Freesurfer August 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
143 discussions

reinstalling
by Ahmed, F, Me <fahmed＠sun.ac.za> 14 Aug '09

14 Aug '09

Hello, I just have a quick question, when reinstalling FS, is it ok to use the license that I initially received when first installing it? Or must I register for a new license? Thank you and Kind regards, Fatima

3 2

installation problems
by Ahmed, F, Me <fahmed＠sun.ac.za> 14 Aug '09

14 Aug '09

Hello, I am trying to reinstall FS, and I am having some difficulties. When I type in the following command: cd /usr/local tar xzvf freesurfer-Linux-<platform>-<release>-full.tar.gz (replacing the -<platform>-<release> with my Linux variant which is freesurfer-Linux-centos4-stable-pub-v4.3.1) I get the following error: tar: freesurfer-Linux-centos4-stable-pub-v4.3.1-full.tar: Cannot open: No such file or directory tar: Error is not recoverable: exiting now tar: Child returned status 2 tar: Error exit delayed from previous errors Please can you advise me on how to correct this? Thank you kindly Fatima

2 7

tksurfer problem
by sina zarei 13 Aug '09

13 Aug '09

Hello I am not able to see the surface by running "tksurfer bert lh pial". I receive the error "surfer: ### redraw failed: no gl window open". I have tried "export doublebufferflag=1". Mesa is installed and updated. Linux ATI drivers is installed. Os: Fedora 11 Graphics: ATI RV515 X1300. I have tried rh9 and CentOS4 versions of the freesurfer on separate Fedora 11 and CentOS 5. On CentOS I see only a small part of the image. I have tried NVIDIA graphic cards too. 3D games work fine. I am very grateful if you may assist me. Sina

1 0

FreeSurfer: fornix segmentation
by Judit Haasz 13 Aug '09

13 Aug '09

Hi, I have run mri_cc -fornix. In some cases I encountered the following problem. Although fornix.mgz was created, and it seems the program has run properly, the file (same size as those who contain fornix) turns to be empty. Looking at the input volume, I could identify fornix. Could you help finding a solution for my problem? Thank you for help! Judit Haasz mri_cc -fornix -aseg aseg.auto_noCCseg.mgz -o fornix.mgz *SES including fornix in segmentation reading input aseg from aseg.auto_noCCseg.mgz writing aseg with cc labels to fornix.mgz reading aseg from /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/aseg.auto_noCCseg.mgz reading norm from /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/norm.mgz 11261 voxels in left wm, 26612 in right wm, xrange [125, 132] global minimum found at slice 128.0, rotations (0.25, -1.50) final transformation (x=128.0, yr=0.250, zr=-1.500): 1.000 0.026 0.004 -3.864; -0.026 1.000 -0.000 3.409; -0.004 0.000 1.000 0.560; 0.000 0.000 0.000 1.000; updating x range to be [126, 131] in xformed coordinates best xformed slice 128 cc center is found at 128 120 96 eigenvectors: -0.001 0.001 1.000; -0.192 -0.981 0.001; 0.981 -0.192 0.001; error in mid anterior detected - correcting... writing aseg with callosum to to /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/fornix.mgz... writing fornix to to /Applications/freesurfer//subjects/AGING_2008_11_16_SES/mri/fornix.mgz... corpus callosum matter segmentation took 0.6 minutes

2 1

manually edit segmentation
by Fischi Gomez Elda 13 Aug '09

13 Aug '09

Dear all, I'm trying to manually edit the -segmentation step in the recon -all -autorecon2 command. Actually, my problem is that I need a cortex parcelisation of a newborn brain and, as far as I know, I cannot run directly the -recon all as it s based on a adult brain template. My idea was, inf act, to reedit the -segmentation step, as I have a manually segmented template of a newborn brain, and then, run this modified recon -all to obtain the parcelisation. Is it possible? Does exist any way to obtain this cortex parcellisation for a newborn brain using FreeSurfer? Thanks

2 1

subject-inflation-sphere
by Zhong Jidan 13 Aug '09

13 Aug '09

Hi Freesurfer experts, I have a question about the sphere transformation from the inflated surface. In the paper "cortical surface-based analysis II", you mentioned that each vertex is put in a normal vector field which is from the center of the sphere to the vertex, then you project the inflated surface onto a unit sphere. The question is, how do you choose the center of the sphere? If you choose a different location as the center of the sphere, the new sphere you get will be different. So how do you make sure that the center you choose is the one you want? Thanks a lot. -- Regards, Jidan

2 1

reinstalling freesurfer
by Ahmed, F, Me <fahmed＠sun.ac.za> 13 Aug '09

13 Aug '09

Hello Experts, I apologise for the stupidity of this question, but I am not used to using Linux at all, but I need to uninstall my Freesurfer and then reinstall it, however, I have no idea how to uninstall in Linux. Can someone possibly assist me in this problem? I'd be extremely grateful. Thank you and Kind regards, Fatima

