Freesurfer November 2008

freesurfer@nmr.mgh.harvard.edu

70 participants
98 discussions

optseq2 question
by Hongchuan Zhang 13 Nov '08

13 Nov '08

Hi, list, I am new to optseq2 so I really need advices to my questions. We have an experiment of 2 factors with 36 trials for each factor, and another 24 null trials. So in total we have 96 trials. We also have 3 random jitters which make our trials could last for either 4.6, 5 or 5.4 seconds. The total session time is thus 480 seconds. Since our TR is 2 seconds, the ntp = 240. My questions are: (1) How can I set the psdwin? My intuition is that dPSD should be divided by both TR and trial duration. That means we can only have a dPSD = 0.2. Would that be too small? I observed that by doing this the largest psdmax is only 2 seconds. (2) What should I do if I want to break the session into two parts? The previous optseq version seems to allow one specify the runs for each sesssion. But I did not find this option in optseq2. Can I just use half the trials to get two sequences and use them for the two parts? Thanks! Your suggestion is appreciated. Hongchuan 2008-11-03 Hongchuan Zhang, Ph.D. Postdoctoral Research Associate Developmental Cognitive Neuroscience Laboratory Northwestern University 2240 North Campus Drive Frances Searle Building, Room 2-356 Evanston, Illinois, 60208 phone: (847)467-1549 e-mail: hongchuan-zhang at northwestern.edu

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Re: [Freesurfer] tksurfer: Load GDF command line?]
by Pratap Kunwar 13 Nov '08

13 Nov '08

HI Tori, I don't think fsgd option is available on the tksurfer or tkmedit command line. It would have nice to load fsgd file on command line instead of loading from tksurfer gui. > Hi All, > I was wondering if there was a flag or command in tksurfer that would > allow me to load a group descriptor file (y.fsgd) using the command > line. I looked through the tutorial and couldn't seem to find anything. I > only found resources for loading a timecourse. This isn't the same thing > right? Any help would be appreciated! they are not same. > Thanks, > Tori > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >

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Functionality of autorecon2-wm
by Ryan Scotton 13 Nov '08

13 Nov '08

Hi all, My team has recently completed a few hundred FreeSurfer runs on young (2-4 year old) children. For the past month or so, we have been using various editing techniques in order to fix different problems with the white matter volumes (these were to be expected considering the ages of our subjects). Since our goal is to get accurate measurements of cortical thickness, this is a crucial step. A few of the images simply stop including the white matter at a certain point, always always toward the posterior/occipital region of the brain. We devised an approach to solving this problem that involves converting formats and orientations, loading the brainmask and white matter volume into a manual brain segmentation editing tool, and using a 'snake tool' that fills in the white matter that was not captured by FreeSurfer. We have ensured that the label we used to fill this in is the same as the label used for manual editing within tkmedit. HOWEVER, after rerunning FreeSurfer with this edited volume (using -autorecon2-wm), the surfaces do not seem to have changed at all. Am I missing something here? I thought that if white matter edits were made that filled in gaps in the original wm.mgz volume, FreeSurfer would adjust the the surfaces accordingly. I've attached two photos to give you an idea of what I'm experiencing. Thanks for any advice on this predicament. Ryan

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converting modified labels from annot
by j janssen 13 Nov '08

13 Nov '08

Hi, using version 4.0.5. i used mri_extract_label on the aparc+aseg.mgz file to extract and convert labels into volume nifti files, which i can view and use outside FreeSurfer. works fine. however, i have manually edited some surface labels, following the instructions found here: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit?action=fullsea… these instructions result in a modified .annot file, which i have. my question: what is the best way to get a nifti volume for the modified (manually edited) label? ideally, this nifti volume should be exactly the same as done with mri_extract_label except for the modified part. thanks, -joost

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Recon Error Message
by Alexa Nardelli 12 Nov '08

12 Nov '08

Hi guys, I also have another question: I am getting the following error message when I run recon-all with a few of my images: Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux meddhcp202-30.dhcp.med.ualberta.ca 2.6.18-92.1.13.el5 #1 SMP Thu Sep 4 03:51:21 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Nov 7 21:17:02 MST 2008 Does anybody have an answer as to why this may be happening? Thanks Alexa

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brainmask.mgz
by Alexa Nardelli 12 Nov '08

12 Nov '08

Hey, I was just wondering if the brainmask.mgz file is the image after normalization? Thanks Alexa

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6 direction mgh gradient sequence
by Victoria Williams 12 Nov '08

12 Nov '08

Hello, Can anyone point me to where I could find a mgh gradient file for dti processing with 6 directions? I am trying to rerun some old data through dt_recon and the gradient_mgh_dti sequence packs start at 13. Any suggestions? Thanks, Tori

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(no subject)
by Burmicz, Ryzarda 12 Nov '08

12 Nov '08

Hello there, We have a subject processed using recon-all that possesses a dimple in the region of the left lateral ventricle. We would like your opinion as to whether or not it requires fixing and how - we are not sure how to go about it (i.e. if it requires a wm.mgz fill how much of it should be filled? It is a tricky subject in that it is quite an asymmetrical brain). This dimple will surely impact upon the mean cortical thickness, a metric which we are interested in using, and therefore we would prefer to fix it if possible. The dimple is approx at talairach -22.0 -40.5 11.8 I attach some screen shots from tksurfer and tkmedit, although I think it might be best seen from different orientations so let me know if I should upload the subject. Many thanks, Rysia

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Recon-all -long
by Juergen Haenggi 12 Nov '08

12 Nov '08

Dear FS experts Is there any difference or problem when running tp2 on the "longitudinally adjusted" tp1 instead on the recommended cross-sectionaly processed tp1? Thanks in advance Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of 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(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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can't display retinotopy fieldsign data
by Xu Cui 11 Nov '08

11 Nov '08

Hi, After doing the retinotopy analysis I find I can't view the fieldsign with command surf-sess <http://surfer.nmr.mgh.harvard.edu/fswiki/surf-sess> -s sessid -a rtopy -retinotopy fieldsign -flat (I can view ecc/polar data though.) What is shown is a very dark patch almost invisible. I read the entire thread in http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07329.html I am using the latest build for Mac Intel. I could not find convert_fieldsign.m Anybody can help? -- ---------------------------------------------------------------- Xu Cui Department of Psychiatry and Behavioral Sciences Stanford University ----------------------------------------------------------------

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Freesurfer November 2008