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Question about dmri_trk2trk to show the corrected results
by Tarumi Takashi 26 Jan '22

26 Jan '22

External Email - Use Caution Dear experts: I performed cluster-wise correction for along-tract measures using mri_glmfit-sim as documented here ( https://secure-web.cisco.com/1YmsMw8LA5K4vjKmpPSbf5iYXXniVrshoE73mbH13u44Iu… Now, I would like to use drmi_trk2trk to embed the corrected statistical results into the template .trk file, as shown by the command below. dmri_trk2trk --in $FREESURFER_HOME/trctrain/hcp/syn/lh.uf.display.trk \ --out trc/stats/lh.uf.overlay.trk \ --over trc/stats/lh.uf.RD_Avg.glmdir/contrast1/sig.mgh \ trc/stats/lh.uf.RD_Avg.glmdir/contrast1/z.mgh Which of the contrast files should I overlay to show the corrected results? Are the "sig.mgh" and "z.mgh" files corrected for multiple comparisons after running mri_glmfit-sim? Running mri_glmfit-sim with positive contrast for example generated the following output files, but which of them correspond to the "sig.mgh" and "z.mgh" files? I would greatly appreciate if anyone who knows the procedure teaches me to do this. perm.th13.pos.max.cwpval.txt perm.th13.pos.pdf.dat perm.th13.pos.sig.cluster.mgh perm.th13.pos.sig.cluster.summary perm.th13.pos.sig.masked.mgh perm.th13.pos.sig.ocn.lut perm.th13.pos.sig.ocn.mgh perm.th13.pos.sig.voxel.max.dat perm.th13.pos.sig.voxel.mgh perm.th13.pos.y.ocn.dat Sincerely, Takashi Tarumi

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Postdoctoral Scholar Position- Stanford University (Cognitive-motor dysfunction in Parkinson's disease)
by Kevin Bryant Wilkins 25 Jan '22

25 Jan '22

External Email - Use Caution The Human Motor Control and Neuromodulation Lab under Dr. Helen Bronte-Stewart (https://secure-web.cisco.com/1f9dUjRrFk6HT1kdt75XvcPOiw09RU7qvJGDFohQet7PqZ…) part of the Stanford Movement disorders Center within the Department of Neurology and Neurological Sciences at Stanford University’s School of Medicine, is seeking a postdoctoral scholar to investigate cognitive-motor dysfunction in Parkinson’s disease. The goal of the research in the laboratory is to understand the pathophysiology of movement disorders such as Parkinson’s disease. At Stanford, innovations in neural interface technology have allowed us to discover how abnormal electrical brain activity contributes to disorders in movement. In the Human Motor Control and Neuromodulation Lab, the first decoding of electrical activity in deep brain structures during abnormal movement in Parkinson’s disease patients was performed using novel and investigative sensing neurostimulators. Our team has deconstructed brain activity to discover both the neural code responsible and kinematic quantification for various motor symptoms in Parkinson’s disease. This has enabled us to reverse engineer brain circuitry and restore movement in Parkinson’s disease using the first closed loop, demand-based brain pacemakers that respond to neural and kinematic markers of movement impairment. We are now working towards expanding this approach to address the currently unsolved problem of cognitive impairment in Parkinson’s disease. The aim of the current work is to characterize the cognitive-motor dysfunction in Parkinson’s disease using a combination of cognitive assessments, motor tasks, and structural neuroimaging to pave the way for a novel deep brain stimulation therapy aimed at improving these deficits. Specifically, you will investigate the role of the cholinergic system in specific cognitive domains in Parkinson’s disease and its overlap with gait and fine-motor tasks. Additionally, the candidate will help validate the use of novel targets for deep brain stimulation using a combination of tractography and DBS modeling. The current position offers an exceptional opportunity for neuroscientists with a background in cognition and/or structural imaging to apply these skills in a clinically-relevant domain. The desired candidate would have a PhD in Neuroscience or a related discipline with experience in cognition, motor control, and structural imaging. Preferred start date is before July 2022 but is flexible. Job Requirements Required: PhD in Neuroscience or related disciplines with expertise in data sciences Experience working in the area of cognition and motor control Experience in structural imaging (tractography, voxel-based morphometry, etc.) Comfortable analyzing data in Matlab, Python, or similar languages Strong data science skills Ability to work well in a diverse team Effective oral and written communication skills Excellent organization skills and demonstrated ability to complete detailed work accurately Excellent problem-solving ability Preferred: Experience with Parkinson’s disease or other clinical populations Experience with deep brain stimulation modeling (volumes of tissue activated, etc.) Experience with larger data sets How to Apply: Apply by sending the following to Kevin Wilkins (wilkins2(a)stanford.edu) CV Cover letter describing interest and relevant experience for the project Three potential reference contacts

