Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

96 participants
153 discussions

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

1 0

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

2 1

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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Color scale in tksurfer
by Oya, Hiroyuki 18 Feb '10

18 Feb '10

Dear All, How can I use my own color scale in tksurfer overlay? Thank you in advance? Hiroyuki

2 1

parcellation problems
by Guang Zeng 18 Feb '10

18 Feb '10

Hi, there, I have a scan with bad gray and white matter contrast, I added some control points, and got results much better than before. However, there are still some problems. For example, the rh_ctx regions at left-bottom have no label in the attached image. Is there a method to fix this problem besides add more control points here. Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469227/direct/01/

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Inflated_surface
by Rajagopalan, Venkateswaran 18 Feb '10

18 Feb '10

Hello All, I am new to freesurfer and i am kind of sensing there is some problem in my inflated surface (i compared it to the one available in the documentation page).I have placed some marks on lh inflated to find out the coordinates these are x = (-28.5, -59.2, 21.1), n = (-0.5, -0.3, 0.8),x = (-31.0, -66.9, 17.0), n = (-0.5, -0.4, 0.8).I am attaching JPEG of rh and lh inflated images (10kb each).Can anyone please tell me what is the problem here and how use these coordinates to fix that problem like is there a direct connection between these coordinates and WM surface where you identify the problem. Thanks in advance. venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 4

gray/white segmentation
by Rutvik Desai 18 Feb '10

18 Feb '10

Hello, We have some signal dropout at the top of the brain in some of our scans. Because of that, the gray/white boundary is not very accurate at the top. The gm tends to be too thick because some of the darkened wm is classified as gm. What particular parameters can we experiment with to correct for this? I am guessing that some things in nu_correct and/or mri_normalize should be adjusted, but what specifically would you recommend? This anatomy is an average of two scans and the FS version is freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5. thanks, Rutvik

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Freesurfer February 2010