Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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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Re: [Freesurfer] Converting an FSL label to Freesurfer space
by Douglas N Greve 29 Sep '10

29 Sep '10

The output has to be a volume (eg, nii or mgh), not a label. If you need a label, run mri_cor2label on the output. doug Massieh Moayedi wrote: > Hi Doug, > > I tried it, and it seems that it's working until the very last step. > > Here's the output I get: > > > $ mri_label2vol --seg > '/storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped.nii.gz' > --temp > '/storage/AllUsers/Massih/FreeSurferData_TMD/fsaverage/mri/orig.mgz' > --reg $FREESURFER_HOME/average/mni152.register.dat --invertmtx > --fillthresh 0.5 --o > /storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label > > Number of labels: 0 > Annot File: (null) > Template Volume: > /storage/AllUsers/Massih/FreeSurferData_TMD/fsaverage/mri/orig.mgz > Outut Volume: > /storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label > > Registration File: > /scratch/freesurfer_43/freesurfer/average/mni152.register.dat > Fill Threshold: 0.5 > Label Vox Vol: 1 > ProjType: (null) > ProjTypeId: 0 > ProjStart: 0 > ProjStop: 0 > ProjDelta: 0.1 > Subject: (null) > Hemi: (null) > UseNewASeg2Vol: 1 > DoLabelStatVol 0 > $Id: mri_label2vol.c,v 1.25.2.1 2008/12/19 23:18:26 greve Exp $ > Template RAS-to-Vox: -------- > -1.000 0.000 0.000 128.000; > -0.000 -0.000 -1.000 128.000; > -0.000 1.000 -0.000 128.000; > 0.000 0.000 0.000 1.000; > Template Voxel Volume: 1 > nHits Thresh: 0.5 > RegMat: -------- > 1.000 -0.004 -0.001 1.195; > 0.001 0.018 1.000 -19.147; > -0.004 -1.000 0.018 -16.617; > 0.000 0.000 0.000 1.000; > Inverting matrix > RegMat: -------- > 1.000 0.001 -0.004 -1.227; > -0.004 0.018 -1.000 -16.266; > -0.001 1.000 0.018 19.444; > 0.000 0.000 0.000 1.000; > Label RAS-to-Vox: -------- > -1.000 -0.001 0.004 129.227; > 0.001 -1.000 -0.018 108.556; > -0.004 0.018 -1.000 111.734; > 0.000 0.000 0.000 1.000; > ASeg2Vol: Building LUT > ASeg2Vol: Sorting > ASeg2Vol: Mapping > ASeg2Vol: Reverse Map > nmisses = 9558488 (2727 filled) > ASeg2Vol: done > unknown file type for file > (/storage/AllUsers/Massih/FreeSurferData_TMD/SMA_Label_1mm_flipped_to_FS.label) > > > Any ideas? > > Thanks, > Massih > On 09/29/2010 11:37 AM, Douglas N Greve wrote: >> I assume the label is a binary mask in MNI152? If so, use >> mri_label2vol and spec the label as a segmenation, use >> $FREESURFER_HOME/average/mni152.register.dat as the registration, >> specify --invertmtx, and use the orig.mgz in fsaverage as the >> template. I *think* this should work. >> >> doug >> >> mmoayedi wrote: >>> Hi everyone, >>> >>> I need to convert an FSL label (3D, MNI 152 space, 2mm brain) to >>> FreeSurfer's fsaverage brain inflated surface. >>> >>> Does anyone know how to do this? >>> >>> Thanks, >>> >>> Massih >>> >>> _______________________________________________ >>> 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 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Changing and Saving Overlay Config in Tksurfer
by Adam Nitenson 29 Sep '10

29 Sep '10

Hi Freesurfers, I was wondering if there was a way to save any configurations you make to functional overlays (sig.mgh / sig.nii) in Tksurfer so you don't need to change them again. When I go to View --> Configure --> Overlay, it seems that the default is "Linear Opaque" with Min = 2.0 and Max = 5.0. For our purposes, I normally switch to "Piecewise" with Min = 1.3, Mid = 2.3, and Max = 3.3. It's an easy change to make normally, but I am having trouble loading these functional overlays into Slicer since it only loads the default settings with no way (as far as I know) to configure the overlay to display my preferences. Is there anyway I can permanently save these changes to a specific overlay so that it would load automatically that way, which will allow me to import it into other programs? I tried File --> Save Overlay As... after applying the changes, but it only saved the default config. Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Converting an FSL label to Freesurfer space
by mmoayedi 29 Sep '10

29 Sep '10

Hi everyone, I need to convert an FSL label (3D, MNI 152 space, 2mm brain) to FreeSurfer's fsaverage brain inflated surface. Does anyone know how to do this? Thanks, Massih

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white screen when opening freeview
by B.T. Thomas Yeo 29 Sep '10

29 Sep '10

Hi, when opening freeview while logged locally on a linux box (at Harvard NCF), we get a blank screen problem. See attached screenshot. Here, we have loaded multiple volumes in freeview, but in practice, we have this issue even when loading a single image. We are using stable4.5, and the linux version is: 2.6.18-194.3.1.e15 (redhat). An interesting thing is that when ssh-ing from a mac into the same linux box, we do not encounter such a problem. Thanks, Thomas

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