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Tract orientation old-new version
by Montserrat Domingo Ayllón 25 Jan '22

25 Jan '22

External Email - Use Caution Dear FreeSurfers, I have a question concerning the morphological correspondence between the tracts obtained with the old version of Tracula, which reconstructs 18 white matter tracts, and the new version of Tracula, which reconstructs 42 white matter tracts. In the old version, FreeSurfer website specified the orientation of tracts as followed *https://secure-web.cisco.com/1SYoGI_oRbxgO5L4bEmgFMAfx6xPgIzVtrNQIuLTiEvH5EvhGD9IXl6E25nUOlBFXSc0VqVzXnyeYYWNesjTaXLlJqCIJyhdr6DNMqE1ItycEUYdvmxiZla0QU6vGPKK67quADF99Q94ZlKP6zR5mAsz7rNwjTAJpcs9r8moNfQX3YwrQ5uFf1aS5Cfjre1VSHy0ipYuVnoKP7F3CE3SfZdPTZCvRTqviHXd__TV0lmhOCjoCvXCgFHP7m-QXwCgZqtJGfg_a2prtUuRwc1o-4-kggFKFwcH6-2OItBxZJdH20SR50vj-xL05ASeldwlqJvpD15S_i_pX1y_eJkXUMw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTraculaStatistics* <https://secure-web.cisco.com/1SYoGI_oRbxgO5L4bEmgFMAfx6xPgIzVtrNQIuLTiEvH5E…> Points are always ordered in the following way: • CST : Brainstem -> Motor cortex • UNC : Temporal -> Orbitofrontal • ILF : Temporal -> Occipital • ATR : Frontal cortex -> Thalamus • CCG (CingulumCingGyrus) : Posterior -> Anterior • CAB (CingulumAngBundle) : Posterior -> Anterior • SLFP : Frontal -> Parietal • SLFT : Frontal -> Temporal • F-MAJOR/MINOR : Left -> Right compared to the new orientation also specified in the website Points are ordered according to the following convention (see also along-tract plots): https://secure-web.cisco.com/1BJUS0uCXEETYGhNl8xz4sva9Wq-7xSyeuy2AmjISeSWeU… For pathways with a right-left orientation: If the pathway is inter-hemispheric: From right to left If the pathway is intra-hemispheric: From medial to lateral For pathways with an anterior-posterior orientation: From anterior to posterior For pathways with a superior-inferior orientation: From superior to inferior I have post-processed my data with the old version and I'm concerned specifically with two tracts, ATR and CCG. Theoretically, ATR has the same orientation in both versions, antero-posterior, from frontal lobe to thalamus, but the FA graph created by voxel-data obtained with the old version has an inverted morphology, meaning that the highest values of FA in the old version are placed in the anterior limb of internal capsule whereas the highest values of FA in the new version are located in the frontal lobe. To make it clear, I will send you attached a pdf. Regarding CCG, the FA graph created by voxel-data obtained with the old version has the same morphology, when I will expect the inverted morphology given that the new orientation (antero-posterior) is inverse to the old orientation (postero-anterior). The other tracts of the old version have a concordance with the tracts of the new version. I would be very grateful if someone could tell me if I can trust the data obtained with the old version and the graphs obtained with by-voxel data. Thank you in advance. Montse Domingo Ayllón

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Re: [Freesurfer] Reading files from a hard drive (on Windows in the Fressurfer Ubuntu VM)
by fsbuild 24 Jan '22

