Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

Error with Talairach Transform during recon-all
by Janani Dhinakaran 08 Mar '10

08 Mar '10

Any idea what this means and what I can do about it? Mon Mar 8 12:46:58 GMT 2010 talairach_avi done #-------------------------------------------- #@# Talairach Failure Detection Mon Mar 8 12:46:58 GMT 2010 /home/s0964091/Desktop/Newdata/JS/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 CRIC-0012 2.6.31-20-generic #57-Ubuntu SMP Mon Feb 8 09:02:26 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Mar 8 12:46:58 GMT 2010 Thank you Jan -- I am the Sun, I know no darkness.

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problem on the grey matter
by Xiaoying Tang 06 Mar '10

06 Mar '10

Hi all, Is there someone who can teach me how to get the separate grey matter like the white matter(wm.seg.mgz)? I have run the commands autorecon1 autorecon2 and autorecon3, but I still can't find the separate grey matter. I would be most grateful if someone who can help me. Best, Xiaoying

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Viewing AFNI data on FreeSurfer surface: The Basics
by Dickinson, Annelise (NIH/NIMH) [F] 05 Mar '10

05 Mar '10

Hi all, Sorry if this is a REALLY dumb question, I'm a total newbie. I'm trying to view some fMRI data (preprocessed and analyzed in AFNI) on a surface in FreeSurfer. I have the subject's completed surface and analyzed fMRI files all ready to go, but I have no idea how to register them together, nor view them in the FreeSurfer GUI. Any FreeSurfer gurus out there who might be able to explain the process? I've tried to work through the FS-FAST tutorial, but I'm getting stuck on what I need to do, since I already have the data preprocessed and analyzed. Please let me know! Thank you so much! Sorry to ask a silly question! ***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona(a)mail.nih.gov

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surface label values
by Gregory Dierksen 05 Mar '10

05 Mar '10

Hi, I'm trying to use a surface label (generated by V1 predict) to extract values that have been painted onto a surface using mri_vol2surf. Is there a FreeSurfer tool that will do this? I've been looking but nothing is popping out at me. Thanks, Greg --

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Standard Desikan map and/or QDEC blurb?
by Dankner, Nathan (NIH/NIMH) [F] 05 Mar '10

05 Mar '10

Hi all, I'm about to start writing up a paper, and was curious as to whether there is a standard figure displaying the Desikan parcellations that is floating around out there, and also whether or not there is a standard blurb describing QDEC's GLM analyses. Thanks! Nathan

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Recon-all times
by Gregory Cogan 05 Mar '10

05 Mar '10

Good morning, I imagine that this problem gets posted about once a week, but I'm having some issues with the recon -all step. Initially, I ran data off of a PC (Duo E8400 3.00 GHz, 4 Gigs of ram) and the reconstruction took overnight (so about 12-15 hours). We've recently purchased a new mac (quadcore 2.66 GHz, 8 gigs of ram) for our lab that is going to be dedicated for freesurfer and MNE and so far I've run 2 reconstructions on 2 subjects and the first one took about 96 hours and the second took about 50 hours. My feeling is that this is far too long. Are there any issues with freesurfer and snow leopard? Can anyone else think of a reason why this would be so slow given that it's running on a new (and relatively powerful) computer? I'm happy to send the log files if that helps, but it is worth noting that the stages that diverged from the guideline times listed on the wiki were different for each subject. Thank you all in advance -Greg Cogan

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Generating contrast images within a ROI
by Lena Palaniyappan 05 Mar '10

05 Mar '10

I want to generate some pretty pictures to help my dopamine levels this weekend!! Hoep someone can help.. I want to display statistical thickness difference in 5 ROIs (based on Destrieux atlas) only across two diagnostic groups. When I run Qdec I get whole brain thickness maps but I am interested in only few of the Destrieux parcellations: is there any way I can do this? 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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Re: [Freesurfer] How to verify cerebellum segmentation
by Gergely Orsi 05 Mar '10

05 Mar '10

Hi Sita and Bruce, Sorry for this, it's the first time I post files here and I wasn't aware of the possibility you mentioned. Humyo sometimes acts like an idiot, but usually works (I make the files public and gave you direct links), sorry for that also. I've uploaded the data to the incoming directory on the ftp site you recommended. I don't see them in the directory (i think it's normal), but the status window shows that they were transfered. Válasz: 226 File receive OK. Állapot: File transfer successful, transferred 305 111 477 byte in 1067 seconds Válasz: 226 File receive OK. Állapot: File transfer successful, transferred 303 600 415 byte in 1115 seconds Best regards, Gergely Orsi (Henceforward: Gergo) 2010/3/5 Sita Kakunoori <sita(a)nmr.mgh.harvard.edu> > > Hi, > > I am trying to download the dataset to work on this issue, but the link > requires me to login or signup. I was wondering if instead it would be > possible for you to upload the data as per the instructions in the wiki and > let me know when it's done. > > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > Thanks, > Sita. > > > > > On Fri, 5 Mar 2010, Gergely Orsi wrote: > > Hi Bruce, >> >> Please follow these links to get the dataset: >> >> http://www.humyo.com/7891739/C1_orig.tar.gz >> >> http://www.humyo.com/7891739/C1_modified.tar.gz >> >> >> The first one is the original before placing the control points, the >> second >> is the modified dataset after correction. >> >> Thanks a lot, and sorry for writing parallel with Gabor on this topic. >> Actually we are working next to each other, and whoever notices your mail >> first, writes the reply. :) >> >> cheers >> >> Gergely Orsi >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >

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Re: [Freesurfer] How to verify cerebellum segmentation
by Gergely Orsi 05 Mar '10

05 Mar '10

Hi Bruce, Please follow these links to get the dataset: http://www.humyo.com/7891739/C1_orig.tar.gz http://www.humyo.com/7891739/C1_modified.tar.gz The first one is the original before placing the control points, the second is the modified dataset after correction. Thanks a lot, and sorry for writing parallel with Gabor on this topic. Actually we are working next to each other, and whoever notices your mail first, writes the reply. :) cheers Gergely Orsi

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the input file of recon-all
by liyuanyuan60 05 Mar '10

05 Mar '10

HI Bruce and freesurfers I have a question about the input file of recon-all I follow the tutorial, first use unpacksdcmdir to convert the original dcm file to a mgz file,then use the recon-all command with the mgz file as the input. I also tried to run the recon-all command with the original dcm file as the input. And I compare the output *.stats files with different inputs, the *.stats files I compared located in <subjectname>/stats/ Then I found a strange thing, the aseg.stats file between the two inputs is the same, however, the aparc file is different,and the difference in some index is larger than we thought. So, I am not sure, which input file is OK for recon-all analysis? I have attached the related results. The version we use is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0 Thanks for your help! ps1, we use siemens machine, so I put *.IMA as the dcm input ps2, the scanning orient we use is sagittal, however, my partner has asked this question and was answered that we need't reorient it. Sincerely, Jin 2010-03-03 liyuanyuan60

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Freesurfer March 2010