Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

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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Insula: Why no label in parcellation?
by Graham Wideman 12 Apr '07

12 Apr '07

Folks: We see that parcellation has insula labelled as "unknown". Is this by design and if so is there a discussion of the rationale? Thanks, Graham

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Volumes for labels
by Alex Fornito 11 Apr '07

11 Apr '07

Hi, I was just wandering exactly how the grey matter volume for a given label is calculated in mris_anatomical_stats. Multiplying the average thickness by the area estimate I get in the output file does not give me exactly the same estimate of grey matter volume as what mris_anatomical_stats returns. Is the mris_anatomical_stats volume estimate calculated on a vertex-by-vertex basis? Thanks, Alex Alex Fornito JN Peters Research Fellow Melbourne Neuropsychiatry Centre National Neuroscience Facility The University of Melbourne Levels 2 & 3, 161 Barry St Carlton South 3053 Vic Australia Ph: +61 3 8344 1861 Fax: +61 3 9348 0469 Email: fornitoa(a)unimelb.edu.au

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Manuals and Scuba
by Sharon Ruso 11 Apr '07

11 Apr '07

Dear FreeSurfer Team I'm a new user of freesurfer and I would like to ask you few questions. 1.Where can I find more information regarding SCUBA? 2.I read very carefully through the freesurfer website, (all the work flow and tutorials) however, I was wondering weather every time I do any kind of changes, do I have to run recon all again,, or there are any single commands that repair/edit my own revisions? 3. What is the newest version of the FreeSurfer Manual and where can I find it Thank You in advance Sharon

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