Freesurfer April 2018

freesurfer@nmr.mgh.harvard.edu

118 participants
177 discussions

mri_deface keeps seg faulting
by Warner, Graham Cary 17 Apr '18

17 Apr '18

Hi, I'm trying to deface an MEMPRAGE dataset using the following command: [jazz:test_deface] (nmr-stable53-env) mri_deface outSubDir/mri/orig/001.mgz talairach_mixed_with_skull.gca face.gca sample_T1_input_defaced.mgz and am getting the output: logging results to sample_T1_input_defaced.log reading 'talairach_mixed_with_skull.gca'... reading 'outSubDir/mri/orig/001.mgz'... changing type of input volume to 8 bits/voxel... MRIchangeType: Building histogram Segmentation fault (core dumped) I'm using the Martinos center's default version of mri_deface located at /usr/local/freesurfer/stable5_3_0/bin/mri_deface. I'm using the talairach_mixed_with_skull.gca and face.gca sample files found on https://surfer.nmr.mgh.harvard.edu/fswiki/mri_deface but the actual input mgz came from a scanner here at the center. Maybe this is a CentOS 7 compatibility problem? Please let me know if there is any other information I can provide. Thank you, Graham

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Group Analysis Contrast (Follow-up)
by David S Lee 17 Apr '18

17 Apr '18

Hi Douglas, Thank you for your reply. To follow up, I am setting up GLM analysis with 1 categorical variable and 1 continuous variable (age X weight). My fsgd looks like this: *GroupDescriptorFile 1* *Title Cortical Thickness Interaction between Age and Weight* *Class class1 plus blue* *Class class2 circle green* *Variable Demean Age X Demean Weight* *Input 001 Class1 500* *Input 002 Class2 433* *...* I want to test for an interaction between age and weight while controlling for group. Instead of putting-in age and weight separately, I multiply them to test for interaction. Can you tell me if following contrast vector will correctly test for this? *0 0 0.5 0.5* Thank you for your time, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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Non-rigid registration approaches
by Hedyeh Javaheri 17 Apr '18

17 Apr '18

Hello all, I am performing DTI analysis and wanted to know if Freesurfer has a tool for non-rigid registration. I performed recon-all and dt_recon on my subject and then used the register.dat file that was generated by dt_recon to convert the dt_recon output files back into the space of my orig.nii file from the recon-all output. Now I need to register the files in the orig.nii space back onto the T1 MRI that is in native space. I have tried using mri_vol2vol to get the files in the orig.nii (recon-all) space into the T1 native space without using a registration file (I used --regheader) and now the registration matrix of my file is the same as the native space, but when I use rview to visualize the registration there are flaws. I've also tried this co-registration using tkregister2 to create a registration file called register.native.dat, and then used mri_vol2vol with register.native.dat; and the results were the same as when I used mri_vol2vol with --regheader. Is there a tool to do actual manual registration in Freesurfer? Using tkregister2 I cannot perform localized changes; and the global changes it is capable of do not improve on the coregistration. Here is a breakdown of what I have done: subject in Native space to Freesurfer conformed space using recon-all, output: orig.nii subject in Native space to other Freesurfer space using dt_recon, output: lowb.nii and register.dat >From the other Freesufer space to Freesurfer conformed space using register.dat, output: lowb2orig.nii attempting to convert from Freesurfer conformed space to Native space: using mri_vol2vol and --regheader --> poor registration using tkregister2 to make register.native.dat, then mri_vol2vol and register.native.dat --> poor registration I am running Freesurfer version 6 on Windows. Thanks in advance! -Hedyeh Javaheri

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Brainhack San Francisco 2018 - May 3-5
by Valentina Borghesani 17 Apr '18

17 Apr '18

Dear Freesurfer mailing list, Join us for Brainhack San Francisco 2018: 2.5 days of fun hacking around brain data! When: May 3-5 2018 Where: UCSF Mission Bay Campus More info: sfbrainhack.github.io The event is open to anyone with a passion for the brain and/or data: neuroscientists, hackers, cognitive scientists, etc... Everyone is welcome, as everyone brings something interesting to the table: whether it is an interesting problem, a cool dataset, a rare skill, or a new question. Looking forward to hacking with you! Valentina on behalf of the Brainhack San Francisco Team

