Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

glmfit with correlated covariates
by L. Schweren 12 Mar '14

12 Mar '14

Dear FreeSurfer experts, I am attempting to disentangle the effects of different features of pharmacological treatment on cortical thickness. I am running glmfit from the commandline, with multiple covariates (a.o. Z_Age, Z_TreatmentDuration and Z_StartAge) in the fsgd-file. These covariates are correlated up to approximately 0.6 , which to my understanding is not ideal yet not inducing collinearity. Running glmfit, I do not get any errors such as ill-designed matrix or so. My question regards the way the different regression weights are calculated in each voxel. If I test the variance in CT of voxel A explained by for example TreatmentDuration, and part of the variance in voxel A is explained by both TreatmentDuration and StartAge, will the regression weigth of TreatmentDuration than include the part that is also explained by StartAge? Or are all other covariates first "regressed out" of the variance, such that the variable I test can only explain the variance that was not explained by any of the other covariates? Thank you very much, your help is very much appreciated! Best wishes, Lizanne

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Group Analysis Age slopes
by pfotiad＠nmr.mgh.harvard.edu 12 Mar '14

12 Mar '14

Hi Doug, I ran a group analysis comparing a trait between two groups (Diseased vs Controls) with one continuous variable (age), with the following design matrices [1 -1 0 0] and [0 0 1 -1]. When I loaded the significance map and the descriptor file, the age slope of the trait in Controls was positive whereas the age slope of the trait in the Diseased cases was negative. Therefore, comparing the intercept between the two groups does not really give that much info, since the slopes are of opposite sign. What do you believe would be the best course of action in order to compare the age-corrected traits: 1) instead of age=0 maybe comparing the groups at age=mean? 2) or going with a DOSS model? Thank you for your time, Panos

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creating a multi-scanner template?
by Markus Gschwind 12 Mar '14

12 Mar '14

Dear all, I am planning to create a "local cortical thickness normal template" in order to test single patients against it. For that purpose I was planning to use 50-100 MPRAGE scans of healthy subjects (balanced for age range and sex). My question is, if I should worry about the scanner where the data comes form. We have three Siemens Trios, the MPRAGES are more or less the same protocols. - when the created template with standart deviation map comes from all three scanners, can I test patients coming from all three scanners? Will it reduce sensitivity? - when the created template comes from only one scanner, it is clear that I will not be able to compare patients coming from another scanner against it. Thank you! Markus

2 2

wm.mgz and lh.orig.nofix not matching
by Harms, Michael 11 Mar '14

11 Mar '14

2 1

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

11 Mar '14

Thanks for your reply. I am using *ICBM 2009a Nonlinear Asymmetric 1×1x1mm template. *I did not expect that it will make much difference in the algorithm. Does freesurfer favor certain template than others? btw: the individual mri is also 1 mm resolution. On Tue, Mar 11, 2014 at 8:46 PM, peng <prion.w(a)gmail.com> wrote: > Thanks for your reply. I am using *ICBM 2009a Nonlinear Asymmetric > 1×1x1mm template. *I did not expect that it will make much difference in > the algorithm. Does freesurfer favor certain template than others? > btw: the individual mri is also 1 mm resolution. > > > On Tue, Mar 11, 2014 at 5:59 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> >> 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=AttachFile&do=get&target=fscoordinates.pdf >>> >>> 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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ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08
by Wanda Truong 11 Mar '14

11 Mar '14

Hello, I would like to conduct an analysis using mri_glmfit but I'm getting this error: ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 My command was: mri_glmfit --y lh.area.fwhm10.fsaverage.mgh --fsgd finalgroupanalysis.fsgd dods --C group_effect.mtx --surf fsaverage lh --cortex --glmdir lh.surfacearea.glmdir My FSGD file is attached. It contains 3 classes and 1 variable (age). And my design matrix is 1 -1 0 0 0 0 1 0 -1 0 0 0 Please help! Thank you for your time, Wanda -- Wanda Truong, MSc

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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/

1 0

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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