Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

Re: [Freesurfer] project locations from template to individual MRIs
by Douglas N Greve 11 Mar '14

11 Mar '14

what template? When discussing coordinate systems you have to be very specific. A template could be a volume template or a surface template. If a volume template it could be MNI305 or MNI152. If MNI152 it could be the 1mm version or the 2mm version. All of these things are important and the questions cannot be answered without these details. doug On 03/11/2014 12:42 PM, peng wrote: > Thanks Doug, I will read the document. But may I ask a simpler > question: in freesurfer, do you use affine transformation to make > correspondence between a individual subject and the template (the > procedure someone calls as normalization)? > > best > Peng > > > On Tue, Mar 11, 2014 at 5:06 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > > Hi Peng, there's a lot going on there, and it is not specific > enough for > me to make recommendations. Take a look at the docs we have on our > coordinate systems > > http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems?action=AttachFil… > > you might get the answer you need from there or at least use our > terminology to point me in the right direction > > doug > > > > > On 03/10/2014 12:20 PM, peng wrote: > > Thanks Doug for your reply. In fact I need both. I do this > mainly for > > computation (in volume); and display (in surface) is also cool. > > > > The dots (e.g. A1, A2, ..., An, ..., AN) were originally defined in > > volume of the template (icbm152). This can be implemented as an Nx3 > > matrix S, where S(n, :) = [nx, ny, nz] indicates the location of > An in > > the volume. > > RAS here I mean such a coordinate system that, [0 0 0] is AC and > the 3 > > dimensions are taking right, anterior, superior as positive, e.g > > An([nx0 ny0 nz0]) indicates a location nx0 mm right, ny0 mm anterior > > and nz0 mm superior of AC. > > The above two systems can be easily transformed by a transformation > > matrix. > > > > I wish to know the correspondent locations of An in individual > > subject(B), as Bn. e.g. if A1 is center of V1 in the template, I > wish > > to find the center of V1 in the subject as B1. > > So far, all the locations are represented in volume. However, I > guess > > to normalise the individual brain to the template, freesurfer will > > extract the volumes to surfaces. I imagine the procedure will be > like > > An (volume representation of dots in template) -> ASn (surface > > representation of dots in template) -> BSn(surface representation of > > dots in individual) -> Bn(volume representation of dots in > > individual). If this assumption is correct, I would like to use > Bn for > > my computation and ASn for display later. > > > > I hope I have made myself clearer. > > > > best > > Peng > > > > > > On Mon, Mar 10, 2014 at 4:21 PM, 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>>> wrote: > > > > > > Do you mean you want to display them in the MRI volume or on the > > surface > > (or both)? When you say that they are in "RAS coordinates", what > > do you > > mean? How are the coords defined? > > doug > > > > > > > > On 03/08/2014 07:26 AM, peng wrote: > > > Dear freesurfers, > > > > > > I have a set of dot locations (300~400) in a template > brain, > > > indicated by indices of a 3-D array of the template MRI > data, which > > > can be easily transformed to RAS coordinates. I wish to > project > > these > > > dot locations to individual MRIs, ideally also as indicated by > > indices > > > in the 3-D array of the individual MRI data. Is it > possible to do it > > > in freesurfer? I guess the surface-based procedure shall work > > well for > > > this. It might be a very junior question, if it was documented > > > somewhere before, please let me know the link. Thank you very > > much for > > > help. > > > > > > best > > > Peng > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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: https://gate.nmr.mgh.harvard.edu/filedrop2 > > 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> > > Outgoing: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@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 <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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Tracula multiple subjects error
by Sarah Banducci 11 Mar '14

11 Mar '14

Hello- I'm having a consistent problem running multiple subjects through tracula. I am able to run single subjects through all steps but whenever I try to run it on multiple subjects I get the same error about a syntax error and one of the items it wants to copy being a directory so its not being copied. I can't figure out what in my configuration file is incorrect. I'm attaching the configuration file to this email. I'm only trying to get the first few steps done at the moment so command I run is: trac-all -corr -qa -intra -inter -masks -c Tracula_config And it outputs this: *set: Syntax Error.* INFO: SUBJECTS_DIR is /Volumes/KramerLab/Projects/HealthAging/FAST/Freesurfer/v5.3 INFO: Diffusion root is /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014 Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scripts/dmrirc.local -log /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scripts/trac-all.log -cmd /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Mar 11 10:08:12 CDT 2014 mri_convert /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1/data.nii.gz /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.nii.gz mri_convert /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1/data.nii.gz /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1/data.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.998367, -0.00222992, -0.0570763) j_ras = (0, 0.999238, -0.0390395) k_ras = (-0.0571199, 0.0389758, 0.997606) writing to /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.nii.gz... cp /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1 /Volumes/KramerLab/Users/banducc2/TraculaResult/Tracula_031014/F109_1/dmri/dwi_orig.mghdti.bvecs *cp: /Volumes/KramerLab/Users/banducc2/forTracula/DTI/F109_1 is a directory (not copied).* Darwin sarahsmacpro.vp.illinois.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Tue Mar 11 10:08:38 CDT 2014 Thanks, Sarah Banducci University of Illinois, Urbana

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Warping a significance map to MNI space
by Thomas Allan 11 Mar '14

