Freesurfer March 2014

freesurfer@nmr.mgh.harvard.edu

147 participants
247 discussions

Resting State Networks on Cortical Surface
by Xuelong Zhao 13 Mar '14

13 Mar '14

Hi, I am trying to display the 20 ICA components in this nifti file http://brainmap.org/icns/maps.zip onto anatomical template they've provided here http://brainmap.org/icns/colin_tlrc_1x1x1.nii My question is: How do I extract only the cortical surface from the anatomical template and overlay it with only parts of each ICA component that intersects with the surface? Thanks!

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Longitudinal stream
by Eduard Vilaplana Martinez 13 Mar '14

13 Mar '14

Dear Freesurfer experts, I would like to perform a longitudinal analysis with freesurfer 5.1 and I have some questions regarding the whole processing stream. I have BL and 1Y follow-up from all patients (110), and moreover I have 2Y follow-up from only some patients (more or less 50). Do you recommend using the 2Y when available in the whole stream? Or, on the other hand, it would be better to perform a BL and 1Y analysis in the whole sample and then, separately, do a second analysis only with those subjects that have 2Y follow-up? My idea is to study rates of change (cortical and ventricles, mainly). I have another more technical question. When running the base (recon-all -base <templateid> -tp <tp1id> -tp <tp2id> ... -all), does the order of the time points matter? In Reuter et al., 2012 says that all scans are treated the same, so I guess it doesn't matter if tp1 is the 1Y and tp2 is the BL. Am I wrong? Finally, to look at ventricle changes, do you also recommend using the longitudinal stream or rather the cross-sectional one? It seems that the longitudinal stream is more cortical specific, but maybe I would be wrong... Thanks Best, Eduard

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convert sig.mgh into *.nii
by charujing123 12 Mar '14

12 Mar '14

Hi FS experts, I want to extract time course from sig.mgh. But the *.y.ocn.mgh cannot be created. So I want to view it in other formats, such as nii. So how to convert it into nii format. Thanks. All the best. Rujing Zha 2014-03-11 charujing123

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12 Mar '14

Hi everybody, I would like to ask a question about trac-preproc, because I'm new to Tracula and I'm studying how the entire trac-all process works. I want to know which is the specific structural image (I mean the name of the file) that is registered to the dwi volume during trac-preproc, and at which point of the process this is done. I'm doing this because I want to track down all the movements of the files used by Tracula. Thanks, Francesco Baldacchini

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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

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

11 Mar '14

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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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Freesurfer March 2014