[Freesurfer] Which boost version is used in CVS, mris_resample

Hi guys, When running mri_cvs_register on linux (5.3.0), I get into problem with mris_resample, which cannot find libboost_programs_options.so.5. I installed the latest version of boost-1.52.0 for my system, but there are unresolved symbols. Which version is suitable for mris_resample? Thanks

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

t; The version of libboost that we use for our latest release is 1.41. > > Lilla > > ----- > Martin Kavec Mon, 04 Nov 2013 14:10:53 -0800 > > Hi guys, > > When running mri_cvs_register on linux (5.3.0), I get into problem with > mr

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

u get the > libboost libraries on your machine, the program will work properly. > > -Zeke > > > > >> On 11/28/2013 05:09 PM, Martin Kavec wrote: >> Hi Lilla, >> >> thanks for coming back. Unfortunately I was not able to compile >> appropriate

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

rms and it > is what freesurfer builds against. All I can suggest is that you install the > same version, or one very close to it. > > -Zeke > > > >> On 12/02/2013 02:50 PM, Martin Kavec wrote: >> Hi Zeke, >> >> Thanks for response. Well it

Re: [Freesurfer] Which boost version is used in CVS, mris_resample

rt LD_LIBRARY_PATH=.../boost_1_41_0/libraries/lib:$LD_LIBRARY_PATH >> Cheers, >> Andre Santos Ribeiro > > > regards > > Andre Santos Ribeiro > > > On Mon, Dec 2, 2013 at 9:57 PM, Martin Kavec wrote: > >> Hi Zeke, >> >> Thanks a lot for expla

[Freesurfer] Label corresponding to coordinate

Hi all, Is there a command in Freesurfer, which would return to which label (e.g. superior frontal white matter left) a coordinate x,y,z belongs to? Thanks, Martin Sent from my iPad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://m

[Freesurfer] Tkmed in VirtualBox and wm parcelation

Hi all, I have two questions: 1. Does tkmedit, or freeview work under VirtualBox 2. Is it possible to parcelate white matter in freesurfer? Thanks, Martin Sent from my iPad ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.m

Re: [Freesurfer] Tkmed in VirtualBox and wm parcelation

gt; > if you have diffusion data you can check out Anastasia Yendiki's excellent > TRACULA tool. > > cheers > Bruce > > On Thu, 5 Sep 2013, Martin Kavec wrote: > >> Hi all, >> >> I have two questions: >> >> 1. Does tkmedit, or fre

Re: [Freesurfer] Tkmed in VirtualBox and wm parcelation

ata you can check out Anastasia Yendiki's excellent > TRACULA tool. > > cheers > Bruce > > > On Thu, 5 Sep 2013, Martin Kavec wrote: > > Hi all, >> >> I have two questions: >> >> 1. Does tkmedit, or freeview work under VirtualBox >> 2.

[Freesurfer] mri_normalize info

Hi, I would like to know what method mri_normalize uses to normalize image intensities of wm around 110. I do not mean to correct the bias field. Thanks a lot. Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harva

[Freesurfer] Custom intensities in aparc+aseg

Dear all, I ran my subjects through recon-all successfully. I am in a need to have custom intensities for segmentation and parcellation in aparc+aseg. Say, 10 - ventricles, 20 - amygdala, 30 - putamen, ... I would appreciate advice on how I could achieve that. Thanks in advance, Martin

Re: [Freesurfer] Custom intensities in aparc+aseg

Read in the aseg, use find to find the indices of all the voxels > with a particular label, then replace the label with whatever intensity > you want. > > cheers > Bruce > On Sat, 12 Aug 2017, Martin Kavec wrote: > > > Dear all, > > > > I ran my subjects thro

[Freesurfer] mri_cvs_register can not find

Hi all, I am trying to run mri_cvs_register but for some reasons it always terminates with: ERROR: Can not find or read $SUBJECTS_DIR/MY_SUBJECTS/cvs/combined_tocvs_avg35__elreg_aseg.m3z My command is as follows: mri_cvs_register --mov MY_SUBJECT Indeed the file is not there, but another one w

