Freesurfer

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30132 discussions

surface tilted
by Nathan Dankner 09 Mar '11

09 Mar '11

Hi all, After running a surface through autorecon2 and checking it I noticed that it is tilted up at approximately a 45 degree angle. Is this a problem? If so, how should I go about fixing it? Nathan

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Still looking for an answer: question about weighted regression analysis
by Katie Bettencourt 09 Mar '11

09 Mar '11

Still looking for an answer to this question: So in doing a more complicated version of the analysis with paradigm weighting, I had another experiment where I wanted to test out two different models, 1) that BOLD activity was related to my behavioral measure alone or 2) that BOLD activity was related to my behavioral activity plus a factor that represented the number of distractors present (which is constant across set size) (had a high and low distractor condition, so that this factor was effectively 0 for the low distractor condition and something like 1 for the high distractor condition). I modelled the second my simply adding the behavior measure and the distractor factor together (which means that in practicality, nothing changed for the low distractor conditions between model 1 and model 2, but that the weight was increased by a constant factor in the high distractor conditions between model 1 and model 2). When I ran this analysis, what I got (shown in the attached picture in a group average) was an increase in the amount of activity and area of activity for model 2 (targets & distractors) compared with model 1 (targets only). Am I right in interpreting this as model 2 being a better fit? Or is can these maps be compared to show areas that are a better fit for model 1 and other areas that are a better fit for model 2? I have ROI data on the unweighted analyses that goes along with the idea of model 2 being better, but I wanted to make sure I was intrepreting the activity in this weighted analysis correctly. Thanks, Katie On Tue, Feb 22, 2011 at 1:35 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > Yes, your understanding is correct. People might choose Version 1 because > they strongly feel that it accurately represents the underlying mechanism. > It saves one DoF, but that's not going to change much. I think the problem > with Version 1 is that, for most designs, it forces you to extrapolate > outside of your data range. Few things are truly linear, but they are often > well modeled by straight lines over a limited range. For your data, you > might really expect the response to be 0 at x=0, but it become a very > non-linear curve in that region. > > doug > > Katie Bettencourt wrote: > >> Ok, so just so that I understand (I realize I'm being a bit dense, and I >> appreciate you walking me through this). If I am weighting my paradigm by >> my behavioral measure, then the activity I see with this weighted analysis, >> is areas where we are seeing a linear relationship between BOLD activity and >> my behavioral measure. In version 1:1vs0, this assumes that my linear fit >> passes through xy=0. However, in version 2:2vs0, we put an offset (or a >> sort of y intercept?) into the model so that the data doesn't have to pass >> through xy=0. And you are saying that the larger amount of activated area >> that I am getting in Version 1:1vs0, is because I'm seeing areas activated >> for the fact that there's an increase from baseline but not exactly the >> linear fit between BOLD and behavioral measures, but for Version 2:2vs0, I >> see only the areas that show this linear correlation? Does that sound about >> right? >> >> And if I am right, why would anyone do Verison1? Is it just because if >> your fit does pass through xy=0, you get more power this way compared with >> Version 2? >> >> Katie >> >> On Tue, Feb 22, 2011 at 1:00 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> >> >> Katie Bettencourt wrote: >> >> >> You should also look at Version2:1v0. I bet a lot of the areas >> from Version1:1v0 will also show up. You can also create a >> Version3 in which you divide your presentations into a >> low-weight >> and a high-weight (but set the weight=1). Then create >> contrasts of >> low+high and high-low. The low+high should look like >> Version2:1v0 >> and the high-low should look like Version2:2v0. >> >> >> >> So, what would this say? That the extra activity I'm getting >> in Version 1 is just the slope/offset, and isn't actually load >> related data that I am trying to get at (ie. isn't activity >> that is increasing as the number of items the subjects is >> remembering increases, but is just baseline visual stimulation >> activity