Freesurfer July 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
140 discussions

data analysis/reduction after autorecon3
by Liukarl 09 Jul '10

09 Jul '10

Hello, Freesurfers After autorecon3, there are cortical measures for the over 30 predefined regions. And for each regions, there are area, volume, and thickness 3 different measures, which means there are approximately 200 measure for both hemispheres. As a preliminary analysis without specific priori hypothesis, what is the standard way to examine the massive data to find possible group difference for a small sample size about 40 subjects with 20 in each group. thanks Karl _________________________________________________________________ 想知道明天天气如何？必应告诉你！ http://cn.bing.com/search?q=%E5%A4%A9%E6%B0%94%E9%A2%84%E6%8A%A5&form=MICHJ2

2 1

"Configure Overlay Display" tksurfer window...
by Gonzalo Rojas Costa 09 Jul '10

09 Jul '10

Hi: How can I display an overlay in such a manner that only values between "min" and "max" are displayed in a color palette, and values less than "min" and values greater than "max" are displayed in gray ?... Sincerely, Gonzalo Rojas Costa

3 3

recon-all not finishing properly
by p.s.bjerkan＠studmed.uio.no 08 Jul '10

08 Jul '10

Hi, Have a question regarding one subject I´m trying to run with recon-all. It´s been run successfully before. The Freesurfer version used is 4.0.4. We discovered one subject having faults, and when checking recon-all-status.log, it is clear that -autorecon2 does not finish properly. The last entry is "ASeg Stats". The step "Cortical ribbon mask" is thus not included. The "recon-all finished with ERRORS" is not listed. The last entry after -autorecon3 is "AParc-to-ASeg", "WMParc" is not finished. The recon-all-status.log file is about 4.1 GB! Therefore difficult to scan the text, but an excerpt of something repeated is: -------------------------------------------------------------------------- No such file or directory MRIScomputeWhiteVolume: src (11, 257, 296) maps to (345, 137, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 297) maps to (345, 137, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 298) maps to (345, 138, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 299) maps to (345, 138, 147) - OOB No such file or directory MRIScomputeWhiteVolume: src (11, 257, 300) maps to (345, 138, 147) - OOB No such file or directory -------------------------------------------------------------------------- Have tried to run it several times. Thankful for any suggestions on what to do! Thanks! Petr

2 1

cortical thickness more than 5 milimeters...
by Gonzalo Rojas 08 Jul '10

08 Jul '10

Hi: Sometime ago I asked about how to show cortical thickness more than 5 milimeters... Bruce answered me, but I could not find his answer... Could you please send me again ?... Sincerely, -- Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

3 2

Gyrification index group differences
by Juranek, Jenifer 08 Jul '10

08 Jul '10

Hi Nathan, Check out this previous posting wrt using Qdec to visualize group maps (or group diff maps) based on pial_lgi data. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg09281.html Cheers, Jenifer

1 0

tksurfer no longer displaying surface data
by aekairys＠umich.edu 08 Jul '10

08 Jul '10

Hi all, I have been using tksurfer just fine until today it randomly stopped functioning correctly. I have not changed any files or done anything to tksurfer. I have only been working with qdec. There is no error by tksurfer, it just only shows a tiny piece of the cortex. it also says" WARNING: color tables not found. I tried to load: lh bert inflated Any help will be greatly appreciated by U of M Best, Anson K.

2 1

Talairach transform failure in 7T
by Lena Palaniyappan 08 Jul '10

08 Jul '10

I am trying to reconstruct some 7T images but they repeatedly fail Talairach step The tkmedit displays normal coronal, sagittal positions for the target. If I use tkregister2 the moveable appears odd please see the attached The error message is #@# Talairach Failure Detection Thu Jul 8 10:58:38 BST 2010 /Applications/freesurfer/subjects/7TMRIData/szanat05a/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) The talairach.xfm shows MNI Transform File % tkregister2 Transform_Type = Linear; Linear_Transform = 2.49591112 0.47519815 2.82347846 13.68270206 -3.58282375 2.34796309 -2.66250205 -5.44943428 -2.31779170 -0.83566302 0.94148278 7.01633883 ; What should I do next? Thanks 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.

2 5

Gyrification index group differences
by Dankner, Nathan (NIH/NIMH) [F] 08 Jul '10

08 Jul '10

Hi All, I've been using the lgi stream to examine group differences at the gyral-based level, and was wondering whether or not there is a way to do this on the surface. Can QDEC be used in conjunction with lgi? If not, is there a way to perform lgi group differences on surface based data? I noticed that the ?h_pial.lgi file can be displayed as an overlay in tksurfer. Is there any way to average these files together so that I can look at the lgi heatmap for an entire group? Thanks, Nathan

1 0

Exporting FreeSurfer surfaces to Blender
by Pedro Paulo de Magalhães Oliveira Junior 08 Jul '10

08 Jul '10

Hi, I just added a quick tutorial on how-to export FreeSurfer surfaces and use it as a render object for Blender http://surfer.nmr.mgh.harvard.edu/fswiki/BlenderModel If someone has other tutorials I think you can use this new section of User Contributions: http://surfer.nmr.mgh.harvard.edu/fswiki/HowTo/HowTo PPJ ---------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom -- For mobile: http://www.netfilter.com.br/mobile

1 0

Linear regression
by Dankner, Nathan (NIH/NIMH) [F] 08 Jul '10

08 Jul '10

Hi All, I have a dataset with two subject groups. I'm looking to see if there are different age effects on cortical thickness by diagnosis. Initially we did this by testing the interaction of two categorical variables, diagnosis and age (with a median split on age). We are now trying to look at this with age as a continuous variable, but QDEC seemingly does not allow you to look at interactions with continuous variables. Is there a way of doing this using the command line? I've looked at the Group Analysis tutorial, but haven't been able to satisfactorily answer this question. Any help would be appreciated. Thanks, Nathan

1 0

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Freesurfer July 2010