[Freesurfer] whole brain volume

to the BrainSegNotVent measure?  Thanks, Dana -- Dana W. Moore, Ph.D. Instructor of Neuropsychology Department of Neurology & Neuroscience Weill Cornell Medical College 428 East 72nd Street, Suite 500 New York, NY  10021 ___ Freesurfer mai

Re: [Freesurfer] whole brain volume

I think it includes corpus > callosum and internal capsule but I defer to Doug who would know for sure. > Allison > > On Thu, 16 Feb 2012, Dana W. Moore wrote: > > >Thanks, Allison.  This actually leads me to another question though.  It > >says in the wiki that SupraTentorial &

Re: [Freesurfer] whole brain volume

I think it includes corpus > callosum and internal capsule but I defer to Doug who would know for sure. > Allison > > On Thu, 16 Feb 2012, Dana W. Moore wrote: > > >Thanks, Allison.  This actually leads me to another question though.  It > >says in the wiki that SupraTentorial &

Re: [Freesurfer] whole brain volume

I think it includes corpus > callosum and internal capsule but I defer to Doug who would know for sure. > Allison > > On Thu, 16 Feb 2012, Dana W. Moore wrote: > > >Thanks, Allison.  This actually leads me to another question though.  It > >says in the wiki that Su

Re: [Freesurfer] whole brain volume

ts > (https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats) > > On Thu, 16 Feb 2012, Dana W. Moore wrote: > > >Hi everyone, > > > >Previous versions of FreeSurfer had a whole brain measure in the aseg.stats > >file called BrainSegVolNotVent. The newest version no

[Freesurfer] whole brain volume

Hi everyone, Previous versions of FreeSurfer had a whole brain measure in the aseg.stats file called BrainSegVolNotVent. The newest version no longer has this.  I am wondering where I can now find a measure of whole brain volume? Thanks, Dana -- Dana W. Moore, Ph.D. Instructor of

Re: [Freesurfer] skull strip error

W. Moore Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] skull strip error try adding -nowsgcaatlas to the end of the recon-all command. n. On Tue, 2010-04-13 at 18:59 +, Dana W. Moore wrote: > Hi everyone, > > I am using freesurfer version 4.5.0, and have just gotten

[Freesurfer] skull strip error

Hi everyone, I am using freesurfer version 4.5.0, and have just gotten an error message that I have never received before.  The end of the recon-all script is pasted below.  what does this mean? #...@# Skull Stripping Mon Apr  5 15:06:52 EDT 2010 /home/fs01/kab2003/FS/133_S_0525/mri  mri_water

[Freesurfer] freesurfer and DTI

Hello everyone, I have a colleague (cc'd) who is interested in using FreeSurfer's segmentation with DTI results he obtained with TBSS. I am not sure how he should go about this. Any advice is appreciated. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuro

[Freesurfer] wm edits and control points

points first, re-run, and then do further white matter edits? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, S

[Freesurfer] tractography and freesurfer

I have a colleague who is interested in the DTI toolkit to coregister DTI results with FreeSurfer's segmentation. Is that available in any form yet? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New

[Freesurfer] recon-all exited with errors

1.050) to 101.6 (was 107.1) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux compute-3-14.v4linux 2.6.18-53.el5 #1 SMP Wed Oct 10 16:34:19 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Dec 4 22:20:24 EST 2009 Dana W. Moore, Ph.D. Neuropsych

Re: [Freesurfer] edits to pial surface

ral white matter. > >cheers >Bruce > > >On Tue, 17 Nov 2009, Dana W. Moore wrote: > >>Hi everyone, >> >>I have an image in which the pial surface left out portions of the >>cortex (see left temporal lobe below). I am not sure how to go >>about e

Re: [Freesurfer] problem starting qdec

you have the solution to resolve it, please give me some clues. Thanks Zonglei Zhen 2009/7/14 Dana W. Moore <<mailto:dwm2...@med.cornell.edu>dwm2...@med.cornell.edu> Hi everyone, I am trying to use qdec for the first time, and I get the following error message: X Error of fa

Re: [Freesurfer] images with poor resolution

/xopts.txt good luck! Nick On Mon, 2009-10-05 at 16:56 -0400, Dana W. Moore wrote: > Hi Nick, > > Below is Bruce's response to a problem I'm having with the gray/white > segmentation. (Pasted below, you can see the brainmask.mgz volume and > surfaces--the entire brain is lab

Re: [Freesurfer] process dying during longitudinal reconstruction

>On Wed, 2009-10-14 at 22:36 +, Dana W. Moore wrote: > > Hi everyone, > > > > I am trying to run the longitudinal stream on some images. I have 3 > > timepoints, and 2 of them finished the stream just fine, but a third > > quits during autorecon1 during the 3

[Freesurfer] process dying during longitudinal reconstruction

Hi everyone, I am trying to run the longitudinal stream on some images.  I have 3 timepoints, and 2 of them finished the stream just fine, but a third quits during autorecon1 during the 3rd and final longitudinal step.  There is no error message or anything, it just stops.  The log file is atta

