Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30090 discussions

longitudinal analyses for one group
by Sandra Preissler 28 Jun '13

28 Jun '13

Dear freesurfer experts, we want to do longitudinal analyses for two different time points in only one group (We do not have a control group or different groups within the intervention). So we did the longitudinal processing as described in the tutorial (http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial#Prepa…) Now we tried to investigate the results with Qdec. We wanted to test whether the averaged change of thickness between pre-test and post-test differs from zero. We had the experience that we could only test the averaged thickness by choosing a discrete factor in Qdec. Our Problem is that we dont have a control group. So we couldn't choose the group variable as discrete factor. Its an pre-post-design with only one group. Is it possible to investigate changes in thickness between pre-test and post-test without choosing a factor? Or do we have to create a group variable as discrete factor? Can you help us in fixing this problem? Thanks in advance! Sandra ---------------------------------------------------------------- This message was sent through https://webmail.uni-jena.de

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mri_label2vol problem
by LAOUCHEDI MAKHLOUF 28 Jun '13

28 Jun '13

excuse me but i don't understand what you mean by "terminal of mri_label2vol" Thank you for help

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trouble in freesurfer v5.3
by R B 28 Jun '13

28 Jun '13

Hi Freesurfer Experts, i have earlier worked in freesurfer previous versions. i was able to get preliminary results. i have trouble with freesurfer version V 5.3, i have error in this step of the analysis " minc_modify_header: posixio.c:210: px_pgin:Assertion `*posp == ((off_t)(-1)) || *posp == lseek(nciop->fd, 0, 1)' failed." progressively the subsequent steps are showing error. requesting your assistance in troubleshooting this issue thanks hsekar

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tksurfer display problem
by Xiangzhen Kong 27 Jun '13

27 Jun '13

Hi all. I want to display a result with tksurfer. The cmd is here: tksurfer fsaverage lh inflated -overlay ./fwhm10lh/c1.contrast/sig.mgh That is, I want to display the result of the left hemi. However, to my surprise, the plot seems like on the right hemi of the brain. In addition, the color bar is also strange. The plot is attached. I wonder whether this is normal or something may be wrong. 【小孔成像】http://www.conxz.net

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Some Questions Regarding W Files
by Zhongtian Dai 27 Jun '13

27 Jun '13

Hi, I want to ask some questions about w files: 1. does Freeview read and display w files? (if not, any plan to support it?) 2. does tksurfer support custom color scale? how to change a color scale's bounds? they seem to change with overlay's min and max but not consistently. 3. does anything resembling a multi-frame w file exist? Cheers, -- Zhongtian (Falcon) Dai B.S. with Honors in Mathematics & B.A. with Honors in Physics University of Chicago 2012 web <http://falcondai.com/> | blog <http://blog.falcondai.com/> | g+<https://plus.google.com/100753323689686892506> | twitter <https://twitter.com/falcondai> | github<https://github.com/falcondai> | weibo <http://www.weibo.com/falcondai>

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Re: [Freesurfer] freesurfer registration
by Martin Reuter 27 Jun '13

