Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

96 participants
153 discussions

recon-all: different results on different systems
by Andreas Berger 13 Feb '10

13 Feb '10

Hi Freesurfers, we have FreeSurfer running on 10 computers: 7 computers with suse 10 32bit, freesurfer 4.5.0 32bit 3 computers with debian 5 64bit, freesurfer 4.5.0 64bit recon-all -all -i finished on all of them without any errors, so i assumed the best. out of curiousity i processed one of the subjects on both systems, and checking the results in tkmedit and tksurfer i noticed that they are visibly different. (thus in this case one of the surfaces does not look quite ok, other subjects processed on that system look fine however, i haven't looked through all of them yet). screenshots attached. also, i just started recon-all -all -s bert on both systems, so i can compare them to the original bert. what could be the reason for this failure at reproducibility? -- Andreas Berger <andreas.berger.01(a)gmail.com>

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Measuring Cortical Volume
by Jeff Sadino 13 Feb '10

13 Feb '10

Hello, I want to measure the volume of my groups' cortex, n=139, mostly males. I am using fs 3.0.5. >From the aseg.stats file, lh + rh white matter is 548,000 and gray matter is 487,000, for a ratio of 1.1. I know the aseg.stats file is not a good place to go for gray matter volume, as it is usually underestimated. Looking in the aparc.a2005.stats file, the average white matter is 606,000 and gray matter is 463,000, for a ratio of 1.3. I was surprised the gray matter actually went down, and the ratio of 1.3 seems a bit high. Is this normal? I see in the aseg.stats file, skin left over after the watershed is counted as cortex and so is a fair amount around the cerebellum. Could partial volumeing also be a possible explanation? I would think that the aparc file would be most accurate, but with these results, I wanted to doublecheck. Thanks Bruce for answering my earlier question. I am still looking at the pallidum differences and will let you know soon. Thanks! Jeff Sadino

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Segmentation fault wmparc a2009s
by Lena Palaniyappan 12 Feb '10

12 Feb '10

I am trying to derive wmparc volumes for a2009s which are by default not available in wmparc (segments read empty) _ is this because Desikan/Killiany atlas is used in wmparc by default? So I decided to run Mri_aparc2aseg for each subject using mri_aparc2aseg --s <subjid> --annot aparc.a2009s --o mri/wmparc.a2009.mgz --labelwm --rip-unknown --ctxseg aparc.a2009s+aseg.mgz I thought this would generate a new wmparc which will now include labels for wm from a2009s Then I ran mri_segstats --seg mri/wmparc.a2009.mgz --sum stats/wmparc.a2009.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject MPRAGE04 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt Hoping that this would allow me to obtain statistics from this wmparc file But for some reason I am getting segmentation fault message as below atlas_icv (eTIV) = 1663710 mm^3 (det: 1.170940 ) Loading mri/wmparc.a2009.mgz Getting Cerebral WM volumes from surface lh white matter volume 277542 rh white matter volume 284002 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1740943 # brainmaskvolume 1740943.0 # nbrainsegvoxels 260991 # brainsegvolume 260991.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1190 segmentations Computing statistics for each segmentation 1 1 Left-Cerebral-Exterior 0 2 2 Left-Cerebral-White-Matter 0 3 3 Left-Cerebral-Cortex 0 4 4 Left-Lateral-Ventricle 3953 3953 5 5 Left-Inf-Lat-Vent 142 142 6 6 Left-Cerebellum-Exterior 0 7 7 Left-Cerebellum-White-Matter 15484 15484 8 8 Left-Cerebellum-Cortex Segmentation fault Could anyone help please? Cheers 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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comparison between three MRI exams of same patient...
by Gonzalo Rojas 12 Feb '10

12 Feb '10

Hi: I have three MRIs of the same patient taken at different dates/years... I need to compare the hippocampus volume (for example) between the three MRI... I want to compare also the cortical thickness between the three MRI... How can I do such computation ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

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execute a freesurfer command at a specificed time/day...
by Gonzalo Rojas 12 Feb '10

12 Feb '10

Hi: How can I execute a freesurfer command at a specificed time/day ?... Any Ubuntu trick ?... Sincerely, -- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Cortical thickness in controls
by Rajagopalan, Venkateswaran 12 Feb '10

12 Feb '10

Hello All, I would like to clarify the following.I couldn't find the answers i was looking for in the archives so here are my questions; 1) In some of our subjects the WM/GM interface is identified correctly but the pial surface falls short of some voxels which i want to manually edit them inorder to include them. Is there a way to only edit the pial surface if so kindly give directions or direct me the documentation page. 2) I would like to check the cortical thickness values measured in our control subjects with any already published or documented control values inorder to make sure that i am doing right. 3) In some our of subjects WM is not filled completely i.e. in filled.mgz volume there are still some ventricle regions that need to be manually filled, i have done the manual editing it there a way to run rest of the steps from this step i.e inflation smoothing etc. Now i am doing them one by one which is time consuming. Thanks in advance. Regards 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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comparison of values of three MRI exams of same patient...
by Gonzalo Rojas Costa 12 Feb '10

12 Feb '10

Hi: I have three MRIs of the same patient took during different months... I need to compare the hippocampus volume fof the three exams (for example), the cortical thickness, etc... How can I do such computation ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

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Problems with tksurfer display on laptop
by jentis＠nmr.mgh.harvard.edu 12 Feb '10

12 Feb '10

Hi, I have a laptop equipped with Centos and Freesurfer but I can't get tksurfer to properly display the surface files of either the fsaverage brain or individual subjects. The surfaces are either small portions of cortex or an assemblage of lines/dots. I have attached a few tiff files as examples. Is there something I can do to fix this? I have tried using freeview instead, and the surfaces do display properly, but the program does not seem to allow me to trace label files. Is there another way around this? Does a newer version of freeview include tracing ability? Thanks, Jon

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tksurfer problem and solution
by David Mischel 11 Feb '10

11 Feb '10

We have had similar problems with displays of tksurfer described in http://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems. I would like to try freeview, the new solution for display. I don't know anything about freeview and no one here has ever used it. To run tksurfer I set the SUBJECTS_DIR and then use the command tksurfer <subjectCode> lh pial where subjectCode is a directory in the SUBJECTS_DIR. Could someone give me the corresponding command to use with freeview? I appreciate the help. < david David Mischel Manager of IT Center for Imaging of Neurodegenerative Diseases (CIND) <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ VA Medical Center 4150 Clement Street, 114M San Francisco, CA 94121 voice: 415-221-4810 x3864 fax: 415-668-2864

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tksurfer fill holes
by Guang Zeng 11 Feb '10

11 Feb '10

Hi, there, Is there are a command-line version of that 'Fill holes", "Dilate" and "Erode" options in tksurfer. Could I select the size of the kernel for dilation and erosion? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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Freesurfer February 2010