Freesurfer October 2018

freesurfer@nmr.mgh.harvard.edu

113 participants
156 discussions

hippocampal subfields error
by Marcel Heers 03 Oct '18

03 Oct '18

External Email - Use Caution Dear Eugenio, I am currently testing the newest version of your hippocampal subfield analysis script. If I process the data on my macbook the files hipposubfields.lh.T2.v21.file_ID contain the volumes of the different nuclei, but on the linux server these files remain empty. On the server I installed freesurfer as local user. Do you have any suggestions how to check what might go wrong? Thanks for your help! Marcel

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Re: [Freesurfer] Overlay electric field distribution on pial surface
by Meusen - Klooster, D.C.W. 03 Oct '18

03 Oct '18

External Email - Use Caution Dear Prof. Fischl, Sorry for the lack of clarity. I used bbregister to generate a registration.dat file. I used simnibs to calculate the Efield distribution and this has the option to convert the Efield mesh files to .nii files. So I registered the high resolution T1 (from simnibs, that aligns with the Efield) to the original T1 data. Consecutively, I used tksurfer to visualize. bbregister --s Dep48_T1_origANAT --mov /home/debby/Desktop/FigModPap_Depr48/fs_HeadmeshDep48_origT1/mri/T1.mgz --reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat --t1 tksurfer FigModPap_Depr48 lh pial -sdir /home/debby/Desktop -overlay /home/debby/Desktop/FigModPap_Depr48/Dep48_DLPFC_normE_CORRECTED.nii -overlay-reg /home/debby/Desktop/FigModPap_Depr48/register_AnatSimnToAnatOrig.dat -fthresh -2 -fmid 150 Best, Debby ________________________________________ Van: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] namens Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Verzonden: zaterdag 15 september 2018 17:21 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Overlay electric field distribution on pial surface Hi Debby you need to give us a lot more information. What commands did you use to sample the field onto the surface? What was the output of those commands? Note that tksurfer is deprecated, so I wouldn't worry about how it looks cheers Bruce On Sat, 15 Sep 2018, Meusen - Klooster, D.C.W. wrote: > > External Email - Use Caution > > Dear all, > I am studying transcranial magnetic stimulation (TMS) and would like to nicely visualize my TMS > induced electric fields over a pial surface, preferably using Freesurfer to stay in line with my > other images. I have a .nii file of the electric field distribution, registered to T1, representing > field strengths in every voxel. Visualization in freeview looks okay, but visualization using > tksurfer does not really give the right results (most of the brain is yellow... no field > distribution visible). I guess something goes wrong in the setting of the colorbar. Preferably I > would like to see the field strengths (min:max) in a blue-red colorscheme. Can anybody tell me how > to accomplish this? > Thank you very much in advance. > Best, > Debby > >

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Deadline approaching: PhD in visual perceptual learning at the Neural Circuits and Cognition lab @ ENI & German Primate Center Göttingen
by Caspar M. Schwiedrzik 03 Oct '18

03 Oct '18

External Email - Use Caution The European Neuroscience Institute in Göttingen (ENI-G) Germany, a partnership between the University Medical Center Göttingen and the Max-Planck-Society, is seeking a *Ph.D. student * About us: The Neural Circuits and Cognition lab of Caspar Schwiedrzik at the European Neuroscience Institute (ENI-G) and the German Primate Center <http://www.dpz.eu/de/startseite.html> (DPZ) in Göttingen, Germany is looking for an outstanding PhD student interested in studying the neural basis of perceptual learning in vision. The project investigates neural mechanisms of learning and perception at the level of circuits and single cells, utilizing functional magnetic resonance imaging (fMRI) in combination with electrophysiology and behavioral testing in humans and non-human primates. It is funded by an ERC Starting Grant (Acronym VarPL; “Specificity or generalization? Neural mechanisms for perceptual learning with variability”). The PhD student’s project will focus on developing new perceptual learning paradigms and investigating the neural basis of perceptual learning in humans using fMRI. In addition, the PhD student will cooperate with other lab members on parallel electrophysiological and fMRI experiments as well as comparative research exploring the same questions in non-human primates. The lab seeks to understand the cortical basis and computational principles of perception and experience-dependent plasticity in the macaque and human brain (see http://www.eni-g.de/groups/neural-circuits-and-cognition) To this end, we use a multimodal approach including fMRI-guided electrophysiological recordings in non-human primates and fMRI and ECoG in humans. The PhD student will play a key role in our research efforts in this area. The lab is located at the ENI (http://www.eni-g.de) and the DPZ ( http://www.dpz.eu) which are interdisciplinary research centers with international faculty and students pursuing cutting-edge research in neuroscience. The PhD student will have access to a new imaging center <http://www.dpz.eu/en/infocenter/> with a dedicated 3T research scanner, electrophysiology, and behavioral setups. ENI-G is engaged in experimental molecular and cellular research on the central and peripheral nervous systems as well as cognitive and systems neurosciences research. ENI is part of the University Medical Center Göttingen and associated with the Max Planck Society. The University Medical Center Göttingen is a tertiary care center. Its 7,400 employees work in over 65 departments and facilities to provide top-quality patient care, excellent research and modern teaching facilities. Göttingen provides a vibrant and stimulating neuroscience community with a strong background in computational as well as experimental neurosciences. The PhD student will have the opportunity to join one of the fourteen programs of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (http://www.ggnb.uni-goettingen.de) Your profile: The position will be available starting in November 2018 with an initial appointment for 3 years and a salary according to 50% TVL-13. Candidates should have a degree (master, diploma or equivalent) in a relevant field (e.g., neuroscience, psychology, biology), and ideally prior experience in fMRI, strong quantitative, programming, and experimental skills, and share a passion for understanding the neural basis of visual perception and its plasticity. Interested candidates should send their curriculum vitae, a description of their scientific interest and the names and contact information of up to two references who are able to comment on your academic background and who agreed to be contacted to c.schwiedrzik(a)eni-g.de, preferably before *October 10th, 2018*, but later expressions of interest will be considered until the position is filled. A good command of English is a requirement, but fluency in German is not essential. Please apply by 10.10.2018 to: Universitätsmedizin Göttingen European Neuroscience Institute Göttingen Neural Circuits and Cognition Lab Dr. Caspar Schwiedrzik Grisebachstr. 5 37077 Göttingen Germany Tel.: +49-(0)551-39-61371 E-Mail: c.schwiedrzik(a)eni-g.de

