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Memory
by Fu, Jason (NIH/NINDS) [F] 15 Jun '16

15 Jun '16

Is there any way to check how many autorecon processes I can run at the same time? I am using a linux with 16gb ram.

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-hippocampal-subfields-T1T2
by Daniele Orlandi 15 Jun '16

15 Jun '16

Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): can't open file >No such file or directory >ERROR: Reading transform from file /media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele _______________________________________________________________________________ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorlandi(a)fatebenefratelli.it; daniele.orlandi.psy(a)gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php)

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Convert ascii to .mgh
by Robby De Pauw 15 Jun '16

15 Jun '16

Dear FreeSurfer users, To address the problem of multiple comparison, I wanted to apply the localfdr-method. For this purpose, I need the F-statistic (which I can extract from the F.mgh scalar overlay I presume?). I converted this to an ascii-file, which I was able to load into R, using the following chink of code: mris_convert -c /Users/robbydepauw/Desktop/FreeSurfer/GLM/lh.Group.volume.glmdir/Groupeffect/F.mgh $SUBJECTS_DIR/fsaverage/surf/lh.white F.asc After performing an local fdr analysis in R, I want to create a scalar overlay “lfdr.mgh”, but I fail at converting the asci file into an “.mgh”-overlay file. Any idea how I could approach this conversion (from asci back to .mgh)? Many thanks, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email Robby.DePauw(a)Ugent.be<mailto:Robby.DePauw@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent Route to my office<https://soleway.ugent.be/routes/1090>

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Coregister the CT image and MRI image
by HARI GURAGAIN 15 Jun '16

15 Jun '16

Dear Freesurfer community, I am relatively new to this community. I was trying to register the CT image and the MRI images (MRI as a the target volume and CT as the movable volume). I used the mri_robust_register to to do the registration as below: mri_robust_register --mov vol1.nii --dst vol2.nii --lta v1to2.lta --mapmov v1to2.nii --weights v1to2-weights.mii --iscale —satit The problem is that: after register, the new image (v1to2.nii) is not exactly aligned with the original MRI image (vol2.nii). It gives a very different output. I wonder if I am missing anything here or I need to do some extra steps after the above command in order to get the correct alignment of the two images. I was hoping to get the resultant image should be well orient with the target volume image (vol2.nii image in my case). I really appreciate any help here. Hari Guragain

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GLM: Define the design matrix by myself
by Hao wen 15 Jun '16

15 Jun '16

Hello, Freesurfer experts: I want to define the design matrix by myself in GLM, I know that in FS, when we deal with the categorized factors, we treat them as classes, So basically, I want to make a design matrix like this: 1) formula_EffectOnGroupWithAgeGenderCovariates = 1 + TermGroup + TermAge + TermGender and 2) formula_EffectOnGroupWithAgeGenderInterectionCovariates = 1 + TermAge + TermGender * TermGroup Here, TermGroup and TermGender are categorized factors, so I know that we can make the design matrix like 2) in FS, cuz here we define it as intersection, but my question is that if wen can define a matrix like the first one? I know in SurfStat, we can define it like 1) Hope to hear from you soon:) thank you in advance!

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concerting surface format
by Trisanna Sprung-Much 15 Jun '16

15 Jun '16

Hi there is there a way to convert .mesh (BrainVisa) to the Freesurfer surface format? mri_convert doesn't seem to do it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Compile and Install on El Capitan
by Aziz Nanthaamornphong 15 Jun '16

15 Jun '16

Hi, Can we compile & install Freesurfer on El Capitan? Unfortunately, I found the document for Lion ( https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_mac_developers_page) Thank you, Aziz

2 1

SIENAX
by Hassan bakhshi 15 Jun '16

15 Jun '16

Hi, I lately heard about SIENAX and when I looked into it it seems like Freesurfer, using the same brain extraction process and etc. I wanted to ask if it is more complete than Freesurfer or not? and why researcher are going after it? It is for Oxford University I think. Kind Regards,

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Final Call for Papers SAN2016
by Tibor Auer 15 Jun '16

