Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30091 discussions

How to calcutate Brain volume?
by Anupa AV 15 Apr '13

15 Apr '13

Dear FreeSurfer Experts, I'd like to know how to measure the volume of a brain region using freesurfer. I know to obtain the volumes after runnin recon-all command. But I don't find the brain volume of my interest which is DLPFC. How can I get the brain volume of my interest.? Thanks for your response in advance.

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using volume label mask in mri_vol2surf
by Fred Dick 14 Apr '13

14 Apr '13

Dear all I am painting some higher-res anatomical data from a volume to a surface, and want to use a mask that excludes the vessels. (The same data but 1x1x1 conformed were used to create the surface). I've created a binary label in the same space >> mri_cor2label --i ./R2Mask.nii.gz --l ./R2s.label --id 1 made sure that it looks ok when I read in hi-res to tkmedit and display label, then ran mri_vol2surf >> mri_vol2surf --mov ./sPQ07082012-0009-00001-000208-01_R1.nii --reg register.dat --surf-fwhm 4 --hemi $hemi --projfrac $frac --interp trilinear --out_type w --mask R2s.label --o ./dancar-0.5-lh.w And got the output (pasted below), showing that the output is all zero. Output is fine without label, or with -cortex. I've also tried this with a conformed version of the label (also verified in tkmedit) and have had the same thing. (I thought maybe it was applying it to orig vol, which I admit would be strange). (I noticed someone had a similar issue a couple of years ago, but it involved a surface rather than volume label, and looked like it had been resolved). Am running current stable version on Mountain Lion. Thanks for any pointers, best, Fred ########################################################## masking output with label R2s.label INFO: output format is paint srcvol = ./sPQ07082012-0009-00001-000208-01_R1.nii srcreg = register.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = trilinear float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Loading label R2s.label Reading surface /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.white Done reading source surface Reading thickness /Applications/freesurfer/subjects/dancar-synth-handnorm/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 108676 Surface smoothing by fwhm = 4 (n=10) Masking with R2s.label Warning: all vertex values are zero

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Freesurfer Mountain Lion Download
by Garikoitz Lerma-Usabiaga 14 Apr '13

14 Apr '13

I cannot download it, do you think the problem is on my side? Terminal paste: Last login: Wed Apr 10 22:01:36 on ttys000 iMacGari2:~ gari$ curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Darwi… % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 3770M 100 3770M 0 0 343k 0 3:07:28 3:07:28 --:--:-- 0 curl: (28) FTP response timeout iMacGari2:~ gari$ curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Darwi… % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 3770M 100 3770M 0 0 838k 0 1:16:43 1:16:43 --:--:-- 0 curl: (28) FTP response timeout iMacGari2:~ gari$ curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0/freesurfer-Darwi… % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 3770M 100 3770M 0 0 134k 0 7:59:41 7:59:41 --:--:-- 0 curl: (28) FTP response timeout

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Regarding cortical thickness
by Bharti Rana 14 Apr '13

14 Apr '13

I am Bharti, a M.Tech./Ph.D student at School of Computer & Systems Sciences, Jawaharlal Nehru University, New Delhi, India. My area of interest is pattern recognition and image processing. In one of my research work, i used freely available freesurfer software to find cortical thickness using recon-all -all command. But, while retrieving cortcal thickness maps using read_curv() function, i am getting different number of vertices for different brains. Are different number of cortical vertices possible for two different brains? I have gone through FAQ provided by Freesurfer but i did not find any related answer. Kindly clarify. Thanks in advance. -- Best Regards Bharti M.Tech./Ph.D. School of Computer & Systems Sciences Jawaharlal Nehru University NEW DELHI, INDIA

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recon-all problems [solved]
by Marcos Martins da Silva 14 Apr '13

14 Apr '13

I had several problems testing freesurfer 5.2 installation, as previously posted. Now it is all OK and I would like to share what I could learn: 1- It does not work on Fedora 18 (segfaults with all tests with tkmedit, tksurfer and recon-all) that is due to a restriction imposed by glibc (only newest version). Only freeview works under Fedora 18 but, even here, I got a misalignment problem among surfaces and volumes. More details at https://bugzilla.redhat.com/show_bug.cgi?id=905638 2- I got partial functionality using VirtualBox (4.2.8 and 4.2.10). I cannot say about previous versions and the latest one (4.2.12 was released on Apriil, 12th). But I had problems with both virtual machines I tried: CentOS6 (fresh install) and the Xubuntu + FreeSurfer 5.1 vdi file I downloaded from FreeSurfer website. Tkmedit, tksurfer and freeview all worked but recon-all failed all time. 3- Fedora 17 and CentOS 6 work flawlessly out of box if you do not use virtualbox. Probably, other distros will work too, except if they are using the latest glibc (2.16-30). So my final setup is a dual boot machine: Fedora 18 (day-by-day tasks) and CentOS6 (freesurfer tasks). You can do it with only one disk but it is a lot easier with two. I hope it can help people with similar problems.