3 6

Extending Pial Volume
by Derek Huffman 12 Aug '09

12 Aug '09

Hello FreeSurfer Team, I am wondering how to add cortex to the pial volume that is already present in the brainmask volume. When I look at the brainmask volume, there is visible cortex located outside the red "pial" line. I have already added white matter control points and corrected all white matter defects. I am wondering if you have any tips for me. I apologize if this is a repeat question but I couldn't find anything in the wiki about correcting this type of error. Thank you, Derek

2 1

conversion
by Lindsay Nagamatsu 12 Aug '09

12 Aug '09

Hi, The output files that I get from our scanner are .par and .rec files, but I am now using fsl and freesurfer to analyze my data. How can I convert my files into a Nifti format to be used by fsl and freesurfer? Is there a way that freesurfer can do this? Thank you, Lindsay -- Lindsay Nagamatsu, BA MA Candidate Department of Psychology University of British Columbia 2136 West Mall Vancouver, B.C. Canada, V6T 1Z4 Tel: (604) 822-3120 Fax: (604) 822-6923

3 2

Re: [Freesurfer] Clusterwise correction
by Dankner, Nathan (NIH/NIMH) [F] 12 Aug '09

12 Aug '09

Another question: I've noticed that when loading the cluster .annot file, tksurfer also loads the desikan parcellation color table. How can I load the clusters by themselves? And also, I know that loading the cluster overlay allows you to see which clusters are significant by looking at their level of transparency, but is there a way to load ONLY the clusters that are significant? Thanks again, Nathan On 8/12/09 3:49 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: The QDEC script runs mri_glmfit-sim, which automatically finds and uses the FWHM, so you should not have to do anything. Recently (about a month ago), I found a bug in some of the simulation software, so you should upgrade to the latest FS version. doug Dankner, Nathan (NIH/NIMH) [F] wrote: > Doug, > > Sorry, I'm still a bit unclear on how/when I need to pass along the fwhm. I have been generating my scripts for the cluster correction through the qdec GUI. Where along the line do I need to pass it the fwhm? Do I need to go into the script itself and add it somewhere? > > > On 8/12/09 2:02 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: > > > > If you are running an MC simulation (not perm) directly from mri_glmfit > (and not mri_glmfit-sim) then you must pass it a fwhm or the results > will be wrong. The smoothing level is measured by QDEC (mri_glmfit) as > part of the analysis. You can't run the simulation from QDEC, so > specifying the smoothing level for the simulation from QDEC is not an issue. > > doug > > > Dankner, Nathan (NIH/NIMH) [F] wrote: > >> Doug, >> >> Thanks for the info. One quick follow-up question: Let's say for example the smoothing before I run the simulation is 2.75. When you say I need to match the smoothing, do I achieve that by adding 2.75mm of smoothness to the data before running the cluster simulation? In the qdec GUI it only allows you to smooth in increments of 5. Is there a command line flag that would allow me to choose my own level? >> >> >> On 8/11/09 5:48 PM, "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> wrote: >> >> 1) The smoother the data, the more likely a cluster will be found by >> chance. When the data are created, they start with some smoothness >> level. When you smooth them you add more. So you need to match the total >> level of smoothing when you do the simulations, otherwise your clusters >> will be way too significant. mri_glmfit creates a fwhm.dat file with an >> estimate of the total smoothness. >> >> 2) Just if they are nearest neighbors. There is no option to tinker with >> this. >> >> 3) Vertices in the maps created by the simulation are thresholded at the >> level you pass. This is what defines the cluster. >> >> doug >> >> Dankner, Nathan (NIH/NIMH) [F] wrote: >> >> >>> Hello all, >>> >>> I have a couple of questions regarding the way the cluster correction simulation in freesurfer works. I've read the wiki pages on the subject, but if I've missed something and any of this is answered elsewhere please let me know. My technical knowledge of these things is not great so I am just trying to get some background. First of all, how does smoothing the data prior to running the simulation affect the results? I've run corrections on the same data smoothed with a 10mm FWHM, and also on completely unsmoothed data, and the cluster results were different. Secondly, what determines whether vertices are neighbors or not? Is there an option to tinker with this or is it predetermined? Lastly, how do the p values of individual vertices factor into the simulation? Are they taken into account when the determination of the max cluster size under the null hypothesis is performed? Thanks in advance, >>> >>> Nate >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)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 >> >> In order to help us help you, please follow the steps in: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >> >> >> >> >> >> >> > > -- > 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 > > > > > > > -- 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

2 1

← Newer
1
...
7
8
9
10
11
12
13
14
15
Older →

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer August 2009