Freesurfer

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Midline errors
by Maxime Perron 16 Oct '18

16 Oct '18

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qdec analysis with more than 2 covariates
by vittal korann 16 Oct '18

16 Oct '18

External Email - Use Caution Hi Doug, Recently I started working on freesurfer for volume based analysis. For QDEC, I need to include more than 2 variables. For example if I include patients who hail from different places like statutory town, census town and rural. In present scenario, can I include all three as covariates. Here is the error that qdec showing while running GLM: "ERROR: Subject 2 seems to have a mismatched number of discrete factors (expected 4, found 1)" "Reading source surface /usr/local/freesurfer/subjects/fsaverage/surf/lh.white ERROR: no contrasts specified." "Error in Analyze: command fai;ed mri_glmfit --y /usr/local/freesurfer/subjects/qdec/qdecAnalys/y.mgh --fsgd /usr/local/freesurfer/subjects/qdec/qdecAnalys/qdec.fsgd dods -glmdir /usr/local/freesurfer/subjects/qdec/qdecAnalys/ -surf fsaverage lh -label /usr/local/freesurfer/subjects/fsaverage/label/lh.aparc.label" Could you help us out in this regard. Would appreciate any help!! Korann

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Postdoctoral positions available
by Chinappen, Dhinakaran Maheswaran 16 Oct '18

16 Oct '18

Three, NIH-supported postdoctoral positions in computational neuroscience are available immediately at Boston University in the labs of Uri Eden and Mark Kramer. The positions center on two projects: Project: Measure, model, and modulate cross-frequency coupling. Team: An interdisciplinary team of researchers at BU (Mark Kramer and Uri Eden) and the University of Minnesota (Alik Widge). Goals: (i) Develop new statistical modeling methods to assess cross-frequency coupling (CFC) in real-time, and deploy these tools in in vivo animal experiments. (ii) Develop simple, biophysical models to identify candidate mechanisms of CFC. Project: Assess human seizure dynamics across spatial and temporal scales. Team: An interdisciplinary team of researchers at BU (Mark Kramer and Uri Eden) Harvard/MGH (Sydney Cash), and Columbia University (Catherine Schevon). Goals: (i) Analyze human seizure activity in a unique data set, consisting of invasive brain voltage recordings across spatial scales - from single units to large brain areas, and temporal scales - from high-frequency oscillations to slow brain rhythms. (ii) Build biophysical models to probe how human seizures start, propagate, and stop. For either project, the successful candidate will have a strong background in statistics and computer programming; experience in interdisciplinary neuroscience research and biophysical modeling is preferred, although not essential. The positions are based at Boston University in the labs of Uri Eden and Mark Kramer. Both projects are highly interdisciplinary and will involve frequent and extensive interactions with neuroscientists at UMN (Alik Widge), or clinicians at Harvard/MGH (Sydney Cash) and Columbia University (Catherine Schevon). To apply, or for more information about the position, please send an email to Mark Kramer (mak(a)math.bu.edu) Please include an updated CV, names and contact information of three references, and a brief statement of your interest in the position and relevant qualifications. Boston University offers a vibrant community of statistical, mathematical, and neuroscience faculty and students, and many opportunities for collaboration within and outside the University. Dhinakaran M. Chinappen Clinical Research Coordinator Neurology Department Massachusetts General Hospital m: 1-267-257-1224

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Postdoctoral positions available
by Manish Saggar 16 Oct '18

