Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

What is the difference between Cerebral-white-matter and Cortical-white-matter in Freesurfer?
by Righart, Ruthger Dr. 20 May '11

20 May '11

Dear All, I am working with the volume-based stream in Freesurfer and I have a question about what is the difference between the volumes given for Cortical-white-matter and Cerebral-white-matter? How are the volumes calculated for both in Freesurfer? Is it the difference of including or not including the subcortical gray matter and ventricles in the calculation? I have read previous mailings ( e.g. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15449.html ) but I am still confused what is the difference between these measures. Thank you very much in advance for your help! Ruthger Righart (PhD) Institute for Stroke and Dementia Research (ISD) Klinikum der Universität München Max-Lebsche-Platz 30 81377 Munich | Germany Ruthger.Righart(a)med.uni-muenchen.de

2 1

ROI analysis in freesurfer
by abdurahman elkhetali 19 May '11

19 May '11

We have a functional image (beta weights generated in SPM and the original BOLD timeseries they came from ) and a structural image. We have flattened the anatomical image using freesurfer and have determined some ROIs based on that (retinotopy). Now we need to apply those ROIs to our BOLD images. What method would you suggest for this? How would you go about taking the BOLD images and transforming to the flattened space for our subject? TanksAboul Alkhtli

1 0

little bug in mri_cvs_register
by GREGORY R KIRK 19 May '11

19 May '11

running mri_cvs_register --mov 004 --template 003 get error executing surf2vol at /apps/x86_64_sci5/freesurfer-latest/bin/elastic_registration_CVS.pl line 162. line 162 is system($cmdLine)==0 or die "error executing surf2vol"; i saw martin kavec posted the same error but did not see a response ' the command is $cmdLine is surf2vol -fixed_mri /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/mri/norm.mgz -moving_mri /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/mri/norm.mgz -fixed_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/lh.white -moving_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/lh.resample.white -fixed_surf_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/rh.white -moving_surf_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/rh.resample.white -fixed_surf_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/lh.pial -moving_surf_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/lh.resample.pial -fixed_surf_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/rh.pial -moving_surf_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/rh.resample.pial -aparc /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/lh.aparc.annot -aparc_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/rh.aparc.annot -aparc_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/lh.aparc.annot -aparc_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -cache_transform /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/transform.txt -penalty_weight 1000 -fem_steps 17 -elt_vol_range 5.0,10.0 -log_summary -poisson .3 -topology_old -compress -pc_type none -ksp_type preonly -pc_type jacobi -ksp_type cg -ksp_view -ksp_converged_reason -out /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/el_reg_to003.mgz -out_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/surf-mfc_to003 -out_mesh /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/el_reg_to003 &> /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/trace_el_reg_to003_004.txt if you cut and paste this in your freesurfer SUBJECTS_DIR it runs fine but executing strace -f -o /scratch/trace.foo mri_cvs_register --mov 004 --template 003 --step2 one of the output lines is 16837 open("iteration.node", O_WRONLY|O_CREAT|O_TRUNC, 0666) = -1 EROFS (Read-only file system) on another computer where i have freesurfer installed in my home directory the program runs fine. so it seems that when the perl script executes the command and freesurfer is installed in a system directory like /usr/bin/... that the perl script home dir at the point of the system call is in the system directory and it is trying to write there rather than somewhere in SUBJECTS_DIR or other user writable location and surf2vol fails when it tries to open a file in write mode in a system directory greg

2 1

error message from fast_selxavg.m
by Yang Liu 19 May '11

19 May '11

Hi, I was running selxavg-sess, and met this error: >> >> >> >> >> >> $Id: fast_selxavg.m,v 1.40.2.2 2009/04/09 20:01:57 greve Exp $ Parsing Arguments RescaleTarget = 1000 UseMRIread = 1, ext = nii Checking Parameters ??? Undefined function or variable "xyzscale". Error in ==> load_nifti_hdr at 138 hdr.pixdim(2:4) = hdr.pixdim(2:4) * xyzscale; Error in ==> load_nifti at 75 hdr = load_nifti_hdr(niftifile); Error in ==> MRIread at 159 hdr = load_nifti(fspec,headeronly); Error in ==> fast_selxavg>check_params at 1529 mri = MRIread(instem,1); Error in ==> fast_selxavg at 51 s = check_params(s); >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (/space/data/stan/cooked/2010/101204Castor): selxavg failed Done... It all goes back to the undefined "xyzscale". Does that mean the nifti fiel I am trying to load is wrong? This problem is quite annoying because it appearance is unpredicatable. Sometimes our analysis go through fine, sometimes it pops out, and I have no idea what is the difference from those successful runs. Thanks, Yang

1 0

recon-all tutorial data
by obregon＠nmr.mgh.harvard.edu 19 May '11

19 May '11

Hi, I'm new to the software and I'm having trouble finding the following file: ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz How can I download the "recon-all" tutorial data? Has it been replaced/relocated? Thanks a lot, Gabriel Obregon

3 2

Fwd: sign mc-z
by René Besseling 19 May '11

19 May '11

Dear all, A beginners question: what does the sign mean in the multiple comparison simulations? I thought it defines the side of the t-test performed on the glm parameter estimates, but since you can run the simulations for a bunch of contrasts simultaneously and since in some cases you might be interested in H1: c^T B<0 and in others in H1: c^T B>0, I think the sign must mean something else... Hope you can help! Best regards, René

2 1

question about voxel size
by Sghedoni Roberto 19 May '11

19 May '11

Hi, I'm looking at a aparc.stats file. I noticed that VoxelVolume is 1 mm^3. However for this patient the voxel size was 0.9 x 0.9 x 1 mm^3 in acquisition. Actually, in the aparc.stats file Nvoxel = Volume_mm3 for each structure. I would like to understand whether the voxel size was resized from the acquisition value to 1 mm^3 and the result is ok or the voxel size reported in aparc.stats is uncorrect and I have to rescale the values for the correct voxel size. Actually the results are quite strange, in particular the intracranial volume is quite large and if I rescale for the above value the result is more similar to our past patients. Thanks Per favore, pensa all'ambiente prima di stampare questo messaggio.

2 1

Error during file browsing
by Allie Rosen 19 May '11

19 May '11

Hello, I am running FreeSurfer v5.0.0. When in tkSurfer, when I am loading any file, I come across a problem when I press "Browse" to search for the file. In the "Filter" bar, the pathway is always followed by " */* ". There are no files listed in the window below unless I delete the */*. This happens every time I enter a new directory. I'm not sure if this problem is due to FreeSurfer or to my computer, so I apologize if it is unrelated. Thanks in advance for the help, Allie Rosen, MSc Candidate Graduate Student, Department of Neurosurgery Toronto Western Hospital 14-327 399 Bathurst St. University of Toronto

1 0

CORRELATION VALUE
by cgomez＠bidmc.harvard.edu 18 May '11

18 May '11

Hi all, My design is very simple: 1-group,1-variable 2-nuisance (age,gender). I just want to see the correlation between Cth and my variable. I obtain one cluster after mc-correction. (using freesurfer5) There is any way to get the intercept,slope or r-pearson (in average) values of this particular cluster. What I've done is transform this cluster in a label to then visually inspect the Graph Average ROI, but I want the numerical results. Thanks in advance for your useful help. Cleo.

2 2

ERROR: gdfOffsetSlope:
by Ilana Hairston 18 May '11

18 May '11

Hi there, When i load he group descriptor file i get the following error: "cannot determine the offset and slope for the given group descriptor because the design matrix creation method is unknown" Why is that? Thanks ilana -- ******************************* peligro! flaca pero mala! ******************************

2 1

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