15 Jun '16

Dear colleagues, please, accept our advanced apologies for any multiple cross-postings... The Society of Applied Neuroscience (SAN, http://www.applied-neuroscience.org/) in cooperation with the Medical School of the Aristotle University of Thessaloniki and the Department of Neurology of the Max Planck Institute for Human Cognitive and Brain Sciences, have the great pleasure to invite you to the biennial meeting of the Society, SAN2016 (http://applied-neuroscience.org/san2016/) which will be held in Corfu Island, Greece between 6-9 of October, 2016. We cordially invite everyone engaged in studies of Neuroscience, to participate in the SAN2016 meeting. Apart from the highly promising scientific program, blended with numerous workshops and special sessions, there will also be a lively social program which will give our guests the opportunity to enjoy Greece and Corfu.We feel confident than you will enjoy SAN2016 both scientifically and socially as one of our main purposes is to give the chance to all colleagues to establish new fruitful international collaborations in areas of mutual academic and clinical interests. SAN2016 will bring together scientists and practitioners from a wide range of specialist fields. These include, but are not limited to: EEG/ MEG/ fMRI/ fNIRS Neurofeedback fMRI-NFB studies Brain Computer Interfaces Trans Cranial Magnetic Stimulation Peripheral Biofeedback Direct Current Stimulation Event-Related Potentials Brain Connectivity Neuronal Reorganization EEG and Cognition QEEG Diagnosis Emerging combined EEG and Virtual/augmented reality technology Instrumentation Audio-Visual Stimulation LORETA & Methodology Clinical, educational, sport and optimal performance applications Rehabilitation Integrative Therapy Complimentary evidence-based applications ...and all fields of applied neuroscience. All the above blended by an attractive selection of keynote and invited speeches, as well as, hands-on pre-conference workshops. There will be a practitioner track focusing on topical issues. The conference committee receives more proposals than space available. Careful attention to Quality of work, clarity and completeness of the submitted materials is likely to increase the chance for acceptance. All the accepted abstracts will be published in the Frontiers in Human Neuroscience. SAN2016 abstract submission is supported by a Frontiers event and are directly submitted through the following link until the 20th of June, 2016: http://www.frontiersin.org/events/SAN2016_Meeting/3717 Numerous special issues and research topics are also planned by Society members as per tradition. We believe that SAN2016 will be a wonderful chance for you, to meet old friends and make new ones. We look forward to seeing you in Corfu, Greece! Panos Bamidis John Gruzelier Manousos Klados SAN2016 Conference Chairs [photo] Manousos Klados, PhD Postdoctoral Researcher, Max Planck Institute for Human Cognitive & Brain Sciences, +49(0)-341-9940-2507<tel:+49(0)-341-9940-2507> | +49(0)-176-6988-1781<tel:+49(0)-176-6988-1781> | http://www.mklados.com<http://www.mklados.com/> | Skype: mklados<http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> | Stephanstraße 1a PC D-04103 Leipzig Germany [https://ci5.googleusercontent.com/proxy/wfND7YmOcmmmhOcWnAPwzldxiMKDQ0ZEH6B…]<http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> [https://ci4.googleusercontent.com/proxy/SOGJyqe3XDVibRzjS7kIHMn0wxxN3gs6crn…] <http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> [https://ci4.googleusercontent.com/proxy/ahUWs7Kb9fTQYqQaKqQOHw_lJ51-8iZCTFV…] <http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> [https://ci5.googleusercontent.com/proxy/I4p-2-DQI2hI3TCSTFL8FU-S6nOJjUSrqaX…] <http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> [https://ci4.googleusercontent.com/proxy/aNqIP9WjyzcakJkPrx4ojYNZW21-IErLJzp…] <http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> ________________________________ [https://ci5.googleusercontent.com/proxy/gNWUZj68l5WWS37gZPrhK0NtyDcg3ynzeRz…]<http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> Call for Papers (Frontiers):Applied Neuroscience: Methodology, Modeling, Theory, Applications and Reviews<http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> [https://ci4.googleusercontent.com/proxy/gqH06Cwh6_YveSPCh8DwhmSl8iQjJKeayHJ…]<http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> Find me at SAN2016 Conference<http://t.sidekickopen53.com/e1t/c/5/f18dQhb0S7lC8dDMPbW2n0x6l2B9nMJW7t5XYg2…> ________________________________ ________________________________

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tkmedit
by kojima_masaki_mail＠yahoo.co.jp 15 Jun '16

15 Jun '16

Hi. I have this error, when I was doing tkmedit PSY1001fs /Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/brainmask.mgz -aux /Users/MRI/Desktop/fsurfer_test_kojima/Surf_data_main/PSY1001fs/mri/wm.mgz -surfs ERROR: Assertion failed: (!c->out.queue_len), function write_vec, file xcb_conn.c, line 195. Abort what is the problem? Kojima

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