16 Oct '18

External Email - Use Caution [https://tr.cloudmagic.com/h/v6/emailtag/tag/2.0/1539198474/b66430ca7e69eb44…] [Apologies for cross-posting] The Brain Dynamics Lab (http://bdl.stanford.edu) at Stanford is looking to hire 1-2 postdocs with expertise in neuroimaging data analysis to develop/apply computational methods that can quantify transitions in brain activity (or connectivity) in health and disease (specifically, major depression and ADHD). We use a number of neuroimaging modalities including simultaneous EEG-fMRI and EEG-fNIRS, structural/functional connectivity, and independent fMRI/fNIRS/EEG. We also use computational modeling (e.g., The Virtual Brain) for realistic bio-physical network model simulations and neuromodulation (e.g., TMS) to gain mechanistic understandings for the observed aberrant brain dynamics in patients with psychiatric illness. Other computational tools used in the lab include Topological Data Analysis (TDA) - including Mapper and Persistent Homology - and Deep Learning (DL). Stanford University is located in sunny northern California, deep in the heart of Silicon Valley and a short train ride to San Francisco. The postdoc will be able to contribute to a number of ongoing research projects in our lab and collaborating labs by analyzing neuroimaging data from those studies. In addition, the postdoc will have the opportunity to develop their own research program with the domain of scientific or methodological problems currently being investigated within the lab (http://bdl.stanford.edu) The successful candidate should: • Have a PhD in a relevant field of study and demonstrated experience with the processing and statistical analysis of neuroimaging data. • Have strong and demonstrated computer programming skills, including Python. Experience with Nipype is preferred. • Have strong skills in statistics and machine learning (esp. TDA, DL, etc.) • Have solid experience with computational data analysis, including strong UNIX/Linux skills and experience using high performance computing clusters. Our lab is strongly committed to diversity in science, and we particularly welcome applications from members of traditionally underrepresented groups. Interested candidates should email the following to saggar(a)stanford.edu: • A cover letter describing your background and research interests • CV • Names and email addresses of two references The initial position is for one year, with the option to renew for 2-3 years, given satisfactory performance and available funding. The positions are available immediately and applicants will be considered on a rolling basis. m- Manish Saggar, Ph.D. Assistant Professor, Psychiatry Stanford University http://bdl.stanford.edu

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fMRI mask for hippocampal subfields
by Buckle, Chanelle [cbuckle＠sun.ac.za] 15 Oct '18

15 Oct '18

External Email - Use Caution Good day I have fMRI data and would like to look at BOLD activation in the hippocampal subfields (particularly the subiculum). I was wondering if there is currently an AAL mask available for the hippocampal subfields or if there is some way to create it using the WFU Pickatlas Tool? Kind regards, Chanelle [http://cdn.sun.ac.za/100/ProductionFooter.jpg]<http://www.sun.ac.za/english/about-us/strategic-documents> The integrity and confidentiality of this email are governed by these terms. Disclaimer<http://www.sun.ac.za/emaildisclaimer> Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende bepalings bereël. Vrywaringsklousule<http://www.sun.ac.za/emaildisclaimer>

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using mris_ca_train
by Maedeh Khalilian 13 Oct '18

13 Oct '18

External Email - Use Caution Dear Freesurfer experts, I have a question, does the number of input subjects matter in using "mris_ca_train" or not? i mean does it affect the results?(maybe the more subjects, the better result) and if yes, what is an approximate number? and the second question is that if there is a way so i can check my .gcs file? for example for reading annotation files u had an m file named "read_annotation.m".it did help me alot. Generally how can i check my .gcs file and evaluate its quality? just by applying it on a subject by "mris_ca_label" ? i really appreciate you if you can help me, Kind regards, Maedeh,

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FreeSurfer Errors
by Sparsh Jain 12 Oct '18

