Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Big lesion
by Lemkaddem Alia 09 Sep '09

09 Sep '09

Hi, One of our subjects has a big lesion in the left hemisphere, which appears on the MRI. Because of this, I obtain a big whole in the cortical parcellation. I have already tried: - To correct the WM mask. - Used control points to fix intensity normalization. Please have a look at the images that I have attached. The lesion is very big and it's very hard to tell where the WM is. Thankful for all the help I can get, Alia

2 1

The error about recon-all -s subjid -autorecon1
by QQ Liu 09 Sep '09

09 Sep '09

Hi all, In order to find the debug of the problem which occurred when I run recon-all -s subjid -all, I run recon-all -s subjid -autorecon1 for a try. Then there is a another error message to report as follows: ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...40 iterations mghRead: encountered error executing: 'zcat /usr/local/freesurfer/subjects/am03/mri/T1.mgz',frame -1, errno 12 mri_strip_skull: done peeling brain Brain Size = 1657531 voxels, voxel volume = 1.000 mm3 = 1657531 mmm3 = 1657.531 cm3 mri_watershed Error: read failed Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Wed Sep 9 15:08:15 CST 2009 I'm confused that when running -all the first step passed. And the test of bert all passed. Is there anything wrong with the conerted data of our raw data? Thanks a lot in advance. -- Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com

2 1

The image display window cannot show up in the top
by QQ Liu 08 Sep '09

08 Sep '09

Hi all, When I use tkmedit and tksurfer to view the volume or surface, the image display window just fleets once. I click the tag and it doesn't show up either. What's more, the menus of tkmedit don't response when I click them, besides the menu of "Edit". I just use the test commands as follows: tkmedit bert orig.mgz tksurfer bert rh pial Thanks. -- Best wishes. Q.Q Liu +8613426232824 qqliu16(a)gmail.com

1 0

problem with intensity normalization control points
by Ritobrato Datta 08 Sep '09

08 Sep '09

Hello All, I followed the steps in exercise C in the following page http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ControlPoints and added control points manually and then saved the Control Points by File > Save Control Points Then I ran recon-all -autorecon2-cp -autorecon3 -s <subjid> After completion, I opened the viewer to check if it is implemented by tkmedit <subjid> brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white But saw that the image where I added the control points didnt get converted to a continuous line. I have attached a figure as an illustration. What am I doing wrong ? Thanks Ri

3 5

tksurfer: "can't find talairach file"
by Philipp Klein 08 Sep '09

08 Sep '09

Hello, I installed version 4.50 of freesurfer on a Ubuntu 8.10 system, the tests listed in the wiki all run well. Starting tksurfer with other data a warning is shown in the terminal (the talairach.xfm can't be found), but the program starts after that. As far as we can judge after a quick examination, everything is working fine, it's just the warning. Another issue is the warning concerning the missing colortable. Hope anyone can help. Greetings Philipp ps: the terminal output: >>> /usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1$ tksurfer FS_spm_CanonicalBrain rh pial surfer: current subjects dir: /usr/local/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1 can't find talairach file '/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1/COR-.info/../transforms/talairach.xfm' surfer: Reading header info from /usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/mri/T1/COR-.info surfer: vertices=171090, faces=342176 can't find talairach file '/usr/local/freesurfer/subjects/FS_spm_CanonicalBrain/surf/../mri/orig/COR-.info/../transforms/talairach.xfm' WARNING: No colortable found! surfer: single buffered window surfer: tkoInitWindow(FS_spm_CanonicalBrain) surfer: using interface /usr/local/freesurfer/lib/tcl/tksurfer.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /usr/local/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /usr/local/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % surfer: dmin=0.1820, vno=121693, x=60.0832, y=26.3634, z=-18.3935 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 121693 marked (curv=0.000000, stat=0.000000) x = (60.1, 26.4, -18.4), n = (0.7, -0.1, -0.8). surfer: dmin=0.8543, vno=79701, x=72.6551, y=-6.2425, z=-27.2842 % surfer: curv=0.000000, fs=0.000000 <<< It has to be added, that COR-.info isn't a folder at all, so the path can't be correct.

2 1

The error maessage about recon-all
by QQ Liu 08 Sep '09

08 Sep '09

Hi all, When I run the FreeSurfer with one scan images(128) of a subject, I am getting the error message as follows: Segmentation fault ERROR: mri_ca_register with non-zero status 139 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Fri Sep 4 23:59:54 CST 2009 /usr/local/freesurfer/subjects/am01/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux qq-desktop 2.6.28-15-generic #51-Ubuntu SMP Mon Aug 31 13:33:16 UTC 2009 i686 GNU/Linux recon-all exited with ERRORS at Fri Sep 4 23:59:54 CST 2009 The commond used is "recon-all -s subjid -all". Can you give some tips to solve this question? Thanks in advance. -- 祝好！刘倩倩 13426232824 qqliu16(a)gmail.com -- 祝好！刘倩倩 13426232824 qqliu16(a)gmail.com

3 2

postdoctoral position at The University of Chicago (on behalf of Dr. Steven Small)
by Anthony Dick 08 Sep '09

08 Sep '09

A 2-3 year post-doctoral position is available at the Human Neuroscience Laboratory of The University of Chicago (www.humanneuroscience.org) The ideal candidate should be interested in the study of the neural basis of language and/or neural plasticity characterized by changes in brain networks during learning or recovery from injury (primarily stroke). Candidates should have a background in psychology, neuroscience, computational biology, and/or communication sciences and disorders. Prior experience with fMRI is desirable but not obligatory. Experience with multivariate statistics/structural equation modeling, EEG/MEG, TMS, behavioral experimental methods, or neuroinformatics would also be advantageous. Applicants should email their CV and a statement of research interests to Professor Steven Small (small(a)uchicago.edu) -- Anthony Steven Dick, Ph.D. Post-Doctoral Fellow Human Neuroscience Laboratory Department of Neurology The University of Chicago 5841 S. Maryland Ave. MC-2030 Chicago, IL 60637 Phone: (773)-834-7770 Email: adick(a)uchicago.edu Web: http://home.uchicago.edu/~adick/

1 0

hippocampus volume comparision
by Guang Zeng 08 Sep '09

08 Sep '09

Hi, there, I converted a subject from nii (160x256x256) to mgz (256 x 256 x 256 ), and then sent it to the FreeSurfer pipeline. Now, I'd like to compare the resulted hippocampus volume with a hand tracing hippocampus using the original volume. What is the best way to do it? I think I can not use the data in the aseg.stats directly, right? Because of the conform. Thanks a lot! Guang Zeng _________________________________________________________________ Windows Live: Keep your friends up to date with what you do online. http://windowslive.com/Campaign/SocialNetworking?ocid=PID23285::T:WLMTAGL:O…

2 1

mesh file...
by Gonzalo Rojas 07 Sep '09

07 Sep '09

Hi: Where I can find the mesh file that freesurfer generates for each patient ?... Sincerely, Gonzalo Rojas Costa

1 0

which files are modified during white matter editing? cluster <-> local editing
by u.h. 07 Sep '09

07 Sep '09

Dear Freesurfer Devs, We ran our FS brains on an cluster with no visualization nodes, and brought the results into a local computer for interactive interventions and QC after recon-all finished. We fixed some minor segmentation errors, and at this point I'm curious to know if this step only affects the wm.mgz file.. If this is the case, would I be correct in thinking that one would only need to upload the wm.mgz file to the cluster and re-run the necessary commands (autorecon2-wm -autorecon3)? I also saw there is one .touch file that seems to be affected by wm editing. Should I worry about it? Thank you for your assistance. Best, Oori

1 0

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