Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

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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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

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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.

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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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cross-sectional analyis error
by Guang Zeng 18 Feb '10

18 Feb '10

Hi, there, I am testing two subjects using cross-sectional FS. Both of they have being processed for almost four days. Both of them are stuck at the mris_fix_topology step, but there is no error message pops up. Subject#1 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $ $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $ before topology correction, eno=-132 (nv=182824, nf=365912, ne=548868, g=67) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 11 iterations marking ambiguous vertices... 71554 ambiguous faces found in tessellation segmenting defects... 39 defects found, arbitrating ambiguous regions... analyzing neighboring defects... -merging segment 22 into 9 -merging segment 29 into 27 37 defects to be corrected 0 vertices coincident reading input surface /data1/radiology/m047599/subjects/027_S_0408_20060510/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -9.2222 (-4.6111) -vertex loglikelihood: -6.1352 (-3.0676) -normal dot loglikelihood: -3.5992 (-3.5992) -quad curv loglikelihood: -5.8849 (-2.9424) Total Loglikelihood : -24.8415 CORRECTING DEFECT 0 (vertices=30671, convex hull=1376) ************************************************************* Subject#2 ************************************************************* Correcting Topology of defect 2 with euler number 1 (0 loops) Nothing to correct for defect 2!! AFTER CORRECTION, EULER IS -262 Surface Diagnostics: eno=-262 (nv=157710, nf=315944, ne=473916) # of border vertices [ #v ~ #f ] 0 # of edges with single face 0 # of edges with more than 2 faces 0 # of corner configurations 0 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX Correcting Topology of defect 3 with euler number -219 (110 loops) computing statistics for defect 3: 23911 vertices location: [ (168,58,111) - average intensity = 83.612 ] -gray ( 77.29 , 6.14 ) -white ( 93.87 , 3.59 ) -gray ( 79.92 , 20.78 ) -white ( 95.75 , 18.72 ) -intensity (77.286301 [log = -2.730186 ]- 93.865768 [log = -2.235836 ]) -curv (k1=-0.170 (0.615) , r1 = 5.894 | k2=-0.052 (0.142), r2 = 19.402 ) -curv (k1=-0.138 (0.656) , r1 = 7.230 | k2=-0.024 (0.219), r2 = 41.547 ) max face = 47468(47468) - loop = 1 (110) - ntries = [18,18997] BEST FITNESS (o)is -9.95545 mri =0.000 curv = 0.865 unmri = 6.496 ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 ) ( f=0.00 , v=0.00 , c=0.86 , q= 1.73 ) BEST FITNESS (M) is 14.81362 mri =0.000 curv = 0.886 unmri = -18.358 ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 ) ( f=0.00 , v=0.00 , c=0.89 , q= 1.77 ) Could any one tell me how to fix this problem, is there a method to ignore this fix_topology step? Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/201469230/direct/01/

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Paradigm file question
by John Richey 18 Feb '10

18 Feb '10

Dear Freesurfer experts, For the first column in paradigm (.par) files in fsFAST, is it necessary for the stimulus onset times to be cumulative across runs? In other words, if I present the same task N times in run 001, run 002, ... run N, is it necessary for the second through Nth .par file to indicate the cumulative time elapsed? Or should each .par file start with time = 0?

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converting nifti to .mgz files - command
by Jenessa Price 18 Feb '10

18 Feb '10

Can you please tell me the exact mri_convert command for converting nifti to .mgz? We had originally done it using .img/.hdr files, but there were errors with the recon because the orientation wasn't correct. We then were able to get a correct orientation using the .nii format but could not convert to .mgz with the mri_convert command. Thank you! -- Jenessa S. Price, B.A. Graduate Student, Clinical Psychology and Neuropsychology University of Cincinnati

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