Freesurfer September 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
131 discussions

Perirhinal cortex
by Kelly Silva 25 Sep '09

25 Sep '09

Hello, Is there any way to calculate the cortical thickness of perirhinal cortex? Thanks in advance, Kelly ____________________________________________________________________________________ Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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LGI:default value of the radius when calculating LGI
by Zhangyuanchao 25 Sep '09

25 Sep '09

Hi, expert, I would to know what is the exact value of the radius when calculating lGI; How could I check that value? Thanks a lot! yuanchao ___________________________________________________________ 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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tksurfer inflated
by africa millan 25 Sep '09

25 Sep '09

Hello everybody, The image I enclose you in this mail (jpeg and gif format) represents 3 images ( the same region but different orientation) of a subject, corresponding to the inflated (tksurfer lh inflated) obtained after 4 times of recon 2 running. As you can see, there are several soft peaks that I couldn't remove although I repeated and corrected the segmentation three times. Do you think it is necessary to repeat the segmentation again? Thanks Africa. _________________________________________________________________ Nuevo Windows Live, un mundo lleno de posibilidades. Descúbrelo. http://www.microsoft.com/windows/windowslive/default.aspx

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Labels for the auditory cortex
by Nasim Maleki 25 Sep '09

25 Sep '09

Dear developers, I was wondering if you would have labels for the Broadman areas corresponding to the auditory cortex for the fsaverage subject. Thank you, Nasim

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how to use mri_surf2surf
by Guang Zeng 24 Sep '09

24 Sep '09

Hi, there, mri_surf2surf resamples one CorticalSurface onto another. If I have two subjects from different time points (tp1 and tp2), I'd like to compare the FreeSurfer analyzed surface data. For example, could I use mri_surf2surf to resample the white matter surface of tp1 onto tp2, so I can overlay the white matter surface of tp2 to tp1 using tkmedit? Thanks! 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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Re: [Freesurfer] FSL to FreeSurfer registration
by Estephan Moana 24 Sep '09

24 Sep '09

Thanks for you input Michael. For some reason, I only saw your answer after Dougla's response. Assuming that I do not want to do volume-based analysis and just want "nice pics" of my blobs over a 3D brain, would Michael's suggestion work? If so, what is the next step after using fslroi, as the input for reg-feat2anat is a feat directory (an not a single example_func file)? An unrelated question: is there a way to get the FreeSurfer mailing list via a RSS feed? This would be help decrease the amount of emails in my inbox... Thanks again. Estephan

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hippocampus volume difference
by Guang Zeng 24 Sep '09

24 Sep '09

Hi, there, I use the following matlab code to find right and left hippocampus in aseg.mgz %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% filename = 'case_1/mri/aseg.mgz'; [vol, M, mr_parms, volsz] = load_mgh(filename); hippo_left = find( (vol > 16.99) & (vol < 17.01) ); hippo_right = find( (vol > 52.99) & (vol < 53.01) ); %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% I found size(hippo_left, 1) = 3075; size(hippo_right, 1) = 3237; However, the value I found in aseg.mgz is 3162 3162.0 Left-Hippocampus 3390 3390.0 Right-Hippocampus Why these values are different (3075 < 3162, 3237 < 3390)? 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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cortex.label stats
by Dankner, Nathan (NIH/NIMH) [F] 24 Sep '09

24 Sep '09

Hi all, In past versions, I have been using this command to generate average cortical thickness across the cortex: Mris_anatomical_stats -l (hemi).cortex.label -f (id)/stats/(hemi).cortex.stats (id) (hemi) However, I have noticed that in version 4.5 the cortex.stats files are no longer in the stats folder. Are they somewhere else, or is there a different method which I should now use to compute these statistics?