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Cohen's D from gamma and rstd: size mismatch
by Kelly Vaughn 17 Apr '18

17 Apr '18

Hello FreeSurfer Experts, I am trying to calculate Cohen's d effect sizes for a contrast I created in QDEC. I have found multiple sources suggesting this code: cd glmdir/contrast fscalc gamma.mgh div ../rstd.mgh -o cohensd.mgh But when I use it (replacing the glmdir and contrast with my own), I get the following error: freesurfer-Darwin-lion-stable-pub-v5.3.0 Darwin Galactica.local 14.5.0 Darwin Kernel Version 14.5.0: Sun Jun 4 21:40:08 PDT 2017; root:xnu-2782.70.3~1/RELEASE_X86_64 x86_64 mri_convert Bi_Eprof_Lthick/lh-Avg-thickness-Eprof-Cor/gamma.mgh Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh mri_convert Bi_Eprof_Lthick/lh-Avg-thickness-Eprof-Cor/gamma.mgh Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from Bi_Eprof_Lthick/lh-Avg-thickness-Eprof-Cor/gamma.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh... ---------------------- mris_calc -o Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh Bi_Eprof_Lthick/tmpdir.fscalc.25880/tmp.mgh div Bi_Eprof_Lthick/rtsd.mgh mghRead(Bi_Eprof_Lthick/rtsd.mgh, -1): could not open file mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) I tried to look into the gamma.mgh and rstd.mgh files and they do appear to be different sizes. Even when I use mri_surfcluster to restrict the gamma and rstd files to a single cluster, the resulting files have different sizes, which leads me to a similar error. Can anyone help with this or is there another way I can attempt to calculate effect sizes? Thank you, Kelly Vaughn -- Kelly Vaughn, M.A. PhD Candidate Developmental, Cognitive, and Behavioral Neurosciences Laboratory for the Neural Bases of Bilingualism | University of Houston

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Postdoctoral position at the NIH/NIMH
by Anderson M. Winkler 17 Apr '18

17 Apr '18

We are seeking enthusiastic applicants for a Post-Doctoral Fellowship position to help with the collection and analysis of large brain-imaging datasets. The successful candidate will use state-of-the-art artificial intelligence methods, with the aim of better understanding psychiatric disorders in young people with mental illness, particularly anxiety and depression. Our goal is to understand better the causes and mechanisms of certain psychiatric disorders, improve their definition and classification, and ensure the best treatment can be offered to psychiatric patients. The successful candidate will develop and apply deep learning algorithms to multi-modal imaging datasets that include MRI (functional, structural), EEG, MEG, and associated behavioral and clinical data. The methods developed by the successful candidate will be used to: - Integrate these diverse sources of information. - Inform the construction computational models in psychiatry. - Test the validity of such models. Candidates with a strong computational background (e.g. PhD in Engineering, Physics, Computer Science, Mathematics, Statistics, Computational Neuroscience, and related areas) who are interested in brain development and psychopathology, are particularly encouraged to apply. Requirements for this position include: - Strong machine learning experience; - Programming experience in Python (preferably), or in R/Matlab/Octave; - Experience with open source machine learning libraries such as Scikit-learn, Theano, and/or Tensorflow; - Excellent interpersonal and written (English) communication skills. Background experience in psychiatry or knowledge of neuroimaging software are not required. However, the candidate will be expected to learn some of these topics as part of their role in our research group. The successful candidate will work jointly with the laboratories of Drs Daniel Pine and Argyris Stringaris, and together with Dr Anderson Winkler, Staff Scientist. Please write to Drs Pine (pined(a)mail.nih.gov) Stringaris ( argyris.stringaris(a)nih.gov) or Winkler (anderson.winkler(a)nih.gov) with your application and CV.