Re: [Freesurfer] images with poor resolution

due to the low contrast. You'll probably need to add some control points and run it with the -gentle option On Fri, 2 Oct 2009, Dana W. Moore wrote: Hi everyone, I am trying to salvage some images that were done with poor gray/white boundary contrasts. First, FreeSurfer includes an area

[Freesurfer] images with poor resolution

boundary and labels the dura as cortex: [] Looking at the raw images, the gray/white boundaries are faint but visible. Is there anything I can adjust to try to make this work with FreeSurfer? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill

[Freesurfer] white matter parcellation

parcellation is why there are large areas of unsegmented white matter. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd St

[Freesurfer] generative group averages

Hi everyone, I am using aparcstatstable2 and asegstatstable2 to generate group information so I can get mean values for a group for certain regions. Is there a way to generate group results for right and left total thickness from mris_anatomical_stats? Thanks, Dana Dana W. Moore, Ph.D

[Freesurfer] failed skill strip

This is the first time this has happened. I am using version 4.4.0. Any thoughts on what the problem is? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neur

Re: [Freesurfer] problem starting qdec

uce Fischl wrote: Hi Dana, are you using vnc or nomachine or something? Have you used qdec in this way before? Bruce On Tue, 14 Jul 2009, Dana W. Moore wrote: Hi everyone, I am trying to use qdec for the first time, and I get the following error message: X Error of failed request: GLXBadRen

[Freesurfer] problem starting qdec

[0x40291b69] I am accessing our linux computer remotely using ssh from a windows machine--I don't know if this is related to the problem. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyt

[Freesurfer] recon-all freezing

ples deleted finding control points in Right_Cerebral_White_Matter found 40735 control points for structure... bounding box (58, 45, 28) --> (131, 156, 177) This is always where the script stops when the process seems to freeze. (I have tried 3 times with the same result). Any id

Re: [Freesurfer] talairach error during recon-all

ng? doug Dana W. Moore wrote: Hi all, I get the following error message during recon-all: ERROR: 'imgreg_4dfp /usr/local/freesurfer/average/711-2C_as_mni_average_305 /usr/local/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t

[Freesurfer] talairach error during recon-all

254 ERROR: mpr2mni305 execution aborted ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Any idea why this is happening? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital

[Freesurfer] images with poor resolution

Hi all, I have a couple images that have poor gray-white boundaries, and the cortical parcellation did not come out well. Is there any way to manipulate thresholds to try to enhance the gray-white segmentation? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell

[Freesurfer] remove random factor

allel processing nodes, and I don't have permission to write to the freesurfer home directory. I was wondering, if I could use the whole path when I enter this command into recon-all, and then save it anywhere I like. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuro

[Freesurfer] total gray and white matter volumes, and total brain volume

gray matter and white matter described above, or I could use BrainSetNotVen from the aseg stats file, or I could add all the structures in the aparc and aseg files. Any recommendation on which is best? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology

[Freesurfer] error estimates

I was wondering if there is any output in stats that generates an error estimate for the calculated stats for an individual subject? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian

Re: [Freesurfer] question about wmparc stats files

t exist in others. This would generate tables that had different labels for each subject. doug Dana W. Moore wrote: In my wmparc.stats file I have noticed that for many structures I am just getting a value of 0. I do get output for ctx and wm values corresponding to the aparc structur

[Freesurfer] longitudinal processing stream

. a color-coded segmentation that shows atrophy)? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New

[Freesurfer] Re: Literature values for cortical thickness

Actually, I have also been looking for cortical thickness normative values. We have run our first few research subjects with FreeSurfer (a normal control and several patients with neurodegenerative disorders), and I wanted to see if the thickness values we're getting are in the normal rang

Re: [Freesurfer] problem downloading freesurfer

: try: wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.3.0/freesurfer- Linux-centos4-stable-pub-v4.3.0-full.tar.gz Nick On Tue, 2009-04-28 at 16:54 -0400, Dana W. Moore wrote: > I am trying to download FreeSurfer onto a different Linux machine. I > am able to download, but when

[Freesurfer] longitudinal processing

time as small as 2%. Is this kind of variability expected, or am I doing something wrong? I just used the first baseline as tp1, processed it cross-sectionally, and then longitudinally, and then I used the second baseline as tp2. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Co

[Freesurfer] problem downloading freesurfer

repeatedly with the same outcome. Do you know what the problem might be? I am downloading the <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/4.3.0/freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz>freesurfer-Linux-centos4-stable-pub-v4.3.0-full.tar.gz file. Thanks, Dana

Re: [Freesurfer] tkmedit error

ivers (ATI/NVidia) are not enabled by default. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 <http://www.netfilter.com.br>www.netfilter.com.br 2009/4/23 Dana W. Moore

[Freesurfer] tkmedit error

an I trust the stats I get in the current mode? Is this just a display problem, or do I need to re-run the entire reconstruction once the problem is fixed? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell Universit

[Freesurfer] ventricles labeled as white matter in hydrocephalus brain

, and/or prevent it when I run more NPH patients? Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York