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fsgd and contrast matrix
by Martin Kavec 24 Sep '09

24 Sep '09

Hi, I would like to study cortical thickness in a cohort of patient with respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR listed: GroupDescriptorFile 1 Title Mytitle Class Male Class Female Variable Age Variable MMSE Variable CDR Class Ctrl Class MCI Input subject1 Male 70 27 0.5 MCI Input subject2 Female 65 28 0 Ctrl My design matrix should thus have 4*(3+1)=16 columns/regressors. I am puzzeled a bit, how would I set the contrast matrix to study only correlation of thickness with MMSE, while ignoring CDR. Or should I have a separate fsgd file? Thanks, Martin

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Re: [Freesurfer] FSL to FreeSurfer registration
by Douglas N Greve 24 Sep '09

24 Sep '09

Hi Michael, while fslmaths has an option to do "2D" smoothing, this is still only smoothing in a slice of the volume and has the same problems as 3D smoothing (ie, smoothing across tissue types and sulci). The "2D" that FS implements with mris_volsmooth is along the cortical surface, which is unrelated to the volume axes. So, unfortunately, you do still have to do two analyses if you want a volume-based analysis with smoothing. doug Michael Scheel wrote: > Hi Estephan, > > you don't necessarily have to rerun the full 1st level Analysis in total. > What you have to find out is which of your volumes is the one that > example_func is created from. > Normally this should be the middle timepoint fmri image of your > functional run (e.g. if you have 99 volumes then number 45 > will be taken as example_func) that's the default if you haven't > specified it otherwise. > You can use fslroi as a command to extract this volume for the above > example e.g.: > fslroi input_fmri.nii.gz middle_volume.nii.gz 44 1 > (fslroi starts counting from 0 thats why it is 44 instead of 45) > > 2D and 3D smoothing can also be done with > fslmaths see the -s and the -kernel option > > Best, Michael > On 23-Sep-09, at 6:52 PM, Douglas N Greve wrote: > >> >> >> Estephan Moana wrote: >>> So what I need to do is to run the 1st level FEAT as usual for the FSL >>> pipeline, and repeat this analysis for FS with the only difference >>> been to set the "Spatial smoothing FWHM" to zero on the pre-stats tab >>> of the FEAT GUI? >> yes >>> >>> Also, can you explain if this smoothing on the FEAT GUI is the 3D you >>> refer to? And how 2D smoothing is accomplished? >> Yes, this the 3D smoothing. 2D smoothing on the raw data is more >> difficult inside of feat. You'd have to use MC and then run >> mris_volsmooth (FS program) outside of FEAT, then pass FEAT the >> preprocessed data and tell it not to do MC or smoothing. >>> >>> Thank you. >>> >>> Estephan >>> >>> Douglas N Greve wrote: >>>> The example_func does not actually get smoothed, so smoothing itself >>>> will not affect the registration. 3D smoothing will smooth values >>>> from WM and CSF into gray and from across sulci into functionally >>>> distinct regions. For this reason we recommend not using 3D smoothing >>>> (or doing 2D smoothing on the surface). Unfortunately, this requires >>>> two different analyses. >>>> >>>> doug >>>> >>>> Estephan Moana wrote: >>>>> Hello all, I took the FS course last June at the OHBM in San >>>>> Francisco, and am now playing with it to get to know it better. One >>>>> of the slides on the talk about FSL-FS integration mentioned that >>>>> the input data (from FEAT) for the reg-feat2anat command should have >>>>> not been smoothed prior to registering to FS. >>>>> >>>>> Considering that FEAT 1st level analysis has a default of 5mm >>>>> spatial smoothing (and that's what I used on my data), it seems >>>>> counterintuitive to need to run a 1st level analysis again so the >>>>> output files are not spatially smoothed. >>>>> >>>>> So my questions are: 1) having the example_func file spatially >>>>> smoothed will necessarily hinder a proper registration to the FS >>>>> anatomical?; 2) if so, should I re-run all my FEAT 1st level >>>>> analysis without smoothing or is there any other way? >>>>> >>>>> I know this is quite a beginners question, but I could not find the >>>>> answers on the FS FAQ or the mailing list archives. I appreciate any >>>>> light on this. >>>>> >>>>> Regards, >>>>> >>>>> Estephan Moana, DDS >>>>> Graduate Student >>>>> Oral Biology PhD Program - Neurobiology track >>>>> School of Dentistry, UNC- Chapel Hill >>>>> 2140 Old Dental Building, CB# 7455 >>>>> Chapel Hill, NC 27599 >>>>> Phone: (919) 966-5680 Fax: (919) 966-5339 Cell: (612) 702-3295 >>>>> moana(a)email.unc.edu <mailto:moana@email.unc.edu> >>>>> ------------------------------------------------------------------------ >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> 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 >> >> >> _______________________________________________ >> 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

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Freesurfer September 2009