by Daniel Callow 10 Oct '19

10 Oct '19

External Email - Use Caution Hello, I am running tracula on some of my DTI data and have had no issues for most of my subjects. However, for one of them I get the following error after mri_segreg MRISread(/Volumes/DANIEL/freesurfer_pin/APOE.269/surf/lh.white): could not open file Loading mov Extracting frame 0 Projecting LH Surfs Loading lh.white surf No such file or directory It doesn't make sense that I am getting this error because when looking in that exact folder I see the following [255a-280:freesurfer_pin/APOE.269/surf] amos% ls lh.area lh.smoothwm.FI.crv rh.area rh.smoothwm.FI.crv lh.curv lh.smoothwm.H.crv rh.curv rh.smoothwm.H.crv lh.defect_borders lh.smoothwm.K.crv rh.defect_borders rh.smoothwm.K.crv lh.defect_chull lh.smoothwm.K1.crv rh.defect_chull rh.smoothwm.K1.crv lh.defect_labels lh.smoothwm.K2.crv rh.defect_labels rh.smoothwm.K2.crv lh.inflated lh.smoothwm.S.crv rh.inflated rh.smoothwm.S.crv lh.inflated.H lh.smoothwm.nofix rh.inflated.H rh.smoothwm.nofix lh.inflated.K lh.sphere rh.inflated.K rh.sphere lh.inflated.nofix lh.sphere.reg rh.inflated.nofix rh.sulc lh.orig lh.sulc rh.orig rh.white.H lh.orig.nofix lh.white.H rh.orig.nofix rh.white.K lh.qsphere.nofix lh.white.K rh.qsphere.nofix rh.white.preaparc lh.smoothwm lh.white.preaparc rh.smoothwm rh.white.preaparc.H lh.smoothwm.BE.crv lh.white.preaparc.H rh.smoothwm.BE.crv rh.white.preaparc.K lh.smoothwm.C.crv lh.white.preaparc.K rh.smoothwm.C.crv It looks like the file it can't open is there? I have attached the log file for recon-all and trac-all the subject in case it might help. Thank you, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Maryland, College Park *ddcc2442(a)gmail.com <ddcc2442(a)gmail.com>* 443-254-6298

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Cerebellar edits to correct aseg
by Zeng,Victor (BIDMC - Psychiatry) 10 Oct '19

10 Oct '19

Hi, according to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview , there is a separate protocol to correct cerebellar errors with rois such as the lingual gyrus, fusiform and etc specially the creation of the brain.finalsurfs.manedit file. I have a few questions about this step: I'm assuming that the recon-2, if it detects a brain.finalsurfs.manedit, it makes a mask out of it, and applies it to brain.finalsurfs? The potential conflict I see here if that's not the case is this scenario: I'm doing all the manual edits for the brainmask, re-run recon23, then I create the brain.finalsurfs.manedit and correct the cerebellum, running the recon-all -autorecon-pial. Then I realize that there are still recon errors, and I edit the brainmask again. Would this second instance of editing the brainmask be negated by the fact that the brain.finalsurfs.manedit file doesn't have these edits? Also, generally, is it okay to do other sort of edits (e.g removing the blood vessel between the cerebral cortex and the cerebellum) @ the brain.finalsurfs.manedit, rather than the brainmask.mgz? best Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab ph: 617 754 1237 -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Error in running make_average_subject
by Himanshu Aggarwal 10 Oct '19

10 Oct '19

External Email - Use Caution Hello Freesurfer Developers I am trying to create an average subject for 20 subjects using the function make_average_subject. But I keep running into a segmentation fault. I have attached the recon-all.log file. I found a few other posts about the same problem which direct the users to the following patch: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ (https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/) But this patch does not have a readme file which can instruct the users about the steps that need to be followed to get rid of this bug. However, I have replaced the files in /usr/local/freesurfer/bin/ (i.e. the $FREESURFER_HOME) with the files given in this patch directory. But the problem still persists. Kindly provide the steps that need to be followed to make use of this patch properly. Regards Himanshu

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Brainhack Global 2019: Call for Local Event Sites and Participation
by brainhack org 10 Oct '19

10 Oct '19

External Email - Use Caution Dear colleagues, *apologise for cross posting* Brainhack Global 2019 is collecting registrations for hosting sites! The event will be run globally, on November 13-17, to share ideas and experiences with colleagues across diverse disciplines and institutes. Don’t forget that you are the designer of your own event! You can run your hackathon around a theme that your institute is working on, hold a train track to share the expertise among your colleagues or broadcast all around the world, propose your own projects to run collaboratively and make them heard across the globe, or work on local proceedings and guidelines that would facilitate open and transparent scientific research for the local and global neuroscience community. Brainhack Global 2019 team is ready to help in hosting local events. Please check our website for more information and FAQs, and our Github repository for guidelines and materials that we provide. If you are interested in running a Brainhack, please fill the form in the Brainhack Global 2019 website! If you are planning to participate in an event, please check out the 2019 event hosts registered with us so far from the Brainhack Global 2019 website. http://brainhack.org/global2019/ Read our FAQs! http://www.brainhack.org/global2019/#faq Follow Brainhack Twitter! https://twitter.com/brainhackorg Join discussions on Brainhack Mattermost! https://mattermost.brainhack.org/brainhack/channels/brainhack-global-2019 Important Dates 13 November 2019 Host confirmation 13-17 November 2019 Brainhack events We look forward to having you all in this very exciting event! The Brainhack Global 2019 Organizing Committee Cameron Craddock, The University of Texas at Austin Dell Medical School, Texas, USA Pierre Bellec, Centre de Recherche de l'Institut Universitaire de Gériatrie de Montréal, Montréal, Canada Daniel Margulies, CNRS, Paris, France Isil Poyraz Bilgin, The University of Reading, Reading, UK Sofie Van Den Bossche, Ghent University, Ghent, Belgium Damion Demeter, The University of Texas, Texas, USA Anibal Sólon Heinsfeld, The University of Texas at Austin Dell Medical School, Texas, USA Peer Herholz, Montréal Neurological Institute & Hospital, McGill University, Montréal, Canada Jon Haitz Legarreta, Université de Sherbrooke, Sherbrooke, Canada