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LME univariate data
by lanbo Wang 17 Apr '18

17 Apr '18

Dear Experts, Hi, There is no example detail on website of LME tutorial. I have some question about it. Could you send me the table of ADNI univariate example data? Thanks, Lanbo

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Re: [Freesurfer] reruns recon-all -long after edits
by Anna Daniels 16 Apr '18

16 Apr '18

Hi Martin, thank you so much for the quick and helpful reply! As I only edited the wm.mgz in the base, there was still some non-wm included there in the long and also some minor edits to the brainmask.mgz were necessary that I had probably overlooked in the cross. To run this command recon-all -long 11904_T1_fs 11904_base -autorecon2 -autorecon3 do I only need to have 11904_T1_fs.long.11904_base (the edited long) and 11904_base in the subjects dir? Or also the cross folder (11904_T1_fs)? I'm submitting the jobs from a HPC system where the upload is time-consuming. Thanks again! Best, Anna --- Hi Anna, yes, long can still be edited, but usually this is not necessary. What kind of edits did you need to do in the long? You would need to call with the long flag, and passing the cross and base name. So just like the regular processing of the -long step, only replace -all with -autorecon2 etc. recon-all -long 11904_T1_fs 11904_base -autorecon2 -autorecon3 for this to work 11904_T1_fs.long.11904_base needs to contain your edits, so maybe backup the old long run and call it backup, then edit this one and run it. You cannot simply append the _edit or you will confuse the naming convention. Best, Martin > On 15. Apr 2018, at 23:07, Anna Daniels <anna.daniels(a)fu-berlin.de> wrote: > > Dear FreeSurfer team, > > using the longitudinal stream in v6.0.0, I edited the cross and base runs, but still had to edit the long runs for some subjects. If I understood the LongitudinalEdits Wiki correctly, the long can still be edited if necessary. > > Rerunning the respective recon-all command with -autorecon2 -autorecon3 and the edited long run as input did not work. How do I rerun the long correctly while incorporating the edits made directly to the long? > > Here you see how I called the procedure: > > anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ ls -lisa > total 20 > 8527874 4 drwxrwxr-x 5 anna anna 4096 Apr 15 21:18 . > 8527873 4 drwxrwxr-x 34 anna anna 4096 Apr 15 12:18 .. > 8544378 4 drwxrwxr-x 10 anna anna 4096 M?r 29 23:54 11904_base > 8527875 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:02 11904_T1_fs_edit.long.11904_base_edit > 8527888 4 drwxrwxr-x 10 anna anna 4096 Apr 12 23:29 11904_T2_fs_edit.long.11904_base_edit > anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ start=`date +%s` > anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ !recon > recon-all -long 11904_T1_fs_edit.long.11904_base 11904_base -autorecon2 -autorecon3 > > Unmatched ". > anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ end=`date +%s` > anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ runtime=$((end-start)) > anna@anna-K56CM:~/FREESURFER/00_DATA_MABT1T2/08a_MABT1T2_long_edits_transfer/c1$ echo $runtime > 10 > > As you can see, the process ends very quickly (10s) and only gives the error 'Unmatched ".' though I did not open any double quotes when calling the procedure. > > Thanks a lot for your help! > > Best, > Anna

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Brainhack Donosti 2018, San Sebastián, Spain
by James Hartzell 16 Apr '18