Re: [Freesurfer] mri_cvs_register can not find

, Nov 4, 2011 at 12:40 PM, wrote: > Hi Martin, > Could you give more details? Which version of mri-cvs-register are you using? > Was there a log file that you could share also? > Thanks, Lilla > --Original Message-- > From: Martin Kavec > To: Freesurfer mailing li

Re: [Freesurfer] mri_cvs_register can not find

tin, > Could you give more details? Which version of mri-cvs-register are you using? > Was there a log file that you could share also? > Thanks, Lilla > --Original Message-- > From: Martin Kavec > To: Freesurfer mailing list > To: Lilla Zollei > Subject: mri_cvs_register

[Freesurfer] Default LGI settings

Hi, I wonder how are the default FS settings to calculate LGI finetuned? More towards large-scale changes, such as in neonal>pediatric cortex, or would it be possible to study rather focal changes, say on a sulcus/gyrus level? Which parameters should I change to become sensitive to "smaller" LG

Re: [Freesurfer] LGI error in make_outer_surface at 31

Hi Jenifer, I don't know what the error exactly means, but sometimes just re-running the analysis helps. Best, Martin On Wednesday 24 September 2008 19:24:40 Juranek, Jenifer wrote: > Hi, > Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB > v7.6.0.324 (R2008a) install

Re: [Freesurfer] Error in recon-all -long on Linux

Jurgen, I think it comes from the fact that FS could not find some file. I had similar situation here a while ago, when I had almost full partition with FS data. FS created about 4GB logfile. Just a guess, didn't you move the data from your mac to linux to be re-analyzed or finish the analysis

Re: [Freesurfer] Creating template rat model

Mark, without prior knowledge of what you do, I can just recommend you the recon-all option "-notal-check". You can find out more about it by running "recon-all -help | less". So your command would look like: recon-all -autorecon1 -notal-check -s $YOURRAT Best, Martin On Monday 13 October 2

Re: [Freesurfer] Rat template creation: MRIstripskull failed

Mark, once I had a similar problem on an autopsied brain, where it was very difficult to obtain an MPRAGE-like contrast. So instead, I acquired T2-weighted and inverted it. This gave me contrast very similar to MPRAGE, though my analysis failed anyway, due to too strong bias field. So you might

[Freesurfer] Qdec questions

Hello all, I have started with a group analysis using qdec and have some questions: 1. loading fsaverage into tkmedit along with rh.white and lh.white surprised me that the pial surfaces do not run under the skull, as I see it on a single subject but copy the white matter. It is also correct, b

Re: [Freesurfer] Qdec questions

Thanks for the replay, Nick! On Monday 27 October 2008 16:48:26 Nick Schmansky wrote: > Martin, > > To answer question 1, the fsaverage surface is used as a target surface > to which the data (ie thickness) of each subject in the group is sampled > and then smoothed, so the accuracy of the recon o

[Freesurfer] Qdec problem?

Hi, I am trying to run a group analysis on cortical thickness between patients and controls. In the qdec.dat I set a MMSE for all the controls 0.0. Now, whenever I try to covariate thickness against age and MMSE, the qdec complains that there is no spectrum in MMSE values. I tried to set MMSE f

Re: [Freesurfer] (no subject)

Hi Rysia, I would look at wm.mgz loaded as auxiliary volume and switch to main volume frequently to see, whether you have anything in wm.mgz, which needs to be fixed. There is a tutorial on fixing wm.mgz on the followning web-page: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatter

Re: [Freesurfer] Autorecon 1 y autorecon 2

Hi Kelly, the analysis of your subject is failing at the point of registration to the Talairach space. Since the status of the registration is FAILED, I would certainly check the result and follow instructions on how to proceed, as explained on the following web-page: http://surfer.nmr.mgh.har

[Freesurfer] Reusing ROIs

Hi, For my group analysis I am thinking of reusing a specific set of cortical ROIs from already published data. I suppose that a target template (fsaverage) and ROIs itself should be sufficient to have. If I use the same fsaverage for my cohort, I should be able to get the data out of the ROIs