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5.2 pial surfaces
by Bruce Fischl 13 Apr '13

13 Apr '13

Hi All we've tracked down the problem with 5.2 pial surfaces that affects some types of acquisitions. We will be testing the fixed version this week and hope to release a corrected mris_make_surfaces in the near future. You should just be able to rerun autorecon2 I believe to update your surfaces and not the whole recon pipeline, but we'll make a more detailed announcement when we are ready with it. Anyone who has had problems with the 5.2 pial surfaces (or anyone else for that matter) is welcome to try it out. Just let us know your hardware/software environment and we'll send you a version. Sorry for the problems. cheers Bruce

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announcement for MGH email list (fwd)
by Bruce Fischl 12 Apr '13

12 Apr '13

FYI ---------- Forwarded message ---------- Date: Fri, 12 Apr 2013 00:27:38 +0200 From: Jorge Jovicich <jorge.jovicich(a)unitn.it> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: announcement for MGH email list Ciao Bruce, would you mind forwarding for me the postdoc position announcement below? Thanks, Jorge ----------------------------------------------------------------------------- POST-DOCTORAL POSITION IN USING BRAIN DATA TO SUPPORT THE DEVELOPMENT OF EMOTIONALLY PLAUSIBLE VIRTUAL AGENTS AT CIMEC/CLIC, UNIVERSITY OF TRENTO A postdoctoral position will soon become available at the CLIC laboratory of the Center for Mind / Brain Sciences, University of Trento (http://clic.cimec.unitn.it/) starting as soon as possible from June 2013. The successful candidate will join a team of computational linguists and computational neuroscientists whose research is focused on using machine learning methods to analyze recordings of neural activity (EEG, MEG and fMRI) to gain insights about conceptual knowledge and other aspects of the cognitive models of agents involved in language use and interaction. This particular position will be in the PRESTO project, a collaboration between CIMEC, Delta Informatica, the University's Computer Science Department, and Fondazione Bruno Kessler (FBK). The objective of the project is the development of training environments based on immersion in virtual reality situations in which the trainee interacts with artificial agents (avatars). The role of the postdoc in the project will be to run experiments testing the emotional plausibility of the artificial agents, and studying the interaction between emotions and decision making in the trainees. The ideal candidate for the position is a cognitive neuroscientist with a strong research curriculum in the use of fMRI and/or EEG to study emotions and interaction. Familiarity with machine learning methods to analyze such data (eg MVPA) a plus. The fellowship has a duration of 1 year with the possibility of renewal for a second year if the results of the first year are satisfactory. The Language Interaction and Computation Lab (CLIC) is a unit of the University of Trento's Centre for Mind/Brain Sciences (CIMEC) (www.cimec.unitn.it) an interdisciplinary Centre for the research in brain and cognition including neuroscientists, psychologists, (computational) linguists, computational neuroscientists, and physicists. CLIC consists of researchers from the Departments of Computer Science and Cognitive Science carrying out research on a range of topics, including concept acquisition and information extraction from very large multi-modal corpora, combining brain data and data from corpora to study cognition, and theoretical linguistics. The official call for the position can be found at: http://www.unitn.it/en/cimec/11882/study-and-job-opportunities Deadline for the application is April 30th. For additional information please contact Massimo Poesio (massimo.poesio at unitn.it), attaching your CV. -- Jorge Jovicich, Ph.D. MR Lab Coordinator 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 http://www.cimec.unitn.it/ http://polorovereto.unitn.it/~jovicich

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problem about cortical area values
by 仙豆 12 Apr '13

12 Apr '13

Dear teacher, I haven't found the page describes the workflow to extract freesurfer cortical area values for a region-of-interest (ROI) defined by myself (used another software), I only saw how to calculate cortical thickness values, please help me~ Thank you very much! Student: He Qin

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mri_glmfit & .nii.gz & FSF_OUTPUT_FORMAT
by Xiangzhen Kong 12 Apr '13

12 Apr '13

Hi, all. I have come across a problem when using mri_glmfit. We know that the output format is controlled by the $FSF_OUTPUT_FORMAT. I have checked that in my environment, $FSF_OUTPUT_FORMAT is nii.gz. But the output fils are all in mgh format. How can I get output files in nii.gz? Thanks! Xiang-zhen 【小孔成像】http://www.conxz.net

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setting thresholds in qdec
by Michael Harms 12 Apr '13

12 Apr '13

Hello, Is it no longer possible to set the Min, Mid, and Max thresholds directly on the Qdec display tab? The only way I seem to be able to change them is via the sliders in the histogram at the bottom, which I don't recall previously being the case. This is Qdec 1.4 (FS 5.2) on a RHEL 5.9 system using freesurfer-Linux-centos4_x86_64-stable-pub-v5.2.0 distribution. I can't change the FDR "Rate" either. thanks, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mharms(a)wustl.edu

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