Freesurfer April 2007

freesurfer@nmr.mgh.harvard.edu

57 participants
78 discussions

aseg visualization question
by Morgan Hough 16 Apr '07

16 Apr '07

I have a quick question about an error we are getting with FS 3.0.5 when we are using tkmedit as described in the tutorial to display the segmentations overlaid on the T1. tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz The first error seems to regard the new requirement that a color LUT be passed with the segmentation option. If we add tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz tkmeditColorsCMA Then the message reduces to a problem of opening the segmentation file which it says is not in the right .cor format. I assume this is a legacy error message but I am not sure if I need to rename the aseg.mgz file or pass in another option with the file type. Thanks in advance for your time. Cheers, -Morgan

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Scripting: Feeding arguments and variables to script?
by Graham Wideman 16 Apr '07

16 Apr '07

Folks: Basic scripting questions: 1. When you launch FS from command line and provide a -tcl command to invoke a tcl script, how do you supply arguments to that script (or is that even possible)? FWIW, I tried things along the lines of: set myvar [lindex $argv 1] ... and this gives an error about "no such variable". 2. Once a script is running, what variables can it look at to find out: Current subject id Path to current subject Details about currently loaded surfaces: especially right or left 3. What assumptions, if any, can a script rely on as to current directory? Thanks, Graham

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Color threshold in freesurfer
by Doug Greve 16 Apr '07

16 Apr '07

Kevin has just made a change to the default way that the DEV version of tksurfer displays colors in overlays. The change has to do with the way the color is displayed near the threshold (fthresh). Previously, as a superthreshold value approached the threshold, its color and opacity would change. The result was that voxels at or just above threshold would be transparent, making them look like they were not active. The default now is to make them opaque regardless of value (as long as they are above threshold). When you look at the overlay configuation GUI, you will now see three items under "Threshold": Linear Linear Opaque Piecewise By default, "Linear Opaque" will be checked. To use the old behavior, check "Linear". Note that you can still control the overall opacity with the slider at the top of the GUI. Kevin is working on changing tkmedit. I'll let you know when that is ready. doug -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Pial Surfaces
by Sharon Ruso 16 Apr '07

16 Apr '07

Dear FreeSurfers I have a problem editing pial surfaces. My pial "borders" do not include Some important brain parts i.e. amygdala. Can anybody help me? Tnx Sharon

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Re: [Freesurfer] Scripting: Feeding arguments and variables to script?
by Graham Wideman 16 Apr '07

16 Apr '07

Bruce: Thanks for that instant reply. I must admit that as soon as I hit "send" on my enquiry, my brain thought "wait a minute -- environment variables?!" and I was just trying that out. Of course, I would never have found the tksurfer-defined ones, so that's a great help. Probably the rest of the bunch would be useful too.... Thanks, Graham

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volume index vertex positions
by burak ozkalayci 15 Apr '07

15 Apr '07

Hi surfers, Last time I asked how to see and access to the thickness values and your advices worked. Thanks a lot. When I checked the asci file, which I acquired by converting the thickness file, I saw that the X Y Z coordinates of the vertices are given in talairach coordinates. However I need them in volume index coordinate. Is it possible? Thanks in advance. Burak

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RE: [Freesurfer] major lobes - frontal, parietal occipital and temporal
by lfriedman10＠comcast.net 14 Apr '07