[Freesurfer] Cortical thickness in WM disease - experience

Hi, I have been running quite a few clinical subjects (close to 300) through FS pipeline and comparing cortical thickness from parcellated cortex for each individual subject to its agematched controls. The subject clinical symptoms are not specific, ranging from amnesia, reduced ability to gene

Re: [Freesurfer] Cortical thickness in WM disease - experience

ults! > at those for the suspicious ones to distinguish damaged wm from gray > matter. David Salat has thought about this much more than I have, and may > have more to add. > > cheers, > Bruce Thanks a lot, Martin > > On Mon, 12 Jan 2009, Martin Kavec wrote: > > Hi, > &

Re: [Freesurfer] Masking brainmask based on surfaces

wrote: > This looks like a problem we had with an older version. What version of > freesurfer are you running? > > Martin Kavec wrote: > > Hi, > > > > I am trying to mask a non-brain tissue left by watershed based on the > > cortical surfaces. I found that all wh

Re: [Freesurfer] Masking brainmask based on surfaces

> > tkmedit subject orig.mgz -seg ribbon.mgz > > aparc+aseg is suppossed to inherit the cortex from ribbon.mgz > > doug > > On Mon, 6 Apr 2009, Martin Kavec wrote: > > Hi Dough, > > > > this data were analyzed using 4.0.4. So indeed it not the latest, which I >

Re: [Freesurfer] Masking brainmask based on surfaces

Greve wrote: > but you are using aparc+aseg to generate the mask, so if aparc+aseg is > perfect, the mask should be as well. Do the mask and aparc+aseg match? > > On Mon, 6 Apr 2009, Martin Kavec wrote: > > Doug, > > > > ribbon (aparc+aseg) looks perfect, and correspond

[Freesurfer] How to complete gracefully

Hi, I have a bunch of analyzes (about 30), for which recon-all -all terminates prematurely at mris_volmask (and core is created). On one case I ran the mris_volmask and the rest of analysis by executing commands manually, which went fine, but it's laborious. Is there quicker way to complete the

Re: [Freesurfer] How to complete gracefully

mestamps > would be wrong on your files to make make all rebuild everything? > > cheers, > Bruce > On Sun, 10 > > May 2009, Martin Kavec wrote: > > Hi, > > > > I have a bunch of analyzes (about 30), for which recon-all -all > > terminates prematurely

Re: [Freesurfer] How to complete gracefully

: > Hi Martin, > > -make all is what we would suggest. Is there any reason the timestamps > would be wrong on your files to make make all rebuild everything? > > cheers, > Bruce > On Sun, 10 > > May 2009, Martin Kavec wrote: > > Hi, > > > > I have a b

Re: [Freesurfer] How to complete gracefully

Hi Bruce, On Tuesday 12 May 2009 13:28:36 Bruce Fischl wrote: > Hi Martin, > > there are probably some files it wants to see early in the stream that > didn't exist in 2006. I think the only cure is to string together the > individual commands you want to run (you can find them in the recon-all >

Re: [Freesurfer] How to complete gracefully

Bruce, but I am running 4.3.0 Thanks, Martin On Tuesday 12 May 2009 14:55:05 Bruce Fischl wrote: > Hi Martin, > > I'll leave this for Nick, but we fixed the atlas eTIV calculations in the > new version. Not sure which step you need to rerun though. > Bruce > _

Re: [Freesurfer] How to complete gracefully

Hi Nick, On Tuesday 12 May 2009 15:39:47 Nick Schmansky wrote: > Martin, > > That etiv number seems high. Does the -tal-check stage pass? did you > rerun the -segstats stage? that calculates etiv. The data were first pushed through the whole FS pipeline in 2006. As I look at the recon-all.log

[Freesurfer] brainmask volume greater than ICV

Hi, I am running FS-4.3.0 and after recon-all -all, I am finding in aseg.stats of quite a few of my subjects that brain mask volume (1735600 mm^3) is greater than ICV (1701891 mm^3). The talairach failure detection passed fine: talairach.xfm OK (p=0.7556, pval=0.6675 >= threshold 0.005 ). The