11 Mar '14

Hi I have proceed my data and produced a significance map across all my subjects and this looks fine on the fsaverage inflated brain. To compare to some other results, I really need to wrap this map into standard MNI152 space. To do this, I have used the following commands but with a problem at the end: 1. mri_surf2vol -sig.mgh -identity fsaverage -template ./fsaverage/mri/T1.mgz -hemi lh -o SIG.fsspace.mgz 2. mri_vol2vol -mov SIG.fsspace.mgz -targ /$FSL_DIR$/data/standard/MNI152_T1_2mm.nii.gz -o SIG_MNI.nii -interp nearest -reg /$FS_DIR$/average/mni152.register.dat So the first step works fine and looking at it using tkmedit shows the surfer as a nice volume in the right place on the T1.mgz or brainmask.mgz for the average brain. After step 2, looking at the final MNI space file, it appears that is has been rotated 180 degrees through the transverse plane (left and right are correct but top and bottom have been flipped and so have anterior and posterior) and the map has also translated. All of the dimensions are correct but the 2 images do not line up. I can easily rotate the image so that all the axis agree with the normal image but then the map is quite a few slices too high compared to the MNI152 brain and I cannot be certain how far it has been shifted. Any help would be appreciated. Thanks Tom

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primary auditory cortex ROI
by Ritobrato Datta 11 Mar '14

11 Mar '14

Hi All, I need to demarcate primary auditory cortex in a group of subjects anatomically and I came across the following papers - https://surfer.nmr.mgh.harvard.edu/ftp/articles/2013/2013_-_Wasserthal_et_a… https://surfer.nmr.mgh.harvard.edu/ftp/articles/Sigalovsky_et_al_2006.pdf Is there a script that I can use on my 3T MPRAGE images to get primary auditory cortex ROI ? That will be very helpful. Best, Ri

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Brain Segmentation blurred at the interhemisphere surface
by Kaiming Yin 11 Mar '14

11 Mar '14

Hi FreeSurfer guys, Just want to ask a quick question. So I have been using freesurfer on the analyses on my brain- however I have noticed in certain parts, there hasn't been any segmentations. I have attached a picture, to show what I mean. Is there a reason for this? The blurry part kind of sweeps across the whole brain. Is there anything then, that I can do in freesurfer to still allow it to calculate the segmentation? Many thanks, Kaiming

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Tksurfer + Histogram
by Saurabh Thakur 11 Mar '14

11 Mar '14

Hello Freesurfer Expert, Can anyone help me with histogram plotting of different surfaces in tksurfer. I looking to calculate the thickness of cortex. Thanks in advance, Saurabh Thakur,

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Cortical thickness measuring algo
by Saurabh Thakur 11 Mar '14

11 Mar '14

Hello Freesurfer, Laplacian based method for measuring Cortical thickness Can u anyone help me to understand how freesurfer has implemented this algo and where to find this algo for better understanding. Thanks, Saurabh Thakur,

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applying Yeo atlas to individual brains
by Jeff Eriksen 10 Mar '14

10 Mar '14

Our lab has a need to apply the Yeo atlas to individual brains. As I understand it, Yeo atlas is only currently available for the FSAverage brain. Any plans to incorporate Yeo on to the default FS segmentation, or have it available as an option? -Jeff Eriksen

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Re: [Freesurfer] applying Yeo atlas to individual brains
by Gregory Kirk 10 Mar '14

10 Mar '14

problem with surf2surf is it deals with scalar fields ( data ) so don't think that will do it. problem with label2label is that it deals with a single label which has a diferent structure than anot. so a way to do it 1. mri_annotation2label ... to convert the yeo anotation file to individual labels 2. mri_label2label ... to map each label from the fsaverage space to the individual subject space 3. then the function that takes the labels on the individual subject space and makes a .annot of it in indiv. subject space. you will need to supply a colormap table to, don't remember the name ( google freesurfer make annotation file, or something like that) seems like a lot of work but just make a little script and you only need to figure it out once. if any problems i could dig in my notes, i did not find one function to map a .annot in 1one space to a .annot in another. gref On 03/10/14, Thomas Yeo wrote: > Hi Jeff, > > I am a little unsure myself since I usually work with data mapped to > fsaverage space. I think you might want to use mri_surf2surf, since > there's a "--sval-annot" option. It's hard for me to check now because > I am away at a conference. > > Can someone chime in if mri_surf2surf is wrong? > > Thanks, > Thomas > > > > > > On Mon, Mar 10, 2014 at 10:59 AM, Jeff Eriksen <eriksenj(a)ohsu.edu> wrote: > > What I need are the ?h.Yeo.annot files for the individual subjects, similar to the default ?h.aparc.annot and ?h.aparc.2009.annot files. Will mri_label2labe give me that directly? > > > > Thanks, > > -Jeff > > > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu](javascript:main.compose() > > Sent: Monday, March 10, 2014 9:50 AM > > To: Jeff Eriksen > > Cc: 'freesurfer(a)nmr.mgh.harvard.edu' > > Subject: Re: [Freesurfer] applying Yeo atlas to individual brains > > > > Hi Jeff > > > > you should be able to use mri_label2label to map the Yeo atlas from fsaverage to any subject. > > > > cheers > > Bruce > > On Mon, 10 Mar 2014, Jeff Eriksen wrote: > > > >> > >> Our lab has a need to apply the Yeo atlas to individual brains. As I > >> understand it, Yeo atlas is only currently available for the FSAverage > >> brain. Any plans to incorporate Yeo on to the default FS segmentation, > >> or have it available as an option? > >> > >> > >> > >> -Jeff Eriksen > >> > >> > >> > >> > >> > > > > > > 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. > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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vtk conversion
by LAOUCHEDI MAKHLOUF 10 Mar '14

10 Mar '14

Hi all i am developping an application for neuronavigation, and i want to use freesurfer cortical parcellation and sub-cortical segmentation, is there any freesurfer command to convert surface files to vtk files ? Thanks

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Freesurfer March 2014