Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

ERROR: comparison in expression
by Xue, Feng 20 Feb '10

20 Feb '10

Dear experts, We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all: $ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression I also checked the recon-all-status.log file, but not error was found. Has anyone met this problem? Is it critical? Thanks in advance. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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Re: [Freesurfer] Freesurfer Digest, Vol 72, Issue 66
by Sebastian Moeller 20 Feb '10

20 Feb '10

Hi Jonathan, On Feb 20, 2010, at 10:15 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Message: 2 > Date: Fri, 19 Feb 2010 17:08:06 -0500 > From: Jonathan Winkle <jwink(a)mit.edu> > Subject: [Freesurfer] Distorted images > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <4B7F0BC6.3020207(a)mit.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi! > > I'm new to freesurfer and I am trying to reconstruct some recent scans > of a rhesus macaque. The dicoms appear to be fine, but after converting > to cor files the images appear distorted. I have attached a screenshot > as an example of what the images look like. For converting the dicoms to > cor I used: > > "mri_convert $path/1500-4-1.dcm $path/001 -ot COR -nc -sc 0.5" > > I am using freesurfer 3 on ubuntu. > > Any help you can give is much appreciated! Have a look at the attached tar.gz, it contains the scripts I use to process rhesus data. Especially myscripts_anat might be helpful (and unpack_CIT.csh for how to import DICOM data). For me it works to go from macaque anatomical scans to reconstructed surfaces (but I never actually used the recons for morphometry so the thickness values might be completely off). I am sure there are other people on this list who can give more experienced advise regarding monkey processing, but until they comment have a look at my scripts :). What I do not know is, is whether the scripts in the attachement will reach the list... Oh, there is also a somewhat old copy of my "myscripts_anat" folder on the freesurfer wiki (http://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData) but I would rather try the attached ones... (Oh well, these scripts were never meant to be distributed so they are full of typos and comments are often actually about older versions of the scripts, but hey better than nothing...) Best Sebastian

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Local GI - euler number and compute_lgi
by Lena Palaniyappan 20 Feb '10

20 Feb '10

Hi all I am running recon-all localGI One subjects image is not getting processed and crashes repeatedly with message that there may be a topological defect in a particular vertex. It asks me to check euler number. The wiki indicates that this crash is a known issue and restrating _mris_compute_lgi must solve this. My questions are 1. how to check the euler number and how to interpret this number in terms of topological defects? 2. mris_compute_lgi does not find lh.pial surface when I TRY TO RESTART - what should I do? I used mris_compute_lgi subjid/surf/lh.pial Many thanks in advance Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Distorted images
by Jonathan Winkle 19 Feb '10

19 Feb '10

Hi! I'm new to freesurfer and I am trying to reconstruct some recent scans of a rhesus macaque. The dicoms appear to be fine, but after converting to cor files the images appear distorted. I have attached a screenshot as an example of what the images look like. For converting the dicoms to cor I used: "mri_convert $path/1500-4-1.dcm $path/001 -ot COR -nc -sc 0.5" I am using freesurfer 3 on ubuntu. Any help you can give is much appreciated!

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mris_expand problem
by Gregory Dierksen 19 Feb '10

19 Feb '10

Hi, I'm trying to make a "midgray" surface by inflating the white surface of a subject by 5% using the following command: mris_expand -thickness rh.white 0.5 rh.midgray.05 I am getting the following output: using distance as a & of thickness expanding surface rh.white by 0.50% of thickness and writing it to rh.midgray.05 reading thickness... freadFloat: fread failed Input/Output error freadFloat: fread failed Input/Output error freadFloat: fread failed Input/Output error ... You get the idea. Usually this command takes about 20 minutes or so to expand a surface... when this message comes up (continuous) I've let it run for a couple hours without completing (I haven't let it go to its conclusion because it takes too long). So, what's going? How can I fix this? Thanks, Greg Dierksen --

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Question.
by jijun wang 19 Feb '10

19 Feb '10

Dear experts, When I tested my FreeSurfer, and when I input the command of *"tksurfer bert lh inflated*", only a bit part of the brain surface could be seen. Also, I often failed to drag the tksurfer window. What is the possible problem? Thank you very much. -- Best regards, Jijun Wang, MD & PhD Shanghai Mental Health Center 600 Wanping Road Shanghai 20030, China. E-mail: jijunwang27(a)gmail.com

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Error with ntrs using mc-sess
by Gabriel A. Tobon 19 Feb '10

19 Feb '10

Hello, I am having trouble running motion correction on a set of block design data. When the matlab script is run, I get an error saying: "ERROR: ntrs = 2 < 6" I am not sure what this error means, except that ntrs, comes from the fmc.mcdat file. Could anyone explain to me what this error message means, why there has to me more values in the fmc.mcdat file? Here is my fmc.mcdat: 0 0.0000 -0.0000 0.0000 -0.0000 -0.0000 -0.0000 0 0 0.000 1 0.0031 -0.0102 -0.0081 0.0577 -0.0003 0.0620 44.93 44.74 0.085 Thank you, gtobon

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tksurfer colortable problem
by jentis＠nmr.mgh.harvard.edu 19 Feb '10

19 Feb '10

Hi Guys, I'm running tksurfer on my laptop and when I try to load the .sulc surface it crashes and tells me WARNING: No colortable found! Everything else seems to work just fine but I need to visualize the sulci to complete my project. Any ideas? Thanks, Jon

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Recon successful- ran for half a minute instead of 30 hours. Visualisation problems
by Janani Dhinakaran 19 Feb '10

19 Feb '10

tkmedit subjectname rawavg.mgz is the way to visualise the volume. The first image. This is what happened. s0964091@CRIC-0012:~/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM$ tkmedit subj001 rawavg.mgz ERROR: cannot find /home/s0964091/Desktop/Allimages/MRIscan/janani/CRIC-0014_5679.adb.DICOM/jan/subj001/mri/rawavg.mgz Error: Loading volume rawavg.mgz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. -- I am the Sun, I know no darkness.

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A basic question about visualising data
by Janani Dhinakaran 19 Feb '10

19 Feb '10

My data is on the desktop. The subjects directory is under usr/local/freesurfer/subjects. I tried setting desktop as SUBJECTS_DIR by using 'export SUBJECTS_DIR="/Desktop/Allimages/MRIscan... and the full path till DICOM" ' but apparently it didn't work because when I tried to run recon, it says SUBJECTS_DIR /Desktop/Allimages/MRIscan/.../....DICOM does not exist If I can't get SUBJECTS_DIR to change to Desktop path, how can I introduce my data into usr/local/freesurfer path? I notice Bert has everything in order. If I mkdir Mine in SUBJECTS_DIR and put my MRI files in there , will it work?

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