Re: [Freesurfer] recon-all : brainmasl.mgz missing

Hi Iwo, you do not say which command exactly you ran. brainmask is created in the "first" step of the processing pipeline, so to obtain it you should have successfully completed the following: recon-all -autorecon1 -s YOUR_SUBJECT Best, Martin On Thursday 28 May 2009 11:24:27 Iwo Bohr wrote:

Re: [Freesurfer] Troubleshooting

Hi Falk, On Thursday 28 May 2009 11:56:51 Falk Lüsebrink wrote: > Hello, > > > > I’m having trouble to generate a correct aseg.mgz for one volume of mine. > The nu_noneck.mgz is also incorrect and therefore I think the -careg stage > of autorecon2 might fail. Is there a way to do some kind quality

Re: [Freesurfer] Segmentation fault during -cortribbon flag in autorecon2

Hi Andreas, I get the same error, in almost the same scenario; while re-running some studies with FS-4.3.x. The I also run them on a cluster with large amount of memory running Gentoo linux, and CentOS4_x64 FreeSurfer binaries. To complete the studies I take them on a 32 bit platform with Kubun

Re: [Freesurfer] vtkMultiThreader error

Hi Don, I am in a similar situation. I am on a IBM BladeCenter cluster (though with one blade only) with 2 Quad core Intels, and I experience intermittent crashes of mri_volmask as well. Similarly as you, when I run the mri_volmask on the crashed subject on a desktop, this passes perfectly fine

Re: [Freesurfer] from dicom to mgz

Guys, I am using Philips DICOMs from INTERA and ACHIEVA generation systems without any problems. So far I have done about 600 analyses. INTERAs are on 11.4 software version and ACHIEVAs went from release 2 up to the current 2.6.1 (and soon release 3) However the images do not go directly from the

Re: [Freesurfer] reinstalling freesurfer

Fatima, try rm -rf $FREESURFER_HOME The command which Pedro gave you assumed that your freesurfer installation directory was /usr/local/, which may not be the case. If you had freesurfer correctly installed before, you must have had the $FREESURFER_HOME variable set correctly. Thus the command a

Re: [Freesurfer] reinstalling freesurfer

his? I’d be extremely grateful. > > > > Thank you and kind regards, > > Fatima > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Martin Kavec > *Sent:* 13 August 2009 11:53 >

[Freesurfer] fsgd and contrast matrix

Hi, I would like to study cortical thickness in a cohort of patient with respect to MMSE and CDR. I prepared a fsgd file where I have both MMSE and CDR listed: GroupDescriptorFile 1 Title Mytitle Class Male Class Female Variable Age Variable MMSE Variable CDR Class Ctrl Class MCI Input subject1

Re: [Freesurfer] fsgd and contrast matrix

e CDR has an effect, I just want to see whether the atrophy areas correlated with CDR and MMSE differ. Thanks, Martin > This will improve both DOF and > efficiency. > > doug > > Martin Kavec wrote: > > Hi, > > > > I would like to study cortical thickness in a c

[Freesurfer] mri_glm-sim

I wonder how log does it ususally take to complete cluster-wise correction for multiple comparisons using mri_glm-sim. I have a group analysis of 19 subjects with 1 continuous and 1 discrete factor (two levels) and the mri_glm-sim is running now for about 4 days. Is there any way to track the p

Re: [Freesurfer] Circle around vertex

Hi Bruce, if I dilate an arbitrarily shaped label in tksurfer, how much is it actually dilated? Thanks, Martin On Sat, Nov 7, 2009 at 8:18 PM, Bruce Fischl wrote: > Hi Yigal, > > yes, you can select the vertex, make a label out of it, then dilate it > however many times you want. This will be a

Re: [Freesurfer] Circle around vertex

Sat, Nov 7, 2009 at 8:36 PM, Bruce Fischl wrote: > once every time you click "dilate label" > > On Sat, 7 Nov 2009, Martin Kavec wrote: > > Hi Bruce, >> >> if I dilate an arbitrarily shaped label in tksurfer, how much is it >> actually >> dilated? &