16 Apr '18

Registration is still open for Brain Hack Donosti, 2018 http://www.bcbl.eu/events/BrainhackDonostia2018/en/conference/ Registration deadline: April 25th, 2018 Project submission deadline: May 1st, 2018 Hacking multimodal neuroimaging techniques to explore brain function and structure Welcome to the very first edition of Brainhack Donostia, taking place in San Sebastian, Spain, between the 2nd-4th of May 2018, hosted by the Basque Center on Cognition, Brain and Language! As an official satellite event for Brainhack Global 2018 (organised by Cameron Craddock and the Neurobureau) this 3-days workshop will focus on tutorials introducing people to Neuroimaging techniques, such as fMRI, Diffusion, MEG, EEG and fNIRS, from preprocessing to data analysis (connectivity and decoding). In a pure BrainHack style, participants are encouraged to bring their own projects to be developed and to recruit collaborators onsite. The projects can focus on fMRI, Diffusion, EEG, MEG and/or NIRS. They can also focus on multimodal imaging if you want! However, given the space available, this edition will be able to host up to a maximum of three project development teams. For this reason, we invite you to submit your project beforehand on this website, specifically here. Yet, before submitting, check the links at the end of this page to verify that your project is eligible! The projects that will be developed will be chosen on the first day of the Brainhack, giving precedence to those pre-submitted. Working papers on the outcomes of the event can appear in the Gigascience Brainhack Thematic Series, and shorter project reports are eligible for the annual Brainhack Proceedings. Can I participate if I don't have a project? Can I do both tutorials and projects? Don't worry, projects are optional, both in proposing them and taking part in them! Their development will take part at the same time as the tutorials. For this reason, we suggest you choose a track on the first day (HackTrack or TrainTrack, as our friends in Singapore like to call them) and not to change it. However, if the projects permit, we will not be strict about it! What about the materials? We will provide the tutorials contents and materials, as well as raw and preprocessed data from Open Databases, on our GitHub RepositoryThis data will be prepared in order to reduce the computational load (hence, the time) required to complete the workshops in a fair amount of time. Nonetheless, if you want to bring your own data to analyse (and, given the possibility, ask specific questions about them), you're more than welcome to do so! What should I bring with me? Participants are encouraged to bring their own laptops (and if they can, a battery change and charger): we will not have a terminal for the attendees. For this reason, we will also communicate what software will be used in the tutorials, so that you can install it in advance (if you prefer to do so). Please try to install it before attending, but if a problem arises during installation, you can ask onsite for help in that step as well! We will also prepare a Virtual Machine with all the software necessary to the tutorials, if you prefer not to install the programs into your laptop Where can i find everything? You can find it in this GitHub Repo! Who can attend? What are the requirements? Do I need a background expertise on something, like programming? Anyone can attend! Although having already a basic knowledge of programming or neuroimaging analysis might help with the tutorials, don't worry: we will not leave anyone behind. If you are a first-timer, have no-clue-on-how-a-computer-works, and are interested in neuroimaging, this could the moment to take your first step! >From Undergraduates to Seniors, from Academics to industrials, we will welcome everyone. Just pay attention to the different fee tiers at the registration. Don't forget: registration is mandatory, and you can do it here. Will there be beverages and food provided? We will not provide free food for lunch nor dinner, but you will be able to go to one of the venues near BCBL to eat, or bring your own food from home. However, what we will do is to have fresh coffeein the main room, as well as coffee breaks. We're also organising a social dinner for Thursday night! It all sounds good, but where can I find more information about Brainhack? There is a quick presentation here, about this satellite edition. If you want to know more about how a Brainhack works, you can find the 2018 global edition website here! If you prefer to have general information about more editions and projects, the general Brainhack website is here. Last but not least, there's also a paper about it on Gigascience, here! Topics We will announce the definitive program asap Programming Introduction to Bash Introduction to Python Virtual Environments Git FMRI & MVPA Preprocessing fMRI data Quality assessment of fMRI data Denoising physiological signals Decoding brain patterns using MVPA EEG & MEG An introduction to electrophysiology techniques to explore your mind From raw data to the insights of your brain Connectivity analysis Connectivity: from theory to practice fNIRS Introduction to fNIRS How to Spectroscope your brain DTI Introduction to DWI Quality assessment of DWI data Preprocessing data Find your path: tractography and group analysis -- James Hartzell, PhD Basque Center on Cognition, Brain and Language (BCBL), Donostia, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

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LGI for the lobar annotation
by Fernanda Hansen P. de Moraes 16 Apr '18

16 Apr '18

Good night, does anyone know if it is possible to calculate the lGI for the ?h.lobesStrict.annot? And if it yes, how can I do it? I've already tried to use: *mri_segstats --annot subjxx/label/lh.lobesStrict.annot --i $SUBJECTS_DIR/subjxx/surf/lh.pial_lgi --sum lh.lobesStrict.annot.pial_lgi.stats* Thank you! -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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Freesurfer April 2018