or something?) >> >> Yes. It's easier to explain if I can draw it out. But imagine an >> xy plot with your weight on the x axis and the fMRI response on >> the y axis. If there is an offset but no change in fMRI with >> weight, then the data points will be on a horizontal line. Now >> what happens if you try to fit that data with a line that is >> forced to pass through xy=0? You'll get some positive slope, but >> overall it won't fit very well. >> >> >> And What exactly to do you mean by divide my presentations >> into low and high weight? What exactly would this be >> comparing? Sorry if I'm being dense. >> >> I mean create a new paradigm file with two non-null conditions. >> Condition 1 would be all presentations with weight < 0.5 (low >> weight); Condition 2 would be all those with weight>0.5. You >> should pick your own weight threshold of course. >> >> doug >> >> >> Katie >> >> >> doug >> >> >> >> >> Katie Bettencourt wrote: >> >> Yes, those are the maps I"ve been comparing. I've been >> comparing it to BV sort of, but that analysis is not >> surface >> based and I"m not used to it, so I can't quite tell >> which is >> more accurate, though Version 2 gives a much smaller >> area of >> activity, which fits with the description of what I've been >> given about what to expect in BV. Attached is two >> pictures of >> the difference I get for Version 1:1v0 (labeled with >> "single" >> in the image name) and Version 2:2v0 (labeled with >> "double" in >> the name). As you can see, Version1 activates a much >> larger >> area than Version 2. >> >> I guess part of my problem is that I'm having trouble >> understanding exactly what these two versions are >> telling me >> about the data and what the differences is. Can you try to >> give me a sort of layman's explanation? >> >> Katie >> >> >> On Tue, Feb 22, 2011 at 11:45 AM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: >> >> I assume that you are comparing maps of Version1:1v0 and >> Version2:2v0 ? I could imagine it going either way. >> If the true >> slope is 0 but the offset is non-0, then Version1 >> will give >> you an >> artificially high slope (and Verion2 will give you >> the correct >> slope at 0, and so no activation). Are you comparing >> this >> to a BV >> analysis? >> >> doug >> >> >> Katie Bettencourt wrote: >> >> So I created a weighted regression analysis to >> look at the >> effect of memory load in a particular brain region. >> Basically, >> I weighted the paradigms by a behavioral measure >> that >> reflected the number of items actually >> remembered (as >> set size >> was increased). As far as Doug told me there are >> basically 2 >> ways to weight your paradigm files. >> >> Version 1: >> Have 2 conditions, baseline (condition 0) and >> all the set >> sizes (condition 1). Condition 1 would then be >> weighted by >> the behavioral measure. >> >> Version 2: >> Have 3 conditions, baseline (condition 0), and >> then I >> represented each presentation as two different >> conditions, one >> with a weight that is always 1 (condition 1), >> the other >> weighted according to the behavioral measure >> (condition 2). >> >> >> The difference, as far as I understand it, in >> version >> 1, it is >> assumed that the response amplitude is ) when the >> weight is 0 >> (ie. that when you are attending to 0 items, brain >> activity = >> 0). Whereas, version 2, tests the slope of the HRF >> amplitude >> vs weight without the assumption above. >> >> However, I'm a bit confused as to the results I got. >> When I >> looked at the data from both versions, version 1 >> provided a >> much higher amount of activation and more areas >> activated than >> version 2. However, I believe version 2 better fits >> with the >> multiple regression analysis that is done in >> Brain Voyager. >> Can anyone give me a better explanation of what the >> difference >> between these analysis models is? >> >> Katie >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> < >> http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> >> 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. >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> ------------------------------------------------------------------------ >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >

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Calculating Euclidean Distance
by Weisinger, Brian (NIH/NIMH) [F] 09 Mar '11

09 Mar '11

Hello, Is there any chance that there is a general table of Euclidean distances for each freesurfer segmented brain region relative to each other. So something like a matrix table for each side of the brain Brain region 1 Brain region 2 Brain region 1 0 12.033 Brain region 2 12.033 0 Thank you, Brian Weisinger