Re: [Freesurfer] updating to aparc.a2009s

Hi Shriks, as far as I can see -cortparc, -cortparc2, -parcstats, and -parcstats2 flags (and possibly beyond) of the autorecon3 stage do the parcallation. But I am not sure whether there have been any significant changes between your version and the current version of the FS, which could impact

Re: [Freesurfer] Circle around vertex

. It's > scriptable, so you can feed it a list of vertex indices to build > circular ROIs about. > > It should be available in the 5.0 release of FreeSurfer, but if you'd > like to use it already, send me an email and I can send you a beta version. > > Cheers > -=R &g

Re: [Freesurfer] ICV Error fs 4.3.1

Hi Jeff, I see this relatively often. Eventhough the talairach registration is fine, the ICV is underestimated. In this case I take old ICV, which helps. mri_segstats --subject $MYSUBJECT --old-etiv-only This is in 99% of these cases a cure. This is not just a blind attempt. In these cases I

Re: [Freesurfer] Replicating qdec analysis with more than 2 continuous variables

Hi Nick, could you please also provide us with a INTEL MAC qdec.bin binary? Many thanks in advance, Martin On Wednesday 17 March 2010 21:18:19 Nick Schmansky wrote: > you have a couple options: > > 1) assuming you are using 64b linux, you can download a new version of > qdec which supports sele

[Freesurfer] Model setup - comparing correlations

Hi, in my group analysis I found a significant difference in correlation of physiological parameter X and cortical thickness Y1 in an ROI. For each subject and each cortical parcel I also have a average of parameter Y2 and its correlation to X (calculated using GLM in SPSS). Y1 ~ X Y2 ~ X My

[Freesurfer] Poor Talairach registration and effect on ICV

Hi, in our population of MCI patients, unfortunately parts of the cerebellum were not completely scanned. I ran the data throught the whole FS-4.5.0 pipeline and I see that the eTIV normalized volumes of the segmented structues have very large variance compared to the eTIV normalized group of i

Re: [Freesurfer] Poor Talairach registration and effect on ICV

Thanks a lot for the opinion, Bruce! >From practical point of view, removing the cerebellum from each subjuct should be rather easy since I have its segmentation. Howabout the template? Is there any segmentation of the cerebellum for the template, or I would have to do it manually? I suppose I

Re: [Freesurfer] Recon-all problem (with talairach)

Hi Jan, the place to look at is http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Best, Martin On Tuesday 30 March 2010 12:30:35 Janani Dhinakaran wrote: > Hello everyone, > I wanted to know what I can do to fix this error- it occurs when I'm > running recon-all -all -s Subject >

[Freesurfer] mri_convert fails for enhanced MR IOD DICOMs

Hi, our MR scanner produces DICOMs with enhance MR IOD, i.e. multiframe image file. When I try to use this format with FreeSurfer mri_convert fails. I assume it is not designed for this type of images, isn't it? Anybody knows a workaround? Thanks in advance for help (and great software), Ma

Re: [Freesurfer] mri_convert fails for enhanced MR IOD DICOMs

in advance > > Bruce > > On Wed, 21 Feb 2007, Martin Kavec wrote: > > Hi, > > > > our MR scanner produces DICOMs with enhance MR IOD, i.e. multiframe image > > file. When I try to use this format with FreeSurfer mri_convert fails. I > > assume it is not desig

[Freesurfer] Reference volumes

Hi, I am wondering, whether there has been any publication, or any other resource, with reference volumes of ALL the segmented subcortical structures for different age categories. I tried to search the mailinglist archives, but no success. Thanks, Martin --

[Freesurfer] Runtime for -subcortseg

Hi, anybody knows, how long does it take to run one subcortical segmentation on a MacPro? It take about 6 hours on my MacBook Pro, so I would expect it should finish faster on the workstation. Could anybody suggest me a hardware configuration, on which it could be about 4 hours? Last question,