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PhD & Postdoc positions – computational modeling and real-time fMRI neurofeedback of language, bilingualism and dyslexia
by Narly Golestani 10 Oct '19

10 Oct '19

External Email - Use Caution PhD & Postdoc positions – computational modeling and real-time fMRI neurofeedback of language, bilingualism and dyslexia PhD and Postdoc positions are available at the Brain and Language Lab (www.brainandlanguagelab.org<http://www.brainandlanguagelab.org>) at the University of Geneva. The PhD position is for 3-4 years, and the postdoc position is for up to 4 years, and salary will be commensurate with experience. Several projects will be done in collaborations with Maastricht University and with the University of Vienna. Applicants should have a strong interest in human brain imaging, and in language function and dysfunction, and should have one of (or a combination of) the following profiles: 1. Candidates with a degree in Biomedical Engineering, Computational Neuroscience, or a related field, and with solid experience in computational modelling (i.e. encoding / decoding) of fMRI data, machine learning, statistics and programming. Projects will include extensions of our recent work on the neural encoding of acoustic information in speech sounds (https://www.ncbi.nlm.nih.gov/pubmed/31285622) to higher levels of language processing. 2. Candidates with a degree in Cognitive Neuroscience, Biomedical Engineering and/or Psychology, with solid experience in the acquisition and analysis of brain functional (and structural) imaging data. Projects will include real-time fMRI neurofeedback training studies, focusing on different levels/aspects of language learning. Candidates for either position (depending on experience) will also have the opportunity to become involved in the analysis of data from a 7T myelin mapping (R1) study. The positions are available immediately, and applications will be considered until the position is filled. Applicants should send me their CV, a statement of research interests, and the names and contact information for 2-3 references, at Narly.Golestani(a)unige.ch<mailto:Narly.Golestani@unige.ch>. ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Prof. Narly Golestani Brain and Language Lab Department of Psychology Campus Biotech 9 Chemin des Mines, 1202 Genève +41 22 379 53 52 <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>http://www.brainandlanguagelab.org https://twitter.com/brain_lang_lab ----------------------------------------------------------------------------------------------------------------------------------------------------------------- <https://outlook.unige.ch/owa/redir.aspx?SURL=5WTo-p-J-W9FrDydU-0WU4PdMytUGs…>

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FS dev install error at mri_surf2vol on mac
by fsbuild 10 Oct '19

10 Oct '19

External Email - Use Caution Hello Jonathan, It could help to add -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON to the cmake command line to see what the compiler is doing when you run make and see the first instance of those errors, but clearly something is not right with the linker options.. You could also try downloading makefile.wiki from, https://drive.google.com/file/d/1IMEWQty_7zjsglbErQOlu_KpXb8Lmgmv/view?usp=… - and then rename it to makefile.   This should go in the same subdirectory as your ./freesurfer folder as created by git. The makefile has targets to  fetch/update/setup everything from github, fetch the archive of 3rd party libs needed to build freesurfer, show you the cmake command it will run, run that cmake command, run the make command to compile the source, then do the install pass.  You can see what the steps are if you type "make help".   This works for me on Mac OS 10.13.6 (High Sierra) with the native clang compilers.  I also use a homebrew installation already on my Mac installed under /usr/local, though the makefile will try and set that up w/o actually installing it under /usr/local. - R. Jonathan DuBois wrote: ld: warning: could not create compact unwind for _MatSetValuesLocal: stack subq instruction is too different from dwarf stack size

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Re: [Freesurfer] Notice about macOS Catalina Notarization and FreeSurfer
by fsbuild 09 Oct '19

09 Oct '19

External Email - Use Caution Hello Aditya, We are aware of the security changes in Mac OS 10.15 such as notarization whereby Apple has decided to extend security rules for applications (*.app bundles) to command line tool/binaries.   From my reading of developer postings it is not clear that the notarization process in the current release of Catalina can actually detect the linkages in and authorize all the Mac software that has been built on and distributed for older versions of Mac OS.  I suspect this is why in the past weeks I have started to receive at least 1 email a day from commercial vendors of Mac software saying not to upgrade to Catalina if you want to use their existing software releases.   So perhaps the the first (10.15.0) release of Catalina cannot support or be backwards compatible with all previous releases of Mac software.   My understanding is that each binary only needs to be authorized once and subsequently the approved state is saved, and the binary will run.  I can imagine writing something to try and authorize each individual command under ./freesurfer/bin starting with the lowest level commands, but I would not start with using the recon-all command.. - R. Aditya Kulkarni October 8, 2019 at 22:26 External Email - Use Caution Hello FreeSurfer team, With Apple’s recent release of macOS Catalina, I wanted to test its compatibility with FreeSurfer. Indeed the executables in the freesurfer/bin folder are subject to the “notarization” problem in the OS, such that every dependent executable that is used in a recon-all stream requires the user to allow it manually through security (a process which becomes cumbersome and interrupts recon-all runs with the many libraries it requires). I know you are all working very hard on the software’s development and just wanted to update with this information in case other users are updating to Catalina and going to run a FreeSurfer stream soon. Best, Aditya Kulkarni _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Freesurfer October 2019