24 Jan '22

External Email - Use Caution You can setup a shared folder in Windows to contain files the VM can see..  if your external hard drive shows up in Windows Explorer, then you can copy files from there into the shared folder. This posting shows an example, https://secure-web.cisco.com/11DgSP6uWEzU9l91wLx_sKr77qIMGn3Bxz8CTqCN1iqTwb… In this example you,- create a shared folder on your C drive using Explorer, i.e., C:\shared- with the VM running, go to the pull down menu for “Devices” in the VirtualBox application and select “shared folder”- click on shared folders- click on the folder icon with a + sign- in the popup menu click on the arrow next to the field for “Folder Path” a navigate to the shared folder on Windows to set the path, i.e., C:\shared- click OK (don’t fill in anything else) to get out of the popup menu- click OK to get out of the shared folders menu… back in the VM in your terminal window do …$ cd$ mkdir guest_shared$ mount -t vboxsf shared ~/guest_shared…an icon for the mounted folder named guest_shared should appear on the Ubuntu desktop … double click on it and/or use the terminal to go there ...$ cd guest_shared Then it should work to copy files into C:\shared on the Windows side and see them in the Ubuntu VM. - R. On Jan 24, 2022, at 04:19, Tim Schäfer <ts+ml(a)rcmd.org> wrote:       External Email - Use Caution        Dear Krystal,FreeSurfer does not know about hard disks, the operating system is responsible for that. In this case the problem most likely is with the Virtual Machine (VM), which needs to get access to the hard disk. You should be able to make a folder on your host system (the physical machine) available to the VM system somehow in the VM software. It should not matter which harddisk that folder is on. This is sometimes called 'mounting' the folder. Once you can see the folder inside the VM, FreeSurfer will also be able to see it. Good luck!TimOn 01/24/2022 1:50 AM krystaly <krystaly(a)hku.hk> wrote:External Email - Use Caution        Hi FreeSurfer experts,I’m trying to open nifty/ DICOM files, which are stored in a hard drive (SEAGATE - Backup Plus Hub; Model: SRD0PV1). However, the files cannot be found in any of the folders on Freesurfer 7.1.0 of which operates on Visual Machine on Window 10.May I know whether I should: 1.  Import those folders to Freesurfer for viewing at Freeview; or 2.  Set anything for opening the files directly from the hard drive?Please kindly advise. Thanks a lot.Best regards,Krystal_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://secure-web.cisco.com/1JG2wguzlymmvbwtzbW0WPy_QcmP7r_KfWhZrRkmOo_9ZelrtECWjbzOVlbro1PvNx1SYxdQ4FGzgF_W-dtI4C1hLXMvEjAy-W3B2RkK-OKt9OwkXa8PQVTTwFI8TLimbJIM7CxxCi6SdfvcPsZDUR1cDemEKirf_qlHbI6XRTzzyRi6ighdVFD1piAnTrgTnP2ywRwPF4ib0UQU0nAuBu4dBsykhlRBOFs3JeCYwPUJqwcTTVNDmjToJ2duYB5DraoFLZSv7J7NhYboH9JC4HUxl7Fh6sejZ0z76ijfG5aThBuRzsFcS7JCEw7SjlavxKsD1zEPX0vfpbqtPw3gCjQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer--Dr. Tim SchäferPostdoc Computational NeuroimagingDepartment of Child and Adolescent Psychiatry, Psychosomatics and PsychotherapyUniversity Hospital Frankfurt, Goethe University Frankfurt am Main, Germany_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Two PhD positions in visual perception and brain development
by Mareike Grotheer 24 Jan '22

24 Jan '22

External Email - Use Caution In the *Department of Psychology *and the Center for Mind Brain and Behavior (CMBB), the Education Neuroscience Lab headed by Junior Group Leader Dr. Mareike Grotheer is currently recruiting *2 PhD Students.* The positions are part of the externally funded project "SFB / TRR 135 Cardinal Mechanisms of Perception, C10 Neural substrates of word and number categorization" (DFG Sonderforschungsbereich 135.3 http://secure-web.cisco.com/1jQDdODSir5uGnA_8UDFMeqSqX3Ws_I_ubLm8iz-gWAUpGX… <http://secure-web.cisco.com/1kdf2doeBrCSErq67tB1e2n-ycuqhvvuZzBKbe7ijgqGMug…>) and are *limited until 31.12.2025, *if no former times of qualification must be considered. The *starting date is as soon as possible*. The positions are *part-time *(*75 % *of regular working hours) with salary and benefits commensurate with a public service position in the state Hessen, Germany (*TV-H E 13, 75 %*). Project C10 investigates how words and numbers are processed in the brain and how the brain changes as we acquire math and reading skills. The successful candidates will be highly motivated to conduct research on the neural substrates of visual perception, reading, mathematical cognition and / or brain development. The lab strives to employ a multimodal approach and the successful candidates will therefore have the opportunity to acquire multiple cutting-edge MRI techniques, such as functional, diffusion and quantitative MRI. By combining these tools with behavioral measures as well as computational models (e. g. convolutional neural networks), the successful candidates will explore the human visual system, the interplay of brain function and structure, learning-induced changes in the brain and brain development. The successful candidates will plan, carry out and analyze experiments as well as prepare publications and conference presentations of their work. The lab is part of a larger research network, with excellent links to scientists in Europe and the US. Marburg is a beautiful university town, located just 90 km north of Frankfurt, right in the heart of Germany. The positions are limited to a time period deemed adequate for the completion of a doctoral degree. As part of the assigned duties, there will be ample opportunity to conduct the independent scientific research necessary for the completion of a doctorate. The limitation complies to § 2, 1 WissZeitVG. The successful applicants will hold an MSc-degree (or equivalent) in Psychology, Neuroscience, Biology, Computer Science, or related fields. The applicants will further be keen to learn new techniques and to expand their quantitative and programming skills. They should also enjoy working in a team, as well as, independently. Experience with MRI, programming in Matlab or Python and good written and verbal English skills are desirable. Disposition to own scientific qualification (e. g. a doctorate project in Psychology) is expected. Feel free to contact Dr. Mareike Grotheer at grotheer(a)staff.uni-marburg.de <mailto:grotheer@staff.uni-marburg.de>for more information. We actively support the professional development of junior researchers, e. g. by the offers of Marburg Research Academy (MARA), the International Office, the Higher Education Didactics Office and the Human Resources Development Office. We support women and strongly encourage them to apply. In areas where women are underrepresented, female applicants will be preferred in case of equal qualifications. Applicants with children are welcome – Philipps-University is certified as a family-friendly university. Sharing a full-time position (§ 8 Abs. 2 S. 1 HGlG) as well as a reduction of working time is possible. Applicants with a disability as described in SGB IX (§ 2 Abs. 2, 3) will be preferred in case of equal qualifications. Application and interview costs can not be refunded. *Please send your application mentioning registration fb04-0002-wmz-2022 as a single PDF file to Zika(a)students.uni-marburg.de <mailto:Zika@students.uni-marburg.de>, before the 28^th of February 2022.*

