Freesurfer

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30086 discussions

squashed ascii coordinates of flattened patch
by Eyal Dechter 03 Oct '10

03 Oct '10

Hi, I'm trying to get the coordinates of vertices on a flattened patch that I've cut out of an inflated surface using tksurfer in fs 4.5.0. I save the patch, use mris_flatten, and then mris_convert -p. However, the coordinates I'm getting render the patch somewhat distorted and I'm wondering how I can recover the original geometry. Loading the ascii file back into tksurfer results in the correct geometry, so is there some distortion that tksurfer accounts for when loading up a patch. At the link below I've put a screen shot of the ascii coordinates plotted (ignore the black line) and the flat patch as it looks in tksurfer. I've also put the patch files I'm using. Note how the patch seems squashed. http://web.mit.edu/~edechter/Public/ After saving the patch I run: mris_flatten -w 10 patch_file patch_file.flat mris_convert -p patch_file.flat patch_file.flat.asc Also, there are a number of extraneous random vertices that show up in the ascii files. They are speckled around the patch in the left hand plot. What are these? And how do I get rid of them? Thanks, Eyal Dechter -------------------------- edechter(a)mit.edu Kanwisher Lab MIT

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connot complete setup (Mac OS X snow leopard)
by Tomita Satoshi 02 Oct '10

02 Oct '10

Hi, I cannot proceed setup using tkmedit ! Fatal Error in tkmedit.bin: could not open display freesurfer ver 4.5.0 Mac OS X snow leopard (MacPro) please give me help...

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correcting segmentation errors near the cerebellum
by Mehul Sampat 01 Oct '10

01 Oct '10

Hi Folks, One of my colleagues has a case which has a strange artifcfact near the cerebellum; it seems like it recognizes the tentorium as part of brain This bright artifact (?) throws off the segmentation and also the main surface. To correct this artifact should he just make manual edits to the wm.mgz ? Thanks Mehul

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Motion correction
by hakon.grydeland＠psykologi.uio.no 01 Oct '10

01 Oct '10

Dear all, we are currently processing a dataset using FreeSurfer 5.0 and in a (very) few subjects (3 of 450) the output is distorted. However, when rerunning the 3 subjects adding the -flirt-motioncor flag to the recon-all -all command, the output is fine (please see http://folk.uio.no/haakongr/files/inflated444.jpg for an example, left side is the -flirt-motioncor version). Any ideas as how to solve this problem without mixing procedures (or rerunning all subjects) would be highly appreciated! Thanks, Håkon Grydeland --- FREESURFER_HOME: /psyklab/local/freesurfer.5.0.0 Build stamp: freesurfer-Linux-centos5_x86_64-stable-pub-v5.0.0 RedHat release: Red Hat Enterprise Linux Client release 5.5 (Tikanga) Kernel info: Linux 2.6.18-194.11.4.el5.usit_CVE_2010_3081 x86_64

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tksurfer display
by Shugao Xia 30 Sep '10

30 Sep '10

Dear Freesurfer experts I am new Freesurfer user, I used the command: tksurfer fsaverage lh inflated -annot aparc.annot In the graph showed in the window are only the vertices, not surface, see the figure in the attachment. how to displace the surface in the window, which operation do I need ? (I tried the differerent option in the manu ''View", and I didn't get the surface) Thank you very much Shugao

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calculate the surface area of pial surface using mris_anatomical_stats
by Zhang, Yuning 30 Sep '10

30 Sep '10

Hi,experts, I am trying to get the total surface area of pial surface using the following command,but it seems the default surface for this command is white matter surface, is there any parameters i could change to get the information from pial surface ? mris_anatomical_stats -l lh.cortex.label -f /freesurfer/subjects_1/stats/lh.cortext.stats subjects_1 lh Thanks a lot best yuning

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calculating percent signal change
by Thomas Janssens 30 Sep '10

