Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

Where are all the segmentation names explained?
by Brain Apprentice 16 Sep '09

16 Sep '09

Hello, Generally speaking the segmentation names are self explanatory like Left-Hippocampus or 5th-Ventricle. There are some segmentation's that I am not sure what they mean like ctx-lh-unknown or ctx-lh-bankssts. Is there any place I can go that would explain these few segmentation names? Is there one place I can go that would explain all segmentation names? Thanks in advance to anyone who can help, even if the answer is that there is no such explanations so far in the FreeSurferWiki. B. Apprentice

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selecting the best structural scan
by sima chalavi 16 Sep '09

16 Sep '09

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. >> >> -- Sima Chalavi, Ph.D. student King's College London Institute of Psychiatry (IoP) Box P040, De Crespigny Park London SE5 8AF. Tel:+44-2078485702 BCN Neuroimaging Center (NIC) University Medical Center Groningen Antonius Deusinglaan 2 P.O. Box 196 9713 AW Groningen www.neuroimaging-DID.com

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displaying retinotopy data with tksurfer and other questions
by Ritobrato Datta 16 Sep '09

16 Sep '09

Hello All, Many thanks for all the help that you provide to freesurfer users. I have a few questions - 1. Where do I find ch2better brain ? I want to pipe it through freesurfer all the way to register to the spherical atlas and plot functional data across subjects to it. 2. I have retinotopy data (expanding rings and wedges) for 6 subjects and I want to generate average functional eccentricity and polar angle data for these subjects in surface or sphere space. Can you tell me how do I average the functional data across subjects in the surface domain ? That will be gr8 help. 3. I was trying to plot the retinotopy data for 1 subject onto the inflated surface using tksurfer (following the instructions http://surfer.nmr.mgh.harvard.edu/fswiki/TkSurferGuide/TkSurferWorkingWithD…) and am able to plot it but I am not able to fit a proper color scale and threshold to show color gradation reflecting the different phases. Can anyone please suggest what am I doing wrong ? I have attached a figure here. This is how it plots before any fiddling. 4. Also is there a way to calculate gray matter thickness of V1 in subjects after it has been registered to the spherical atlas. I have already generated V1 labels using Dr. Fischl and Dr. Hind's method. Thanks a lot for your help Ri

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make_average_subject and qdec problems
by Drosos, Athena 16 Sep '09

16 Sep '09

Hello all, I am trying to create an average subject from our pediatric brains and run group analyses with qdec. After I ran the make_average_subject command, the terminal exited with no errors. I then open qdec, load our data table, select our common-space subject, select our variables, and hit analyze. An error message pops up that reads: Couldn't find file: /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.curv When I look in this directory all ?h.curv, ?h.pial, ?h.sulc, ?h.thickness, ?h.sphere are shown as shortcuts. Are these files supposed to be created, where should they be, how can I fix this? The qdec display opens with a gray inflated brain, and the only options on the left side of the gui are to select inflated, pial or white. The end of the terminal window has errors that read: Writing to /Users/athenadrosos/CRPS/CTgroup_analysis/qdec/rh.avgpermissions/contrasts.s ig.mgh reading group avg surface area 907 cm^2 from file ERROR: could not find volume /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.white.avg.area.m gh reading group avg surface area 1131 cm^2 from file ERROR: could not find volume /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/../mri/orig. Does it exist? Reading in average area /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.pial.avg.area.mg h reading group avg surface area 907 cm^2 from file ERROR: could not find volume /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/../mri/orig. Does it exist? Couldn't find file /Users/athenadrosos/CRPS/CTgroup_analysis/fsaverage/surf/rh.curv ============================================================ Completed loading of analyzed data. How can I point to the correct /mri/orig. And where should it be? Is it created by the make_average_subject script? Thank you so much for any help on this matter. Athena

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center of gravity of the aparc.a2005s parcellations
by Jürgen Hänggi 16 Sep '09

16 Sep '09

Dear FS experts Sorry for reposting this question. I am looking for the MNI or Tal-coordinates of the center of gravity (COG; "middle-point of a particular parcellation") of the aparc.a2005s parcellations of the FS average brain. I need these coordinates to visualize the results of a graph-theoretical network analysis where the nodes are defined by the aparc.a2005s parcellations Do these coordinates exist or how can I compute them? Any idea is appreciated Thanks Regards Jürgen ---------------------------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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Something wrong with the display image of tksurfer
by QQ Liu 16 Sep '09

