Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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

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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.

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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.

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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

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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

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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

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Freesurfer file
by wen miao 08 Jul '10

08 Jul '10

Hello, Freesurfer experts I'v got a work with the freesurfer files. As we all know, there are many files in the freesurfer subject directory, and each file has its usage. My question is, what's the particular usage for each of these files and how can I read these files using Matlab or any other softwares rather than the freesurfer tools? Is there a list for this? Thanks in advance. -- Lab of Complex System and Artificial Intelligence, Institute of Automation,Chinese Academy of Sciences(CASIA) Beijing, 100190,P.R.CHINA

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probabilistic white matter mask
by Mehul Sampat 08 Jul '10

08 Jul '10

Hi Folks, I believe that I can create a binary white matter mask using "mri_wmfilter". I was wondering if there is a way to create a probabilistic white matter mask ? (for each voxel, I would like to obtain the probability of it being white matter) I did a search on the mailing list and found the following related message: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11786.html The message suggests to use "-write_probs" flag with the mri_ca_label command but I dont see this flag as on option in the usage instructions for mri_ca_label. If this is the right way, should i just add "-write_probs wm.mgz" to mri_ca_label to get a probablistic white matter mask ? Thanks Mehul

2 1

ERROR selxavg-sess
by 卯野賢太 07 Jul '10

07 Jul '10

Hi,Freesurfers I'm going to analyze the functional data. By now I finished reconstruction of anatomical data and maiking hierarchy, mc-sess,spatialsmooth-sess,inorm-sess,mkanalysis-sess and fslregister. But selxavg-sess output following ERROR. please tell me about -ipr. Keta kenta@localhost[retino1] % mkanalysis-sess.new -analysis retino -TR 2 -paradigm para.para -designtype blocked -funcstem fmcs -nconditions 4 -timewindow 34 -motioncor -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force Completed successfully kenta@localhost[retino1] % selxavg-sess -analysis retino -s sekiguchi001 -df sessdirfile -noomnibus INFO: WhitenFlag = 0 -------------------------------------------------------------- selxavg-sess logfile is /home/kenta/data/sessions/retino1/log/selxavg-sess-bold-retino-100708112251.log -------------------------------------------------------------- ------------------------------------------- /home/kenta/data/sessions/retino1/sekiguchi001 2010年 7月 8日木曜日 11:22:51 JST INFO (sekiguchi001): RunList = 001 002 003 004 -------------------------------------------------------- /home/kenta/data/sessions/retino1/sekiguchi001/bold selxavg2 -TR 2 -parname para.para -o retino/h -i 001/fmcs -i 002/fmcs -i 003/fmcs -i 004/fmcs -cfg /home/kenta/data/sessions/retino1/retino/analysis.cfg -ipr -------------------------------------------------------- here --- Parsing Config File: /home/kenta/data/sessions/retino1/retino/analysis.cfg ---- -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: flag -ipr requires one argument ERROR (/home/kenta/data/sessions/retino1/sekiguchi001): selxavg failed

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editing labels in tksurfer
by Keefe, Helen L 07 Jul '10

07 Jul '10

Hi Everyone, I remember a post in March when Allison referred someone to this page: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit and I think this will be really helpful for me if I can figure out how to make it work. I have a scan with corpus callosum bleeding into the caudalanteriorcingulate. When I try to change the label, I am able to select the region by clicking on it. However, when I try to "Draw a complete outline path that encloses the desired "incursion"", every time I click to draw the path, the image refreshes. Here are the instructions: "Create outline path: * Possibly start with Edit > Unmark all vertices * Make a series of clicks along the desired outline path. tksurfer shows marked vertices." Is "create outline path" the same as "Make Path" on the TkSurfer tools box? What would make the decision between "Possibly start with Edit > Unmark all vertices" and not doing that? I succeeded once in getting the path drawn, but have no luck replicating that. Also, when I tried to relabel the part inside the path, I was able to turn it into label = "None" or turn 90% of the brain into caudalanteriorcingulate. I'm missing something really simple here - help, please. Also - can this be done also on the pial surface using this command? I can see the boundaries better on this view than on the inflated tksurfer $i lh pial -annotation aparc Thanks for any help - let me know if you need more information Helen Keefe

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