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Re: [Freesurfer] amygdala segmentation atlas influence
by Iglesias Gonzalez, Eugenio 02 Oct '18

02 Oct '18

External Email - Use Caution Thanks, Raj. I’d argue that, if the volumes of the nuclei were completely driven by the global volume of the amygdala, e.g., in an extreme case, V_nuc = alpha x V_whole, then the effect size of the nucleus at hand would be the same as for the whole amygdala. Whether such effect size is higher or lower than the “real” effect size in presence of perfect segmentation… depends on the nucleus ;-) Doug: any thoughts? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: "Dr Rajendra Morey, M.D." <rajendra.morey(a)duke.edu> Date: Monday, 1 October 2018 at 21:53 To: "Iglesias Gonzalez, Eugenio" <e.iglesias(a)ucl.ac.uk>, Freesurfer support list <Freesurfer(a)nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] amygdala segmentation atlas influence Hi Eugenio Thanks for your response it is helpful. In the dataset that I just analyzed with about 375 scans I suspect that the segmentation for some nuclei is heavily driven by the atlas. This is resulting in relatively low variance in both the patient group and the control group. The implication is that the between-group statistical test is overly sensitive and therefore produces higher than the expected chance of a significant result. Is this a reasonable concern. The counterargument is that the means of the two groups are closer to each other than the true means because of a heavy reliance on the atlas. The implication here is that the between group statistical test is going to be more conservative than the true difference. Or does it mean the significance of the test is not affected but that the effect size is artificially low. Let me know your thoughts! Thanks raj From: Iglesias Gonzalez, Eugenio [mailto:e.iglesias@ucl.ac.uk] Sent: Sunday, September 30, 2018 10:44 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Cc: Dr Rajendra Morey, M.D. <rajendra.morey(a)duke.edu> Subject: Re: [Freesurfer] amygdala segmentation atlas influence Dear Raj, A few years ago, we published a paper on how Monte Carlo sampling could be used to quantify this. Unfortunately, the method was incredibly slow and difficult to tune, and the performance gain was tiny, so we never put it in FreeSurfer. But this is a direction I’m still interested in, and which I’m planning to revisit in the future. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Emily K Clarke <ekc23(a)duke.edu<mailto:ekc23@duke.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, 26 September 2018 at 15:15 To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Cc: "Dr Rajendra Morey, M.D." <rajendra.morey(a)duke.edu<mailto:rajendra.morey@duke.edu>> Subject: [Freesurfer] amygdala segmentation atlas influence External Email - Use Caution Hello all, I have run the amygdala segmentation in my datasets to obtain volumes of nuclei. I am aware from the fswiki that the volumes should be interpreted with caution because of the reliance on the atlas. When running FS, is there a way to get some metric about how much the segmentation relied on the atlas relative information from the T1 being segmented. If this metric is not available to the user, is some version of it calculated by the software and therefore available internally. Thanks in advance for your help! raj

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Re: [Freesurfer] Mac OS free surfer instalation
by Hoopes, Andrew 02 Oct '18

02 Oct '18

Hi Eduard, we’ll need some more information. What kind of errors are you running into? Are you trying to download v6.0 or the dev version? best Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Vasile, Eduard" <EVASILE(a)mgh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Tuesday, October 2, 2018 at 4:31 PM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Mac OS free surfer instalation Dear Free Surfer Developers, I have installed freesurfer on my laptop and followed all steps you suggested online for a mac computer but freesurfer is still not working. Could you please assist me in installing it? Kind regards Eduard

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Mac OS free surfer instalation
by Vasile, Eduard 02 Oct '18