Re: [Freesurfer] Reference volumes

Thanks for this Sunday reply Bruce, On Sunday 04 March 2007 16:32, Bruce Fischl wrote: > Hi Martin, > > Anders Fjell and Kristine Walhovd did some work that may be relevant > (their publications are on our wiki). I found it, after all. > We are also almost done with the > analysis of Randy Buck

[Freesurfer] recon-all failing from script

Hi, I am trying to further script (Bash) the autorecon1 and subcortseg. The script just sets the path to the received dicom data, gets some info from the dicom header and starts the autorecon1 followed by subcortseg. The things work well when executed from the command line, but if I execute the

[Freesurfer] Situation with OASIS

Hi, I was wondaring, what is the situation with OASIS data? Could you please share with us, in which form you will make the results of your great effort available? Thanks in advance for the great job (and reply of course). Martin ___ Freesurfer maili

[Freesurfer] few oasis question

Hi. I have few questions regarding the recently published OASIS data analyzed using Freesurfer: 1. How did you produce $SUBJECT_ID/mri/wmparc.mgz. I am running recon-all -all on my subjects, but I don't get this file. 2. How did you produce segmentation of the corpus callosum. I am running rec

Re: [Freesurfer] few oasis question

; I'll leave 3 for Doug. > > cheers, > Bruce > > On Wed, 11 Jul 2007, Martin Kavec wrote: > > Hi. > > > > I have few questions regarding the recently published OASIS data analyzed > > using Freesurfer: > > > > 1. How did you produce $SUBJECT_ID/

Re: [Freesurfer] few oasis question

set. It has been taken down until we > resolve it. > > doug > > Martin Kavec wrote: > >Hi. > > > >I have few questions regarding the recently published OASIS data analyzed > >using Freesurfer: > > > >1. How did you produce $SUBJECT_ID/mri/wmparc.mg

[Freesurfer] Mapping segmentation to orig

Hi, how can I map the aparc+aseg.mgz back to $SUBJECT_ID/mri/orig/001.mgz, but without suffering from interpolation? Thanks, Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] Displaying cortical thickness

Hi, I would really appreciate a help (steps or a link to description) on how to display cortical thinning on an inflated surface. I ran a subject through recon-all -autorecon3 and now I would basically want to see, where (s)he has abnormal thickness of the cortex. Thanks a lot in advance, Mar

[Freesurfer] Interpretation of cortical thickness result

Hi folks, I have been puzzled for a while with the results from couple of my subjects. They all have clearly visible cerebral atrophy (says neuroradiologist). I ran them through FS-4.0.1 and aseg.stat gives me, as expected, severe loss of gray matter (and others as well) as follows: GM ICV nor

Re: [Freesurfer] Interpretation of cortical thickness result

al atrophy could get buried in the mean overall thickness. Thanks, Martin > > cheers, > Bruce > > On Tue, 16 Oct 2007, Martin Kavec > > wrote: > > Hi folks, > > > > I have been puzzled for a while with the results from couple of my > > subjects. They al

[Freesurfer] OT - animating ?h.pial or aparc+aseg

Hi, sorry to bring an off topic, but I could not find a solution myself. I was asked to prepare a short fly-by animation of a ?h.pial for a TV who interviewed my boss last week. Would you have any recommendation on how to do that? The ?h.pial is a mesh, which is ideal, because the surface of th

Re: [Freesurfer] OT - animating ?h.pial or aparc+aseg

Hi Bruce, and thanks for the idea. On Monday 05 November 2007 14:45:10 Bruce Fischl wrote: > what kind of animation? You should be able to do this with a tcl script > in tksurfer, saving consecutive tiffs from slightly different viewpoints. I had in mind some complex rotation, zoom-in zoom-out,

[Freesurfer] Mapping group fMRI on surface

Hi, I can not find my way to map the results of the FSL fMRI group analysis (FLAME1+2) from different subjects on their average surface. Here is in more details what I have done: 1. fMRI analysis of each subject in FSL 2. group analysis (FLAME1+2) in FSL 3. cortical reconstruction of each subje

