Freesurfer

freesurfer@nmr.mgh.harvard.edu

13 participants
30061 discussions

physical sizes too big
by Sasha Wolosin 25 Apr '06

25 Apr '06

Dear FreeSurfer, During mri_convert, I get the following warning, and then an error during mri_em_register in -autorecon2. Would greatly appreciate any help, Thanks, Sasha WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (307.20 mm, 307.20 mm, 186.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 308 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ========================== #@# EM Registration Fri Apr 7 15:08:40 EDT 2006 /data/subjects/2154/mri mri_em_register -mask brainmask.mgz nu.mgz /freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-22.0.2.ELsmp #1 SMP Tue Jan 17 06:12:06 CST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 7 15:08:49 EDT 2006 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 1

problems converting to nii
by Michele Perry 24 Apr '06

24 Apr '06

Hi, I am running FreeSurfer version 3.01 and am trying to convert some .mgz files to *.nii format. When I run >mri_convert in_vol.mgz out_vol.nii or >mri_convert -ot nii in_vol.mgz out_vol.nii mri_convert runs without errors but the resulting .nii file cannot be opened by AFNI. Do you know how I can create an nii file that will open in AFNI? ~Michele

2 1

libs and APIs ??
by mweiss＠cbs.mpg.de 24 Apr '06

24 Apr '06

Are there libraries included in the freesurfer-download which contain the used algorithms an data-types? If so, where can I find the according APIs? greetings M.Weiß Leipzig University of Applied Sciences Max Planck Institute for Human Cognitive and Brain Sciences

2 1

renaming
by Sasha Wolosin 23 Apr '06

23 Apr '06

Dear all, I am using freesurfer stable 3.0.1. If I want to rename a subject after the subject has been fully processed, are there any extra steps I would need to take to ensure that the subjects files are referenced correctly in group analysis/ future processing? Thanks, Sasha Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 3

FS on Fedore Core5
by Ryu-Ichiro Hashimoto 20 Apr '06

20 Apr '06

Hello, I have been using FreeSurfer on Dell Linux computer (64 bit) with Fedore Core 4 by downloading [freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.1-full] and had no problems. Recently our lab changed Linux distribution from Fedore Core 4 to 5 and I got the following message when I ran test commands. ---------------------------------- tksurfer test1 rh pial surfer: current subjects dir: /projects/fmri/fs_data surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /projects/fmri/fs surfer: Reading header info from /projects/fmri/fs_data/test1/mri/T1.mgz surfer: vertices=147407, faces=294810 surfer: single buffered window Received X error! Error code : 165 Request code : 145 Minor code : 2 Error text : 'GLXBadLargeRequest' (repeat) ----------------------------------- The other test commands for tkmedit (tkmedit test1 orig.mgz, tkmedit test1 norm.mgz -segmentation mri/aseg.mgz ...) displayed the results correctly. If you could give me any suggestion what to do (without going back to FC4 ... I have no control over it), it would be much appreciated. Thank you, Ryu Hashimoto

4 5

tkregister segmentation fault
by Sungeun Kim 19 Apr '06

19 Apr '06

Hi, I experienced one problem with tkregister. I tried to register local low-res. anatomical data to high-res anatomical data using tkregister. So, I did tkregister -mkdefault modified some parameters. This was OK, but when I did tkregister local I got the segmentation fault message like: tkregister: starting register register: cwd scan => subject's T1/COR's register: reg image transform matrix: -0.999945 0.000000 0.010472 0.207543 0.010406 -0.111469 0.993713 -22.441641 0.001167 0.993768 0.111463 12.550290 0.000000 0.000000 0.000000 1.000000 register: done reading target COR images register: input file type: bshort (x,y,t: <prefix><z>.bshort) Segmentation fault I am using the latest stable version from the web site and I didn't have this problem with the previous version. I tested with another data which worked good with the previous version. But, I still have the same problem. Is there any solution or suggestion to this problem? Thank you in advance. Sungeun Kim.

2 4

problems on installing freesurfer
by mweiss＠cbs.mpg.de 19 Apr '06

19 Apr '06

Greetings, after following the instructions in the Freesurfer-Wiki step by step i still can't run Freesurfer properly... in example: after > tksurfer bert rh pial the following error is prompted: " tksurfer: error while loading shared libraries: libglut.so.3: cannot open shared object file: No such file or directory " all pathes and environment variables are set according to the instructions and all scripts are sourced. i'm running a Debian 3.1 on a i686 machine. .license-File is in place, too. please help! thanks a lot. Marcel Weiß Max Planck Institute for Human Cognitive and Brain Science Student at the Leipzig University of Appied Sciences

3 2

Cortical surface measurement.
by Goradia, Dhruman D 19 Apr '06

19 Apr '06

Hello All, Is it possible to find ROI based cortical surface measures using freesurfer? I am interested in manually tracing ROI and then obtaining thickness, surface area and curvature measures for the ROI. Is there a way to do this in freesurfer? Thank you -Dhruman

2 1

using Analyze
by Chacko Cherian 18 Apr '06

18 Apr '06

Hello all, Can freesurfer use data in Analyze format or does everything have to be converted to .mgz?? Thanks in advance. Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

2 1

masking regions on volume data
by trinity＠nmr.mgh.harvard.edu 18 Apr '06

18 Apr '06

Hi - I'm trying to make a picture for a manuscript submission. We'd like to show group amygdala activation on a volume but we'd only like to show the amygdala activation and mask all the other activation out of the picture. How do we do this? Thank you. Trinity

2 1

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