Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

hippocampus volume comparision
by Guang Zeng 08 Sep '09

08 Sep '09

Hi, there, I converted a subject from nii (160x256x256) to mgz (256 x 256 x 256 ), and then sent it to the FreeSurfer pipeline. Now, I'd like to compare the resulted hippocampus volume with a hand tracing hippocampus using the original volume. What is the best way to do it? I think I can not use the data in the aseg.stats directly, right? Because of the conform. Thanks a lot! Guang Zeng _________________________________________________________________ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:O…

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mesh file...
by Gonzalo Rojas 07 Sep '09

07 Sep '09

Hi: Where I can find the mesh file that freesurfer generates for each patient ?... Sincerely, Gonzalo Rojas Costa

1 0

which files are modified during white matter editing? cluster <-> local editing
by u.h. 07 Sep '09

07 Sep '09

Dear Freesurfer Devs, We ran our FS brains on an cluster with no visualization nodes, and brought the results into a local computer for interactive interventions and QC after recon-all finished. We fixed some minor segmentation errors, and at this point I'm curious to know if this step only affects the wm.mgz file.. If this is the case, would I be correct in thinking that one would only need to upload the wm.mgz file to the cluster and re-run the necessary commands (autorecon2-wm -autorecon3)? I also saw there is one .touch file that seems to be affected by wm editing. Should I worry about it? Thank you for your assistance. Best, Oori

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skull strip - how lenient can one be?
by Lena Palaniyappan 06 Sep '09

06 Sep '09

Hi all I am not grasping the concept of skull strip correction full, Im afraid. I have attached a brainmask 128th slice sagittal of which shows some uneven stripping (I couldn¹t attach the huge T1 image to overlay) - is this degree of tissue separation acceptable? Where does one set a limit? The example set in tutorial data shows some very obvious stripping errors, but the data I have shows really minor stuff and I am always unsure whether to continue auto recon 2 or correct them. Any help? Many thanks in advance Cheers LKP 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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Windows VirtualBox freesurfer v4.5.0
by Nick Schmansky 04 Sep '09

04 Sep '09

For users wishing to run Freesurfer on Windows, there is now a VirtualBox instance of Ubuntu with freesurfer 4.5.0 installed available for download from the site: http://surfer.nmr.mgh.harvard.edu/fswiki/Download Note the link to README file which provides brief installation notes of the download .rar file. Also note that it is possible to run this virtual machine on Linux or Mac OS (after installing VirtualBox). Thanks for Pedro Paulo Oliveira Jr. for creating this virtual machine. Nick

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Re: [Freesurfer] Wrong boundaries at ventricle.
by Zheng Hui 04 Sep '09

04 Sep '09

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weird tksurfer display
by jeungchan lee 04 Sep '09

04 Sep '09

i setup freesurfer out of MGH, and run the following command as you recommend to test the installation. tksurfer bert rh pial and i got this; surfer: current subjects dir: /disk3/ans2/ansfreesurfer/subject/ surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /disk3/ans2/ansfreesurfer/subject surfer: Reading header info from /disk3/ans2/ansfreesurfer/subject//bert/mri/T1.mgz surfer: vertices=131860, faces=263716 Loading /usr/local/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(bert) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... with attached weird figure... where i can see is only a part of the brain. this is my environment; Linux pucca 2.6.18-128.2.1.el5 #1 SMP Tue Jul 14 06:36:37 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux on CENTOS5.3 did i make mistake when i installed freesurfer? it happened when i did tksurfer on my data, too. thanks for your time. -jeungchan -- -- Jeungchan Lee Athinoula A. Martinos Center for Biomedical Imaging. MGH

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Re: [Freesurfer] Fwd: selecting the best structural scan
by Pedro Paulo de Magalhães Oliveira Junior 04 Sep '09

04 Sep '09

I have an experiment with 3 different sequences, but the maximum difference I've found was 5% ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business 2009/9/4 sima chalavi <sima.chalavi(a)gmail.com> > Hi Pedro, > Thanks for your reply, > > Actually I am using 6 different sequences for scanning the same subject, so > a small part of the difference could be because of randomness, but there > should be a way to select the best scan from these 6 different scans. I need > to know how to select the best. > > any suggestion? > > Regards, > Sima. > > 2009/9/4 Pedro Paulo de Magalhães Oliveira Junior <ppj(a)netfilter.com.br> > >> Hi Sima, >> I've run 6 versions of the same scan of the same subject I got some >> differences too. Not so big as you found but still some differences >> >> Probably it's the -randomness flag in the recon-all >> >> Check: >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html >> <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11235.html> >> cheers >> ----------------------------------------------------------- >> Pedro Paulo de M. Oliveira Junior >> Diretor de Operações >> Netfilter & SpeedComm Telecom >> --- Novo Netfilter 3.2 www.Netfilter.com.br >> --- Novo Netfilter Small Business >> >> >> >> 2009/9/4 sima chalavi <sima.chalavi(a)gmail.com> >> >>> >>> Dear Freesurfer experts, >>> >>> We performed 6 different (pilot) structural scans from the same subject >>> and analyzed the data using Freesurfer in order to find the best scan to >>> be used in our real experiment. >>> >>> We have checked the Freesurfer output visually and there do not seem to >>> be any problem as described in the trouble shooting manual. So all 6 scans >>> manage to get through the Freesurfer process just fine. >>> >>> >>> However, There are a lot of differences between the numerical results for >>> the different scans. Please find Attached graphs of (some of ) the results >>> of segmentation and parcellation of these 6 sequences from the statistical >>> outputs. >>> Now, the problem is how to select the best scan from these results. >>> >>> Does any body have a standard protocol for assessing images for analysis >>> or a standard metric, e.g. goodness of fit, from the software that we can >>> assess without having a gold standard? >>> >>> Or any other tip is also appreciated. >>> >>> Thanks in advance, >>> >>> Sima. >>> >>> >

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selecting the best structural scan
by sima chalavi 04 Sep '09

04 Sep '09

Dear Freesurfer experts, We performed 6 different (pilot) structural scans from the same subject and analyzed the data using Freesurfer in order to find the best scan to be used in our real experiment. We have checked the Freesurfer output visually and there do not seem to be any problem as described in the trouble shooting manual. So all 6 scans manage to get through the Freesurfer process just fine. However, There are a lot of differences between the numerical results for the different scans. Please find Attached graphs of (some of ) the results of segmentation and parcellation of these 6 sequences from the statistical outputs. Now, the problem is how to select the best scan from these results. Does any body have a standard protocol for assessing images for analysis or a standard metric, e.g. goodness of fit, from the software that we can assess without having a gold standard? Or any other tip is also appreciated. Thanks in advance, Sima.

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FDR corrected figure
by 류철형 03 Sep '09

03 Sep '09

Dear all. I'd like to make a thickness difference figure with FDR corrected color scale bar. For example. FDR corrected p<0.05 p<0.01 p<0.001 Color scale bar ============================== However, in the qdec or tksurfer, only the uncorrected p value image can be generated. The FDR corrected image can be visualized only with the uncorrected p value color scale bar. How can I make the FDR corrected image with FDR corrected p value color scale bar? Chul Hyoung Lyoo

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Freesurfer September 2009