27 Jun '13

Hi Chris, for the motion correction step there is no bias-field correction. First it is assumed that bias field is not very different (scans are from the same session) and also the robust register can down-weigh regions that differ a lot. However the methods estimates a global intensity scale parameter simultaneously during the registration to adjust intensity values across the images (that's in the robust register paper). Best, Martin On 06/27/2013 06:45 AM, Parker, Christopher wrote: > Hi Martin, > > Are the images bias-field corrected before registration in recon-all? > If so, which method is used for this? Is there a paper for > reference/citation also? > > Many Thanks, > Chris > ------------------------------------------------------------------------ > *From:* Martin Reuter [mreuter(a)nmr.mgh.harvard.edu] > *Sent:* 25 June 2013 18:53 > *To:* Bruce Fischl > *Cc:* Parker, Christopher; freesurfer(a)nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] freesurfer registration > > Hi Chris, > > we actually do use my robust registration tool for it since a while > (FS 5.0, Aug 2010), replacing FLIRT which was used before. Here is the > citation: > > M. Reuter, H.D. Rosas, B. Fischl. *Highly Accurate Inverse Consistent > Registration: A Robust Approach*. /NeuroImage 53(4):1181-1196, 2010/. > > It is a robust rigid registration, using the tukey biweight function > on the residuals. The statistical robustness makes it less sensitive > to outliers (e.g. differences in jaw, neck, eye regions) by > identifying regions with local differences during the registration and > reducing their influence on the registration. This leads to very > accurate alignment in the regions that do not change (the brain). > > Cheers, Martin > > On 06/25/2013 12:05 PM, Bruce Fischl wrote: >> yes, it's rigid and used to be sum of squares but in the newer versions we >> will be using Martin's robust registration (which is a tukey biweight >> instead of SSE) >> >> On Tue, 25 Jun 2013, Parker, Christopher wrote: >> >>> Hi, >>> I understand that the recon-all script registers and then averages two >>> anatomical images (after bias field correction) if two are provided in the >>> "orig" folder, before performing the other parcellation stages. I am writing >>> a report and it might be good to mentioned what registration is used. I'm >>> guessing this is a rigid registration using sum of squared differences cost >>> function? >>> >>> Best, >>> Chris >>> >>> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: > mreuter(a)nmr.mgh.harvard.edu > reuter(a)mit.edu > Web :http://reuter.mit.edu > > 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. > -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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further description of 'mris_divide_parcellation' for high resolution atlas of the cortex
by Montillo, Albert (GE Global Research) 27 Jun '13

27 Jun '13

Does anyone have further documentation on 'mris_divide_parcellation' ? Is there a picture of what it does? It is referred to in the FreeSurfer FAQ Q. How can I get a high resolution atlas of the cortex in Freesurfer? A: This can be accomplished using 'mris_divide_parcellation'. You can pass your preferred max area of a parcellation and it will keep subdividing along the primary eigen-axis until no units are above that surface area.

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Bad resolution of recon-all -autorecon1
by ye tian 27 Jun '13

27 Jun '13

Dear freesurfers, After executing recon-all with -autorecon1, I opened the image Barba50527_2 *T1.mgz* from tkmedit. The bad resolution leads me to doubt that my input format wasn't correct. I input two sequences of images. Each image resembles the attachment Sample Input. There are 439 such image in each sequence. Would you please shine some light on my bad resolution? Thank you very much! Sincerely, Ye

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cortical parcellation: atlas modification and speed/accuracy trade-off
by Montillo, Albert (GE Global Research) 27 Jun '13

27 Jun '13

At times, I would like to use FreeSurfer to just produce cortical parcellation and do not need other results like subcortical parcellation and cortical thickness. How can I run the bare minimum number of steps to generate the cortical parcellation labeled volume? (Does anyone have a script that runs just these steps?) Similarly if I want to speed cortical parcellation and can accept lower accuracy as a tradeoff, are there parameters I can set to enable such a speed/accuracy tradeoff? Now on the flip-side, for other subjects I would like to change the granularity of the cortical parcels that FreeSurfer uses, to use finer parcels. How do I construct a new cortical parcellation atlas with more labels? Best, Albert

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How are time point exclude files used in FSFAST?
by Caspar M. Schwiedrzik 26 Jun '13

26 Jun '13

Hi Freesurfer experts, I was wondering how exactly time point exclude files are used by FSFAST. Are the time points removed from the time series before the GLM, or is the time point exclude file used to build a nuisance predictor (as in FSL's motion outliers routine, http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FSLMotionOutliers)? If the time points are removed from the time series, how is that accounted for when calculating the autocorrelation for the whitening / during (high pass) filtering? Thanks, Caspar

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