12 Oct '18

External Email - Use Caution Hey! I have recently started using FreeSurfer. I have encountered multiple errors over the past few days, and I would like to mention them all. 1. While testing the installation, the code ran for roughly 4-6 hours and generated the T1 and wm output images. The brainmask image failed to load even after multiple attempts. 2. We have patient data from a Seimens 1.5 T MRI machine. They are DICOM images (about 120-145 images). Running dcmunpack on the directory to locate the suitable T1 weighted image (to pass as the input image to freesurfer) returns an error message 'Element not found'. It fails to generate a list of usable input images. The log file also only mentions the error message. Basically, I am having trouble working with DICOM images using Freesurfer. Please advise me on how to go about it. 3. I tried using the dcm2nii tool on the DICOM images. The software gave out three (nearly identical) nii.gz files as output, each about 7 MB in size. I tried running reconstruction on all three one by one. Only the 'compressed' version output underwent reconstruction for a long time without giving any errors. However, the reconstruction process went on for 150 hours without completion. There were no errors during this time, and the mris_fix_topo process went on for about 74 hours until tonight. It was working on 'correcting defect 48' for most of this time, and then the PC suddenly stopped responding. The process had been utilizing 100% of the CPU and 87% of the RAM for a long time, but the computer was always responding. However it suddenly stopped responding after about 74 hours of mris_fix_topology process. My machine has 8 GB RAM and more than 3.4 GHz processing speed (Acer Veriton). 4. Previously, I tried running reconstruction on a different subject's data after converting it to nifti using dcm2niix. After 70 hours of execution, it terminated with an error which showed that the fsaverage folder was inaccessible. Further digging revealed that the folder was somehow pointing to itself. The original error said failed to read from the label file. I had to eventually reinstall FreeSurfer. 5. I tried running iElvis pipeline. After some time I got an error which said that the sphere.reg file couldn't be opened. I tried fixing this but nothing worked. I kept getting the error that lh.sphere.reg file could not be opened and so on. Please help. I have been trying to run it for weeks now. I hope you will be able to address each of these problems soon. Thank You Sparsh

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mri_watershed Error
by Boris Rauchmann 12 Oct '18

12 Oct '18

External Email - Use Caution When I run recon-all i get the follwing error message: mri_watershed Error: GLOBAL region of the brain empty ! Linux 02f92500bcfb 4.15.0-36-generic #39~16.04.1-Ubuntu SMP Tue Sep 25 08:59:23 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-XYZ exited with ERRORS at Thu Oct 11 15:10:22 UTC 2018 The .nii file looks fine. Can someone help me with this? Best, Boris

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Re: [Freesurfer] denoising and recon-all
by Glasser, Matthew 12 Oct '18

12 Oct '18

External Email - Use Caution What are you using for denoising? Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Lisa Crystal Krishnamurthy <lkrishnamurthy(a)gsu.edu<mailto:lkrishnamurthy@gsu.edu>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Thursday, October 11, 2018 at 11:05 AM 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>> Subject: [Freesurfer] denoising and recon-all External Email - Use Caution Hi, I have found that denoising the MPRAGE prior to FS recon-all seems to improve the segmentation (see attached pdf). However, it is not clear if the denoising algorithm may cause some signal intensity changes (especially in voxels with partial voluming at the edge of the brain) that violate assumptions of recon-all. Could you help me understand what the assumptions of your algorithm are, and what I need to do to make sure my images conform to those assumptions? Your help is greatly appreciated. Best, -Lisa ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Postdoctoral position open to work on brain MRI function & microstructure (Italy)
by Jovicich, Jorge 11 Oct '18

11 Oct '18

External Email - Use Caution [Apologies for cross-posting] The MRI Group of the Center for Mind/Brain Sciences, University of Trento, Italy (https://r.unitn.it/en/cimec/mri/) has an open postdoctoral position to develop/apply MRI acquisition and analyses methods to characterize structural and dynamic functional connectivity (deadline October 30, 2018). More information about our group, the call and application links can be found here: https://r.unitn.it/en/cimec/mri/opportunities Feel free to distribute this announcement to potentially interested people. Best, Jorge Jovicich -- Jorge Jovicich, Ph.D. MR Lab Head Center for Mind/Brain Sciences University of Trento, Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3064 Fax: +39-0461-28-3066 Email: jorge.jovicich(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri CIMEC: http://www.cimec.unitn.it/

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