30 Sep '10

Hello, I am trying to calculate the percent signal changes for my monkey data. I did this by running the command selxavg3-sess and looking at the cespct values (or equivalently by using h.nii divided by h-offset.nii). I found in the mailing list that this value should be corrected by a scaling factor scalef if freesurfer-4.5.0 is used (see below). If I apply this correction factor I got values that at first sight look reasonable but if i calcultate the psc using JIP (the imaging program from Joe Mandeville), i find different values. And looking at the raw data I have to conclude that the value from JIP are the correct ones... For example if i look at the same voxel in MT if find: with JIP: -14.45% with FS: -8.15 % notice that the values are negative and pretty large due to the fact that we use and iron oxide contrast agent. If, instead of applying the scaling factor scalef (defined below), I apply the factor max(x.X(:,1)) as a scaling factor (which according to me is the maximum value of the convolved design matrix,or 'the EV' in FSL lingo), then I end up with a value of -15.09%. Which is pretty close to the value obtained with JIP. I got the last idea from mumford.fmripower.org/perchange_guide.pdf Do you have any clue where the differences come from? or if I am doing something wrong? Also, one of my colleagues used both the gamma model and FIR model to calculate the percent signal change (psc) for his event-related designed experiment, and the values are also quite different. He applied the scaling factor for the values from the gamma model, and didn't do it for the fir model. What he got is 0.6% signal change if he takes the peak of the time course (which looks quite ok) that fitted from the FIR model and 1.5% signal change from the gamma model. It seems that there is more than 2 times differences between these two values. Is it normal, or we need another scale factor for the fir model? Thanks for the answers! regards, Thomas Janssens ps: My selxavg3-sess analysis was done using the following parameters in the analysis.cfg file: -gammafit 0 8 -gammaexp 0.3 -timewindow 40.00000000000000000000 -prestim 0 -acfbins 10 -fix-acf -autostimdur -no-fsv3-st2fir -no-fsv3-whiten -polyfit 2 -TER .10000000000000000000 -autowhiten 30 -nskip 0 -fwhm 0 -rescale 1000 ---------------------------------------------------------------------------------------------- >[Freesurfer] Calculating % Signal Change from roisummary-sess readout > >Douglas N Greve >Wed, 04 Aug 2010 14:25:52 -0700 > > >That's right, though you may/will run into the problem of very small >values in which case you can use this fix: > >cd bold/analysis >x = load('X'); >tirf = x.flac0.ev(3).tirf; >Xirf = x.flac0.ev(3).Xirf; >scalef = sum(Xirf .* repmat(tirf,[1 size(Xirf,2)])); > >scalef will be something like 184. Multiply the percent signal change >you get by this number. BTW, this problem is fixed in version 5. > >doug > > >Adam Nitenson wrote: > Hi Freesurfers, > > I am trying to analyze functional activity in individual subjects. > The structural constraint is a dACC label and the functional > constraint is positive activation at a specific timepoint (6 sec > after stimulus). I was just wondering what the numbers following the > "# of estimates per condition" row actually represented, and how I > could convert these to % signal change. I saw in an archived email > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg00171.html > that someone mentioned taking those values, dividing by the baseline > offset value (row 4) and multiplying by 100 to get % signal change. > Is this a valid method? > > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital ---------------------------------------------------------------------------------------------- Thomas Janssens, PhD student Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School Herestraat 49, B-3000 Leuven (Belgium) phone +32 16 33 00 35 cell phone +32 494 115 509

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Re: [Freesurfer] Surface Area and Cortical Volume
by Michael Harms 30 Sep '10