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surface based group analysis
by David 24 Jan '22

24 Jan '22

External Email - Use Caution Hello FreeSurfer Developers, Hello, I would like to ask if there are other correction methods besides multiple comparison correction when surface based group analysis.

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Reading files from an external hard drive
by krystaly 24 Jan '22

24 Jan '22

External Email - Use Caution Hi FreeSurfer experts, I’m trying to open nifty/ DICOM files, which are stored in a hard drive (SEAGATE - Backup Plus Hub; Model: SRD0PV1). However, the files cannot be found in any of the folders on Freesurfer 7.1.0 of which operates on Visual Machine on Window 10. May I know whether I should: 1. Import those folders to Freesurfer for viewing at Freeview; or 2. Set anything for opening the files directly from the hard drive? Please kindly advise. Thanks a lot. Best regards, Krystal

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Using SPM segmentations in FreeSurfer
by Nathan Kindred (PGR) 24 Jan '22

24 Jan '22

External Email - Use Caution Hi, I have been trying to incorporate segmentation files from SPM into FreeSurfer to improve the surfaces, but I am not sure if I am going about it in the right way. I have been replacing the wm.mgz file with a file from SPM and then running ‘recon-all -s ${subject} -autorecon2-wm -autorecon3’, but I keep getting errors. I have tried using both conform and conform_min as part of mri_convert when replacing the wm.mgz file with an SPM file but in both cases I still get errors. Are there other steps I should be taking or a different line of code I should run to get this to work? Thanks, Nathan

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Tracula -prep error: cannot stat dwi_orig_las.1.bvecs
by John Pap 23 Jan '22

23 Jan '22

External Email - Use Caution Hello to everyone! I'm trying to run the preprocessing step of tracula to my subject and I keep getting the following error: mv: cannot stat '/home/ioannis/FFF/KORO/T1_nii/trc/Subj_koro/dmri/dwi_orig_las.1.bvecs': No such file or directory As a matter of fact this file was never created during the process. My files are in nifti format and I try to reconstruct the corticospinal tracts. I attach my configuration file and the log file. Thanks in advance for your help! Ioannis P.

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VM password
by REEM ABU BAKR BAHATHIQ 23 Jan '22

23 Jan '22

External Email - Use Caution ---------- Forwarded message --------- From: REEM ABU BAKR BAHATHIQ <rbahathiq0001(a)stu.kau.edu.sa> Date: Wed, Jan 19, 2022, 3:11 PM Subject: VM password To: <freesurfer(a)nmr.mgh.harvard.edu> Dear Freesurfer mailing list, I have just downloaded the virtual machine + ubuntu package, as outlined on the website when running a VM in windows. However, ubuntu is asking for a developer password to open within the VM. I see on the help page (on the website) that the log in ID could be in the README doc, but I can't actually get the VM open to get there. Does anyone know the password so I can set up the VM and get started with freesurfer? Thanks so much in advance!

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