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FreeSurfer 5.1
by Alan Francis 09 Mar '11

09 Mar '11

Hi Bruce, Nick & Doug: Any chance of FS 5.1 coming out in the near future? We have 2 longitudinal data sets that we are holding back till we have this installed. Thanks so much, Alan

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open .gca file
by Tetiana Dadakova 09 Mar '11

09 Mar '11

Dear FreeSurfer list, I try to open RB_all_2008-03-26.gca by typing mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz and get an error: mri_convert RB_all_2008-03-26.gca -nth 0 means.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from RB_all_2008-03-26.gca... reading frame 0 of gca TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to means.mgz... mghWrite(means.mgz, -1): could not open file ERROR: failure writing means.mgz Could you please tell me what can be wrong? Thank you, Tanja.

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Fixated brain
by Auer, Tibor MD. Ph.D. 09 Mar '11

09 Mar '11

Dear Users, Is there a way to process fixated brain (after autopsy) with Freesurfer? I have read somewhere that I should just "invert" the image, but what does it mean? And would it not increase the noise and the signal from the CSF? Of course, the brain is without any skull, pia and dura mater. Does it cause no problem for Freesurfer? Thanks, Auer, Tibor M.D. Ph.D. Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone/Work: +49-(0)551-201-1725 Mobile: +49-(0)176-8012-7921 E-Mail: tauer(a)gwdg.de <mailto:tibor.auer@gmail.com>

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Miao Wen wants to stay in touch on LinkedIn
by Miao Wen via LinkedIn 09 Mar '11

09 Mar '11

LinkedIn ------------Miao Wen souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Freesurfer, I'd like to add you to my professional network on LinkedIn. - Miao Wen Accepter l'invitation de Miao Wen http://www.linkedin.com/e/-qq80um-gl1us5y3-j/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… Voir l'invitation de Miao Wen http://www.linkedin.com/e/-qq80um-gl1us5y3-j/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59… ------------------------------------------ SAVEZ-VOUS que votre profil LinkedIn vous permet de contrôler votre image professionnelle sur le Web ? Si vous le rendez "public", votre profil LinkedIn apparaîtra quand un internaute effectuera une recherche en ligne sur votre nom. Soignez votre image sur le Web ! http://www.linkedin.com/e/-qq80um-gl1us5y3-j/ewp/inv-22/ -- (c) 2011, LinkedIn Corporation

1 0

Newbie - problems compiling project tree
by Shay Ohayon 08 Mar '11

08 Mar '11

Hi All, I am having some problems compiling freesurfer . I checked out the recent development version from the CVS, ran "setup_configure" successfully, but upon "./configure", I end up with the following annoying message: checking for nccreate in -lnetcdf... no configure: error: FATAL: netcdf lib not found. Set LDFLAGS or --with-mni-dir. I attempted to install the netcdf-bin and libnetcdf6 packages using Synaptic, but this did not seem to help. How do I continue from here? -- Shay

2 2

Pial view
by Allie Rosen 08 Mar '11

08 Mar '11

Hi Everyone, I am hoping to visualize the insula using the pial view in TkSurfer. Is there a way to make the surfaces translucent, or to crop away specific areas? I would like to use the pial view instead of inflated views to do this. Thanks, Allie Rosen, MSc Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

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Intensity Problem
by Matt Russell 08 Mar '11

08 Mar '11

Dear FreeSurfer Experts, I'm currently working with a data set that seems to have a systematic problem with intensity. I attached an image of a brain with this problem for your reference. As you can see, the unprocessed MRI file has an intensity problem in the temporal lobe, almost like a flashlight is lighting it up. When FreeSurfer processes this part of the brain it fails to detect it. My question is a) is this data still usable? We aren't actually looking for any effects in this area of the brain, but are worried that it is a bigger symptom of problematic data and b) if this data is still usable, is there anything we can do to work around it? Thanks, Matthew Russell

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