30 Sep '10

Jeff, Posting this back to the list so that others can see your reply. cheers, -MH -------- Forwarded Message -------- From: Jeff Sadino <jsadino.queens(a)gmail.com> To: Michael Harms <mharms(a)conte.wustl.edu> Subject: Re: [Freesurfer] Surface Area and Cortical Volume Date: Wed, 29 Sep 2010 17:29:45 -1000 Hi Michael, After reading your answer, I can see it as valid for each individual subject. If I wanted to picture the average surface area for my controls, I think the approach would break down. I would have to transform all the surface areas onto a common space subject (fsaverage), and then all of the controls would have the exact same surface area, and so would the study group for that matter. My understanding was that the surface area is a measure of how much each triangle needs to be squished or stretched in order for it to match the triangles in the common space (fsaverage), and so it is a measure of "squishiness", not surface area. I may be getting my understanding of vertex-wise analysis mixed up with something else. Your insight is appreciated! Mahalo, Jeff Sadino On Wed, Sep 29, 2010 at 4:35 PM, Michael Harms <mharms(a)conte.wustl.edu> wrote: > > Hi Jeff, > Where do you get the idea that the area measures are not a "real surface > area"? Once the surface is parcellated, the area of each surface > parcellation as provided in the aparc files is simply the area represented > by the triangles in the mesh of the white matter surface. If you want the > area of the pial surface instead, you can generate those using the > appropriate flag in mris_anatomical_stats. But they are "real" areas, at > least at the parcellation level. (It is questionable, as I understand it, > whether VERTEX-WISE analyses across groups of the area and volume files > are meaningful or informative, but that is a different beast). > > Yes, for cortical quantification, you want to use the stuff in the aparc > files, since it is based on the surface analysis stream. > > cheers, > -MH > >> Hello, >> >> As I understand it, the surface area measure is not a real surface >> area measure. It is more a measure of how much the brain has to be >> stretched in order to get into a common space. My question is that if >> the cortical volume is calculated by multiplying the thickness and the >> surface area (right?), then is it a real volume that can be compared >> between subjects? >> >> Also, is it is more accurate to use the cortical volume measures from >> the aparc files rather than the aseg files, since the aseg files >> overestimate the white matter due to the manual tracing it is based >> on? >> >> Thank you, >> Jeff >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> 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. >> > >

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Re: [Freesurfer] Surface Area and Cortical Volume
by Don Hagler 30 Sep '10

30 Sep '10

The area maps do contain the actual surface area of each vertex with units of mm^2. The problem is that the area at a given vertex depends on how many vertices a given patch of cortex was divided into, which is initially uniform but then varies arbitrarily due to topology correction, rendering it useless for making statistical maps. If you are interested in making statistical maps of between-group differences in surface area, the best way to do that is by calculating the areal expansion measure. This is not a normally used feature of freesurfer, but is possible by using make_average_subject separately for each subject. If you use the area values in the aparc stats files, those are the sum of area for all vertices in each parcellation, and they have units of surface area (unlike measures of areal expansion). > From: jsadino.queens(a)gmail.com > Date: Wed, 29 Sep 2010 15:57:38 -1000 > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: [Freesurfer] Surface Area and Cortical Volume > > Hello, > > As I understand it, the surface area measure is not a real surface > area measure. It is more a measure of how much the brain has to be > stretched in order to get into a common space. My question is that if > the cortical volume is calculated by multiplying the thickness and the > surface area (right?), then is it a real volume that can be compared > between subjects? > > Also, is it is more accurate to use the cortical volume measures from > the aparc files rather than the aseg files, since the aseg files > overestimate the white matter due to the manual tracing it is based > on? > > Thank you, > Jeff > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. >

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Surface Area and Cortical Volume
by Jeff Sadino 30 Sep '10

30 Sep '10

Hello, As I understand it, the surface area measure is not a real surface area measure. It is more a measure of how much the brain has to be stretched in order to get into a common space. My question is that if the cortical volume is calculated by multiplying the thickness and the surface area (right?), then is it a real volume that can be compared between subjects? Also, is it is more accurate to use the cortical volume measures from the aparc files rather than the aseg files, since the aseg files overestimate the white matter due to the manual tracing it is based on? Thank you, Jeff

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