Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

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,

2 1

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…> ________________________________ ________________________________

1 0

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

2 5

Combining cross sectional and longitudinal analyses
by William Baare 14 Jun '16

14 Jun '16

Hi I have two groups I want to compare, in total 172 scans Of these 78 got a a follow up. Groups are approximately evenly distributed. I want to do first a cross sectional comparison and subsequently a longitudinal analysis for the 78 subjects only. My question is: (1) Is it is valid to analyse all data using the longitudinal processing stream ( e.g. recon-all -all, recon-all -base, recon-all -long), even though I do separate cross sectional and longitudinal analyses? Or (2) should I analyse first the 175 using the cross sectional stream and then separately analyse the 78 with a follow up scan with the longitudinal stream? Of course I would prefer option 1 as that would reduce potential editing/adjusting many thanks in advance William

2 1

SAVE REG in tkregister2
by Hao wen 14 Jun '16

14 Jun '16

Hello: I am using tkregister2 to do some manual registration, but I can not save reg with the button in the GUI here is my terminal output: register: ### can't create file NULL/rgb/NULL I think maybe this is a very stupid question:) But FS is really complicated... Thanks in advance

2 7

output file from running mri_glmfit-sim
by Yu Sun Chung 14 Jun '16

14 Jun '16

Hi, all, While working on gyrification data using Freesurfer, I have a question to confirm one of output files. First, I did run mri_glmfit using age x IQ itneraction. fsgd file in which I included intracranial volume and gender to covary out. then, I am running mri_glmfit-sim for age x IQ interaction using the following commands; mri_glmfit-sim --glmdir lh.ageIQ.glmdir --cache 3 abs --cwp 0.05 --2spaces After running simulation, I see there are several output files. Especially, I have a question about "*cache.th30.abs.y.ocn.dat*" *my question is whether these values are raw values of lgi or residualized values? * I think that these values in "cache.th30.abs.y.ocn.dat" refers to raw, non-residualized values of local gyrification index. so I extract those vales into SPSS and covaried out by running regression with ICV and gender as covariates. but I want to confirm whether my understanding is correct. Anyone who used this can confirm? Many thanks in advance!! Best, Yu Sun

2 1

Segmentation fault in mri_convert
by Christopher Finuf 14 Jun '16

14 Jun '16

I'm trying to convert the dicom to the original 001.mgz file using the following command on a Mac OSX Yosemite version 10.10.5. My SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/ . My current working directory is /Users/csfinuf/Desktop/freesurfer/morerepeat/ . The following is the output and error that I get. I'm running the latest version v 5.3.0 of freesurfer. Any suggestions on what the problem is? What is strange that it works with half my data set but the other has this error. I've run this command in the exact way many times before and have never had this issue. bash-3.2$ recon-all -i /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm -subjid Bigler_Repeatability_0005Ad_M1 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1 \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz \n mri_convert /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm... Getting Series No INFO: Found 178 files in /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1 INFO: Scanning for Series Number 2 Scanning Directory INFO: found 176 files in series INFO: loading series header info. RunNo = 1 INFO: sorting. INFO: (224 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; FileName /Users/csfinuf/Desktop/freesurfer/morerepeat/Bigler_Repeatability_0005Ad_M1/IM-0027-0001.dcm Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName Bigler_Repeatability_AD_M Date and time StudyDate 20160512 StudyTime 075942.531000 SeriesTime 081401.859000 AcqTime 080647.620000 Acquisition parameters PulseSeq *tfl3d1_ns Protocol t1_mpr_sag_iso_ave2_ipat2_(mprage) PhEncDir ROW EchoNo 1 FlipAngle 9 EchoTime 2.26 InversionTime 900 RepetitionTime 1900 PhEncFOV 218.75 ReadoutFOV 250 Image information RunNo 1 SeriesNo 2 ImageNo 1 NImageRows 256 NImageCols 224 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 75.8389 136.8499 125.0000 VolRes 0.9766 0.9766 1.0000 VolDim 224 256 176 Vc 0.0767 -0.9971 0.0000 Vr -0.0000 0.0000 -1.0000 Vs -0.9971 -0.0767 0.0000 VolCenter -3.5106 21.0460 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) Segmentation fault Darwin NS112201PSY2.byu.edu <http://ns112201psy2.byu.edu/> 14.5.0 Darwin Kernel Version 14.5.0: Tue Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 recon-all -s Bigler_Repeatability_0005Ad_M1 exited with ERRORS at Wed Jun 8 13:39:08 MDT 2016 For more details, see the log file /Users/csfinuf/Desktop/freesurfer/morerepeat/subjects/Bigler_Repeatability_0005Ad_M1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

2 1

fs development version
by shi yao wang 14 Jun '16

14 Jun '16

Dear Experts: I set up FS development version. And now it shows error message: -------------------------------------------------------------------------- GNU libc version: 2.17 ERROR: Systems running GNU glibc version greater than 2.15 require a newly formatted license file (it's free). Please download a new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -------------------------------------------------------------------------- How can I upgrade this license? thanks Lawrence Emory

2 1

swapped dimensions?
by Marja Caverlé 14 Jun '16

14 Jun '16

Hi guys, Just a quick question; I have converted my original DICOMs into niftis. After the conversion I manually checked whether the orientations were still the same, and they were not, so I swapped them. After this I did a recon -all. A lot of my results are at one side while I expected them in the other hemisphere. Is there any chance that the recon -all swapped left and right? How to check for this? I just want to be sure that I am really talking about the right hemisphere. Thanks! Best, Marja

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Freesurfer