16 Sep '09

Hi all, I have a problem about the tksurfer. When I use tksurfer to show the surface of the cortex. The window of the tksurfer is normal, but the image cannot be seen in the front window. And I cannot fix the image, but I click it then the image can display. Is there something wrong when installing the tool? Or is the Graphics card of the system not suitable? Thanks in advance. -- Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com

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-notalairach flag
by Fischi Gomez Elda 16 Sep '09

16 Sep '09

Hi all, i'm trying to run only the -autorecon1 step of the cortical reconstruction process, but I don't want my data to be transformed into a Talairach template. As I've read on the Freesurfer wiki, I can remove any step of the process using the -no<step> flag, so in my case should be -notalairach. I've tried both: recon-all -autorecon1 -notalairach -subjid <subjid> recon-all -notalairach -autorecon1 -subjid <subjid> and both exited with the same ERROR: "Tailarach failure detection" ################################################################################################################### Wed Sep 16 12:34:37 CEST 2009 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Wed Sep 16 12:34:37 CEST 2009 /home/elda/freesurfer/subjects/Tamara/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux localhost.localdomain 2.6.29.4-167.fc11.x86_64 #1 SMP Wed May 27 17:27:08 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 16 12:34:37 CEST 2009 ####################################################################################################################### It means that is still trying to make compute the talairach transform that maps the input volume to the MNI average_305. ? What should I do to avoid this transformation? Thanks Elda Fischi Gómez Ecole Polytechnique Fédérale de Lausanne (EPFL) Signal Processing Laboratories (LTS5) EPFL-STI-ITS-LTS5, ELD 224 (Bâtiment ELD) Station 11 CH-1015 Lausanne, Switzerland

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Re: [Freesurfer] errors
by Zhangyuanchao 16 Sep '09

16 Sep '09

Dear Doug, Here I attached one of the .dc3 data so that you can help me fix the problem. Some of my data can run smoothly, while others can not. The one I attached exited with errors. Thanks a lot! yuanchao --- 09年9月16日，周三, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 写道：发件人: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> 主题: Re: [Freesurfer] errors 收件人: "Zhangyuanchao" <woshizhangyc(a)yahoo.cn> 抄送: Freesurfer(a)nmr.mgh.harvard.edu 日期: 2009年9月16日,周三,上午12:36 what kind of file is it? where did it come from? Zhangyuanchao wrote: > Dear experts, > I have some data of format .dc3, I would like to calculate the cortical thickenss of the data. > I launched the command "recon-all -i subjectname/***.dc3 -s subjectname", In addition, I also tried "recon-all -i ****** -force", For some of the subjects, It runs without error, while for others it exited with errors. > The error log is "file not find or unknown file type for file **/**/**/**.dc3". > How can I fix this problem? > Thanks a lot! > yuanchao > > > ------------------------------------------------------------------------ > 好玩贺卡等你发，邮箱贺卡全新上线！ <http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___________________________________________________________ 好玩贺卡等你发，邮箱贺卡全新上线！ http://card.mail.cn.yahoo.com/

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FreeSurfer course in September
by Pedro Paulo de Magalhaes Oliveira Jr 15 Sep '09

15 Sep '09

One suggestion that may be useful for the FS Users: You could record the course in video and share some classes using YouTUBE Cheers PPJ Enviado do meu celular Nokia

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Editing labels - How to get the altered structures volumes?
by Amorim, Edilberto 15 Sep '09

15 Sep '09

Dear freesurfers, Foremost, I want to thank all the fellows freesurfeers that help us out in the mailing list. This is an amazing support. I'm a beginner working with FreeSurfer - your help is very appreciated. I've also searched in the e-mail list archives, but did not find the answer to my question. After troubleshooting my output and running recon-all - autorecon-2cp –s <subjid>, some new labeling errors were created in tksurfer when opening the file aparc.annot. So, I expanded the boundary of existing regions, fixing the labels that were misplaced (http://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit) Posteriorly, I exported this new annotation, re-opened the file, and the changes I made were there still. I’m analyzing volumes using the aparc2table volumes in the SPSS. So, after editing the labels, I created an aparc2table, but my edits did not cause any change in the parcellation volumes. I tried running –autorecon3, however the tksurfer surface generated did not keep the changes I made previously, erasing the edits back to the previous boundaries. How should I proceed to have the edits included on an aparc2table. Is it possible? Do you have any other suggestion about how to proceed with that? Is this editing used only for qdec analysis? Thank you all for your help! Best Regards, Edilberto Amorim

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Freesurfer September 2009