Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

Volume calculation
by Walimuni, Indika S 21 Sep '09

21 Sep '09

Hi FreeSurfer List I have been running Freesurfer for some time now and I want to calculate brain structure volumes of all the subjects. I used the command " mri_segstats --seg aseg.mgz --ctab-default --sum out.sum" within the subject's mri directory to get the volume segmentation results from the out.sum file. I want to calculate total brain volume with and without the cerebellum, volumes of total gray and white matter, sub-cortical gray matter objects such as Putaman and Caudate, the volumes of white matter structures such as CC and the volume of the Thalamus. I searched through the earlier postings and found a lot of information regarding this matter. However, due to overwhelming ideas, suggestions and some were very old, I am now kind of confused with the correct method to follow. So, I appreciate if freesurfer expert could help me with following questions, 1. Is above command and the resulting out.sum file, the correct method to use? 2. If not ,what is the best methods and commands that I should use to get above volumes 3. Is the volume under the name "Unknown" the total brain volume with or without the cerebellum. 4. What is the best way to get the inter cranial volume ? 5. Why there are zero volumes under the Left-Thalamus or right-Thalamus ? Please forgive me if this is a repetition of a previous posting. Thank you in advance Truly, Indika Walimuni Research Associate University of Texas Health Science Center Houston, TX.

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tkregister2 question
by Guang Zeng 21 Sep '09

21 Sep '09

Hi, there, I have a case_1.hdr file and case_1.img file, but no the corresponding .mat file which contains the necessary direction cosine info. So everytime when I try to register another nifti file case_2.nii to it using tkregister2 or mri_vol2vol, it always complains that "INFO: could not find ../../case_1.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ../../case_1.mat file" Just want to know if there are other methods I can use to register case_1 and case_2? Any kinds of method! Thanks a lot! Guang _________________________________________________________________ Bing™ brings you maps, menus, and reviews organized in one place. Try it now. http://www.bing.com/search?q=restaurants&form=MLOGEN&publ=WLHMTAG&crea=TEXT…

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Correlating two surfaces in glmfit
by Nicolas Cherbuin 21 Sep '09

21 Sep '09

Hi I am not sure my last query below was circulated to the list. If somebody has an answer it would be great. Cheers Nic _____ From: Nicolas Cherbuin Sent: Friday, 11 September 2009 10:49 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Correlating two surfaces Dear All, I would like to correlate two surfaces with glmfit e.g. thickness and curvature but I don't seem to be able to find any document explaining how to do that. In addition, is it possible to correlate left and right hemisphere surfaces and if yes how? Could you please point me in the right direction? Thanks Nic

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Qdec white matter
by Jose Soares 21 Sep '09

21 Sep '09

Hi all, I am using qdec and I would like to know if it is possible to do any comparison with whit matter in qdec. Thank you for the help, Miguel. ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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job opening
by Bruce Fischl 21 Sep '09

21 Sep '09

Department of Clinical Neurology, FMRIB Centre Postdoctoral Research Assistant: Decisionâmaking and learning Grade 7: Salary Â£28,839 â 35,469 p.a. The Centre for Functional Magnetic Resonance Imaging of the Brain (FMRIB) and the Wellcome Trust Centre for Brain Imaging, UCL, seek a postdoctoral research assistant to work with Dr Tim Behrens in decisionâmaking research. The successful candidate may make a case for working at either location. Employment could begin from December 2009 and is funded by the Wellcome Trust for a period of 2 years. Candidates must have a doctorate in a relevant discipline, experience in functional neuroimaging and, ideally, prior experience of research into decisionâmaking. Expertise in computational models of decisionâmaking and behaviour would also be beneficial, although not essential. For an outline of the lab's research interests and links to further information see http://www.fmrib.ox.ac.uk/ and www.fil.ion.ucl.ac.uk . Applications, including a curriculum vitae and details of three referees, should be sent to Mrs Marilyn Goulding, FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU, fax: (01865) 222717; eâmail: marilyn(a)fmrib.ox.ac. uk. Please quote reference HM09-014. The closing date for applications is October 9th 2009. Further information and application procedures can be found at http://www.fmrib.ox.ac.uk/vacancies .

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Using tksurfer to dispaly the surface
by QQ Liu 20 Sep '09

20 Sep '09

Hi all, When I use tksurfer to display the results of group analysis, there is a problem. I have to put the mouse on the image then it can be in the front. However, there is not the smooth surface as that in the tutorial of group analysis in wiki. The image showed up is just some dots in the black ground. What's wrong about this? and how to solve this problem? The image captured is attached in this mail. Thanks a lot. QQ -- Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com

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transforming of the spherical atlas Right --> Left hemisphere ??
by Ritobrato Datta 18 Sep '09

18 Sep '09

Hello All, we are considering combining some data from the left and right hemispheres. Is there a way to implement a transform of the spherical atlas Right --> Left hemisphere? Topologically, this probably corresponds to turning the sphere inside-out (plus registration of residual hemispheric differences in gyral pattern). Please let me know if there are ways to do this. Thanks Ri

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hippocampus volume are different after step.3
by Guang Zeng 17 Sep '09

17 Sep '09

Hi, there, I ran a subject through FreeSurfer pipeline. I found that the size of left and right hippocampus in aseg.stats are larger than that of left and right hippocampus in wmparc.stats after step. 3. If I want to compare the FreeSurfer segmented hippocampus with a manually traced hippocampus, which value I should use, the result from step.2 or step. 3? Thanks a lot! Guang _________________________________________________________________ Hotmail® has ever-growing storage! Don’t worry about storage limits. http://windowslive.com/Tutorial/Hotmail/Storage?ocid=TXT_TAGLM_WL_HM_Tutori…

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grey/white matter
by africa millan 17 Sep '09

17 Sep '09

Hi, Is there any tool or function to create a histogram to check if I am distinguishing in the right way the white matter from the grey matter?? _________________________________________________________________ Con Vodafone disfruta de Hotmail gratis en tu móvil. ¡Pruébalo! http://serviciosmoviles.es.msn.com/hotmail/vodafone.aspx

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Hippocampus
by Kelly Silva 17 Sep '09

17 Sep '09

Hello, I would like to know: 1) How can I use the mri_binarize for the hippocampus? How are the input and output image that I have to put? 2) How can I visualize (generate) an hippocampus mask to see with the tksurfer command? Thanks a lot, Kelly ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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Freesurfer September 2009