Re: [Freesurfer] Mapping group fMRI on surface

of the latest FSL. I' am not 100% sure it is in common space, but I would guess it is. Thanks, Martin > Martin Kavec wrote: > > Hi, > > > > I can not find my way to map the results of the FSL fMRI group analysis > > (FLAME1+2) from different subjects on their

Re: [Freesurfer] Mapping group fMRI on surface

Bruce, it's auditory cortex I am interested in. If there is a tutorial or explanation somewhere, could you please point me to it. Is this already available in FS? Thanks Martin On Tuesday 13 November 2007 14:38:52 you wrote: > what areas specifically? We have analyzed their data and have a pape

Re: [Freesurfer] Folding Index question

Very interesting debate you keep here, gentlemen. I went on and divided FI by the area in one reference and one pathological subjects (and age matched references). Now it seems that the "NewFI" is quite correlated with cortical thickness. It even decreases from the frontal, through parietal to

Re: [Freesurfer] using BET prior to recon-all?

In my experience, the FreeSurfer's brain extraction works better than the BET. Although, now with an option of iterative BET in the latest FSL, the outcomes are much better than before. In cases where brain extraction failed in my analysis, I found that it was the bias field correction which di

[Freesurfer] Problems on MAC 10.5

Hi, I have upgraded my Mac OS X to 10.5 and after that nu_correct says: Can't locate MNI/Startup.pm $FREESURFERHOME/mni/bin/nu_correct line 37 Anybody has an idea, what could be wrong? Obviously, the file is there. Thanks, Martin ___ Freesurfer

Re: [Freesurfer] Problems on MAC 10.5

software updates. Nick On Fri, 2008-02-01 at 15:29 +0100, Martin Kavec wrote: Hi, I have upgraded my Mac OS X to 10.5 and after that nu_correct says: Can't locate MNI/Startup.pm $FREESURFERHOME/mni/bin/nu_correct line 37 Anybody has an idea, what could be wrong? Obviously, the file is

Re: [Freesurfer] finding WM hypointensities

Hi Bruce, On Friday 22 February 2008 16:36:34 Bruce Fischl wrote: > Hi Thomas, > > the aseg includes hypointensities, but there's only so much you can do > with only a T1-weighted image. We do have some beta versions that use a Could i possibly have the betas for testing? Thanks, Martin ___

[Freesurfer] mri_ca_label segfaults

Hi, I have an emergency here with recon-all -all on a VIP, which segfaults on mri_ca_label -align -nobigventricles ...I tried to run it from the command line and left out the -nobigventricles argument, since actually the subject has enlarged ventricles, but it didn't help. After running for ab

Re: [Freesurfer] Cannot download new Leopard release

Hi Jurgen, the same happens here. The reason for that is that guys pointed the link on the webpage to an nonexisting file. The file uploaded on the server is called freesurfer-Darwin-leopard-i686-stable-pub-v4.0.3-full.dmg while the webpage refers to freesurfer-Darwin-tiger-i686-stable-pub-v4.0

Re: [Freesurfer] Cannot download new Leopard release

Sorry, misspelled harvard in the link. ;) This should work better. ftp://surfer.nmr.mgh.harvard.edu/pub/dist Martin On Tuesday 01 April 2008 11:19:16 Martin Kavec wrote: > Hi Jurgen, > > the same happens here. The reason for that is that guys pointed the link on > the webpage to an

[Freesurfer] Experience with -localGI on Mac

Hello folks, I am trying -localGI on Mac, with working Matlab2007. 1. I think that the getmatlab script is not designed to work on Mac out of the box, since it is not by default in the $PATH, so it could be caught by "which". So I uncommented the three lines and set it hard. 2. That was easy,

Re: [Freesurfer] Experience with -localGI on Mac

Hi Nick, I am just giving a try to the new mris_compute_lgi matlab script kindly provided by Marie, and so far so good. I would appreciate the new binary for: Mac OS X 10.5.2, linux_x86, and linux_x86_64. Thanks a lot. Martin On Thursday 24 April 2008 18:40:12 Nick Schmansky wrote: > Martin a

