Freesurfer April 2013

freesurfer@nmr.mgh.harvard.edu

131 participants
220 discussions

creating new curv/thick/area files using tweaked white/pial
by Fred Dick 15 Apr '13

15 Apr '13

Hi there [Doug/Bruce, sorry for storm of enquiries!] V quick question: I've fixed up some small defects in white and pial surfs (using reposition), and need to regenerate area/thickness/curv etc without changing them. Is there a straightforward way to do this with mris_make_surfaces, or should one use mris_thickness and mris_curvature? (Not sure which binary makes area). Is there a straightforward way to use mris_make_surfaces to create these without altering the pial & white? (Maybe with --white NOWRITE --pial NOWRITE?) cheers, Fred

2 2

Very different results between 5.1.0 and 5.2.0
by Yang, Daniel 15 Apr '13

15 Apr '13

Dear FreeSurfer Experts, I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in particular. Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in 5.2.0. They are significantly different, t(160) = 56.71. The correlation between the two versions is r = .33 Is this something possible?? I can't see what went wrong in my procedures. Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

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convert MNI152 mask to label file
by Emily Boeke 15 Apr '13

15 Apr '13

Hi all, I want to convert a mask I made in MNI152 space using the Harvard-Oxford Atlas into a (subcortical) label file so that I can run an ROI analysis using func2roi-sess. Does anyone know what commands I would need to do so? Thanks! Emily

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32 bit ubuntu in a 64 bit workstation- Problem
by Anupa AV 15 Apr '13

15 Apr '13

Dear All, I'm working with a system, where 32 bit ubuntu is loaded on to a 64 bit computer. Previously there were graphics problem (Screen gets stuck-- So I restarts it and 'll log in again). Now I'm facing a problem where I cannot enter into ubuntu. Any solutions for this problem will be greatly appreciated.

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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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Freesurfer April 2013