02 Oct '18

Dear Free Surfer Developers, I have installed freesurfer on my laptop and followed all steps you suggested online for a mac computer but freesurfer is still not working. Could you please assist me in installing it? Kind regards Eduard

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Error during decompression of DICOM JPEG compressed series
by k3ops＠free.fr 02 Oct '18

02 Oct '18

External Email - Use Caution Hi FS team, I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything runs well for most of the subjects that I process so first thanks for this great tool. I am facing an issue with a JPEG compressed DICOM series that I am not able to precess, I always get the following error during "mri_convert" procedure (before calling recon-all), I also wrote the last command that produces this error: fsdcmdecompress --i freesurfer_18/6858304 --o /tmp/root.tmp.decompressed.dcm.v1uqEv --jpeg >& /tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out sh: 1: Syntax error: Bad fd number After some investigations, it looks it is related to the way standard outputs are redirected to "/tmp/root.tmp.decompressed.dcm.v1uqEv.dcmdjpeg.out" file (which is missing by the way). It looks like ">&" redirection is not a correct syntax in bash (the shell I am using), so I tried with others but unfortunately none of them worked so far (zsh, tcsh, csh, sh). Do you have any recommendation for the way to use "mri_convert" tool? or any other tool that could convert DICOM to nifty efficiently? Thanks for your feedbacks. Regards, Florent

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analyzing and reporting parcellation results
by Tamir Eisenstein 02 Oct '18

02 Oct '18

External Email - Use Caution Hi FS experts, When I'm analyzing regional volumes/thickness using one of the atlases ROI's parcellation, and for example want to compare all the ROI's between two groups, should I correct for multiple comparisons (for the entire number of the atlas ROI's)? or is it acceptable to report the results as it is? Best, Tamir

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Convert sig.cluster.mgh file to a binary mask in .nii format
by Carme Uribe Codesal 02 Oct '18

02 Oct '18

External Email - Use Caution Dear FreeSurfer users, I am trying to extract a binary mask from the file cache.th13.abs.sig.cluster.mgh (I want a ROI from the clusters p<0.05) and convert this mask into a .nii file. I have found a previous message in the forum that reccomends using mri_binarize: mri_binarize --i cache.th13.abs.sig.cluster.mgh --min 1.3 --o lh_AP.mgh And from this output I have run: mri_convert --in_type mgh --out_type nii --out_orientation RAS lh_AP.mgh lh_AP.nii However, I can't visualize the lh_AP.mgh and of course the lh_AP.nii is not created properly when I try to visualize it with mricron. Another command that I have tried without success is: mri_surf2surf --sval lh_AP.mgh --tval test.nii --hemi lh How can I get the mask to operate with it in FSL for example? Thanks in advance! Carme Uribe

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Postdoctoral position at the National Institute of Mental Health, National Institute of Health
by Narun Pornpattananangkul 01 Oct '18

01 Oct '18

External Email - Use Caution The Mood Brain and Development Unit (MBDU) at the NIH led by Dr Argyris Stringaris is looking for a post-doc. The focus of the MBDU is on how reward processing aberrations impact on human mood and may lead to pathologies such as depression. There is a lot of promise that reward processing abnormalities underlie psychiatric disorders. Yet, only if causal links reward processing aberrations and mood still are elucidated, will they form the basis of targeted treatment design. To resolve these questions, we use a variety of tools, benefitting from the unique scientific environment and resources that the NIH offers. In particular, we use longitudinal imaging protocols at three different time scales, work on methodological development of resting-state and task-based imaging data fusion, leverage treatment designs (such as psychological or pharmacological therapies) and develop closed loop devices for mood manipulation. We are a team that works closely together, has many regular science and social meetings and collaborates extensively with others in and out of NIH. Candidates with a strong background in MRI and at least an interest in neurophysiological methods such as EEG/MEG, as well as a keen interest in methodology and computational modeling will be most suited for the job. Advanced coding in R, Python, Matlab or Shell scripts is a requirement. Cognitive neuroscientists, engineers and other candidates with strong numerical and computational skills are particularly encouraged to apply. The postdoctoral community at the NIH is large (approximately 4,000) strong and vibrant. Trainees come from across the U.S. and around the world. Salary for this position is defined by type of training and years of experience. https://www.training.nih.gov/postdoctoral_irta_stipend_ranges Benefits include health insurance for the trainee and his/her family, and support for coursework related to the trainee's research and travel to meetings is often available. https://www.training.nih.gov/programs/postdoc_irp The NIH is among the largest and best communities of neuroimaging researchers in the world, with opportunities to collaborate with leaders in the field of fMRI, MEG, machine learning, computational psychiatry and neuromodulation. Our group has access to high performance computing, has been allocated timeslots to use fMRI and has our own in-patient unit with full-time clinicians. See more information here https://www.nimh.nih.gov/labs-at-nimh/research-areas/clinics-and-labs/edb/m… For more information, please write with CV and expression of interest to Argyris Stringaris: argyris.stringaris(a)nih.gov and Narun Pornpattananangkul: narun.pornpattananangkul(a)nih.gov . The National Institutes of Health is an equal opportunity employer.

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Freesurfer October 2018