[Freesurfer] LGI of annotated cortex

Hi, is it possible to obtain LGI values of cortices, similarly as curvature indices in ?h.aparc.stats? Could this value possibly be included in the ?h.aparc.stats files? Thanks in advance, Martin -- ** Senior Clinical Research Associate MRI Unit of the Depart

Re: [Freesurfer] LGI of annotated cortex

; You can create another stats file (can't add it to the one that is > already there). > > doug > > Martin Kavec wrote: > >Hi, > > > >is it possible to obtain LGI values of cortices, similarly as curvature > >indices in ?h.aparc.stats? Could this value possibly

Re: [Freesurfer] LGI of annotated cortex

al_lgi as a surface file, whereas it is > indeed a thickness / curv file > > Have a nice day, > > Marie > > On 9 mai 08, at 10:29, Martin Kavec wrote: > > Thanks for responce, Dough. > > > > I've looked at recon-all as you suggested, and came up with the > >

Re: [Freesurfer] LGI of annotated cortex

Thanks a lot for clarification, Marie. On Friday 09 May 2008 14:37:46 Marie Schaer wrote: > Martin, > > As lgi is read like a thickness file, the lgi values in your tabular > output replaced the value where you had thickness before. So mean lgi > is in column 4 (note that average lgi values per pa

[Freesurfer] Freesurfer vs. VBM

Gentlemen, I am giving a lecture about aging brain. I only discuss freesurfer, since that's the method we use for the brain volume and cortical thickness assessment. There are other methods, such as VBM and SIENA potentially providing similar information. I would appreciate if you could point m

Re: [Freesurfer] Freesurfer vs. VBM

Thanks to all of you for ideas. You may also find interesting to look at: http://www.wikibooks.org page on VBM, which has large section of Criticism. The most striking for me is the inaccuracy of the spatial normalization, which may account for as much as 10.8 mm. On Thursday 15 May 2008 18:58

[Freesurfer] Color scheme settings frustratration

Hi folks, I am scratching my head, how did you guys set the color scheme of the lgi overlay on: http://surfer.nmr.mgh.harvard.edu/fswiki/LGI the image with text "Example of lGI overlay on the brain using a colocoded scale" What I do is I load pial surface and overlay ?h.pial_lgi, but can not

[Freesurfer] Topological defects in LGI

Hi, I get the following warning followed by error in LGI calculation: ... remeasuring lGI value for vertex iV = 6301. It may take a few minutes. WARNING -- Problem for vertex iV = 6301, lGI value is aberrantly high (lGI=48.6447)... ...lGI

Re: [Freesurfer] Topological defects in LGI

Hi Maria, On Monday 09 June 2008 15:00:10 Marie Schaer wrote: > Martin, > > Which version of freesurfer did you use to generate the surfaces? with the latest one, 4.0.4 > Because the number of topological defects in your surface (64) is very > high. You may have to relaunch the surfaces (orig an

Re: [Freesurfer] Topological defects in LGI

On Monday 09 June 2008 21:14:35 Michael Harms wrote: > No, I don't have any examples (although we haven't been looking either). > However, Martin's email regarding problems he is encountering on the LGI > computation seems premised on having surfaces with topological problems > even under v4 -- hen

Re: [Freesurfer] Topological defects in LGI

On Monday 09 June 2008 21:57:36 Bruce Fischl wrote: > I guess it's possible but the -make switch is designed to prevent this. Are > the surfaces topologically incorrect? What is the euler number for them? Bruce, this depends on at which point the topology fixing was interrupted. For this thread I

[Freesurfer] Reanalyzing some OASIS cases

Hi, I would like to rerun recon-all (from the latest freesurfer) on a few cases from OASIS brains study, to get control values for my patient group. Since my computational options are rather limitted, I would like to avoid running redundant steps, which would anyway give me the same results, or

[Freesurfer] tkmedit problem with XQuartz-2.3.0

Hi, On my macbook pro (MAC OS X 10.5) I have recently updated my X to 2.3.0 and now I can not launch tkmedit: $ tkmedit $SUBJ brainmask.mgz rh.white -aux-surface lh.white Converting main surface: 100% done. Converting main surface: 100% done. Converting original surface: 100% done.

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