14 Apr '07

Hi Bruce, I am using freesurfer to generate masks for fmri data from a breath hold task. As you are probably well aware, this task activates much of the gray matter. I have been content to consider all gray matter as one large ROI but one of my colleagues on the project (Danny Mathalon) has suggested that we might want to look at the BH response more regionally. We have a smallish sample and don't want to go to far with data. So we thought that a reasonable comprimise might be to go for the 4 major lobes. Does this make sense? I do all of my fmri work in MNI space so what I have been doing is registering the freesurfer output to MNI space using SPM tools to get masks and then do the rest with afni. Lee -------------- Original message ---------------------- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Lee, > > what is your goal? Are you just trying to measure lobar volume? > > Bruce > > On Sat, 14 > Apr 2007 lfriedman10(a)comcast.net wrote: > > > Burce and Rahul, > > > > thanks so much for your help. > > > > So I am a little new to freesurfer. > > I have been using lh.ribbon and rh.ribbon as neocortical masks and aseg.mgz > for > > subcortical gray structures, with labels from FreeSurferColorLUT.txt. > > > > What I want to do now is to further subdivide the *h.ribbon masks into > frontal, temporal, > > occipital and parietal lobes. > > > > How would one go about this? > > > > Lee > > > > -------------- Original message ---------------------- > > From: rahul(a)nmr.mgh.harvard.edu > >> Hi Lee, > >> > >> Bruce is correct in that some ROIs cross two or more lobar boundaries > >> (i.e. fusiform) while others (i.e. cingulate subdivisions) can be > >> considered separately or can be included to follow the 4 lobes. To the > >> best of my ability, if you are using the *h.aparc.annot, you can add up > >> the individual ROIs as such to get the lobes: > >> > >> Frontal: > >> Superior Frontal > >> Rostral and Caudal Middle Frontal > >> Pars Opercularis, Pars Triangularis, and Pars Orbitalis > >> Lateral and Medial Orbitofrontal > >> Precentral > >> Paracentral > >> Frontal Pole > >> > >> Parietal: > >> Superior Parietal > >> Inferior Parietal > >> Supramarginal > >> Postcentral > >> Precuneus > >> > >> Temporal > >> Superior, Middle, and Inferior Temporal > >> Fusiform > >> Transverse Temporal > >> Entorhinal > >> Temporal Pole > >> Parahippocampal > >> > >> Occipital: > >> Lateral Occipital > >> Lingual > >> Cuneus > >> > >> Cingulate (if want to include in a lobe): > >> Rostral Anterior (Frontal) > >> Caudal Anterior (Frontal) > >> Posterior (Parietal) > >> Isthmus (Parietal) > >> > >> Best, > >> > >> rahul > >> > >>> Hi Bruce, > >>> > >>> Are you saying that you don't think I even could build these lobar groups > >>> using the existing codes in the LUT.txt file? > >>> > >>> Lee > >>> > >>> -----Original Message----- > >>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > >>> Sent: Saturday, April 14, 2007 2:21 PM > >>> To: lfriedman10(a)comcast.net > >>> Cc: freesurfer(a)nmr.mgh.harvard.edu > >>> Subject: Re: [Freesurfer] major lobes - frontal, parietal occipital and > >>> temporal > >>> > >>> Hi Lee, > >>> > >>> sorry, not really - we've never done a lobar parcellation, and I don't > >>> think the existing units break down that way. > >>> > >>> Bruce > >>> On Sat, 14 Apr 2007 > >>> lfriedman10(a)comcast.net wrote: > >>> > >>>> I know that I could go thru the > >>>> FreeSurferColorLUT.txt > >>>> file to get codes for different cortical structures. > >>>> Is there an easier way to get the major lobes: > >>>> frontal, parietal occipital and temporal. > >>>> > >>>> Lee > >>>> _______________________________________________ > >>>> 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 > >>> > >>> > >>> > >> > >> _______________________________________________ > >> 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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RE: [Freesurfer] major lobes - frontal, parietal occipital and temporal
by lfriedman10＠comcast.net 14 Apr '07

14 Apr '07

Burce and Rahul, thanks so much for your help. So I am a little new to freesurfer. I have been using lh.ribbon and rh.ribbon as neocortical masks and aseg.mgz for subcortical gray structures, with labels from FreeSurferColorLUT.txt. What I want to do now is to further subdivide the *h.ribbon masks into frontal, temporal, occipital and parietal lobes. How would one go about this? Lee -------------- Original message ---------------------- From: rahul(a)nmr.mgh.harvard.edu > Hi Lee, > > Bruce is correct in that some ROIs cross two or more lobar boundaries > (i.e. fusiform) while others (i.e. cingulate subdivisions) can be > considered separately or can be included to follow the 4 lobes. To the > best of my ability, if you are using the *h.aparc.annot, you can add up > the individual ROIs as such to get the lobes: > > Frontal: > Superior Frontal > Rostral and Caudal Middle Frontal > Pars Opercularis, Pars Triangularis, and Pars Orbitalis > Lateral and Medial Orbitofrontal > Precentral > Paracentral > Frontal Pole > > Parietal: > Superior Parietal > Inferior Parietal > Supramarginal > Postcentral > Precuneus > > Temporal > Superior, Middle, and Inferior Temporal > Fusiform > Transverse Temporal > Entorhinal > Temporal Pole > Parahippocampal > > Occipital: > Lateral Occipital > Lingual > Cuneus > > Cingulate (if want to include in a lobe): > Rostral Anterior (Frontal) > Caudal Anterior (Frontal) > Posterior (Parietal) > Isthmus (Parietal) > > Best, > > rahul > > > Hi Bruce, > > > > Are you saying that you don't think I even could build these lobar groups > > using the existing codes in the LUT.txt file? > > > > Lee > > > > -----Original Message----- > > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > > Sent: Saturday, April 14, 2007 2:21 PM > > To: lfriedman10(a)comcast.net > > Cc: freesurfer(a)nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] major lobes - frontal, parietal occipital and > > temporal > > > > Hi Lee, > > > > sorry, not really - we've never done a lobar parcellation, and I don't > > think the existing units break down that way. > > > > Bruce > > On Sat, 14 Apr 2007 > > lfriedman10(a)comcast.net wrote: > > > >> I know that I could go thru the > >> FreeSurferColorLUT.txt > >> file to get codes for different cortical structures. > >> Is there an easier way to get the major lobes: > >> frontal, parietal occipital and temporal. > >> > >> Lee > >> _______________________________________________ > >> 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 > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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major lobes - frontal, parietal occipital and temporal
by lfriedman10＠comcast.net 14 Apr '07

14 Apr '07

I know that I could go thru the FreeSurferColorLUT.txt file to get codes for different cortical structures. Is there an easier way to get the major lobes: frontal, parietal occipital and temporal. Lee

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bad white surface
by Derin Cobia 13 Apr '07

13 Apr '07

I have two subjects where the white surface does not follow the gray-white gradient (see attached pic for example). Is there any way to fix this? I'm assuming it has to do with the limitations of my scan too (it's FLASH data). I'm running 3.0.4, thanks. -Derin

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Freesurfer April 2007