Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

T1 and T2 in one recon-all
by Samuel Inverso 30 Nov '09

30 Nov '09

Hi Freesurfers, Looking through the mail archives it seems T1 and T2 runs for a single subject should not be combined when doing recon-all. Is this still the case? Thank you for your time, Cheers, -Sam

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Re: [Freesurfer] convert/reconstructing with mrdc
by Jesse Bledsoe 29 Nov '09

29 Nov '09

I have T1volume+org.BRIK - should I use those with mri_convert? Thanks again, Jesse On Tue, Nov 24, 2009 at 4:23 PM, Saad, Ziad S. (NIH/NIMH) [E] < saadz(a)mail.nih.gov> wrote: > mri_convert usually work with BRIK files. > > Alternately, 3dAFNItoNIFTI could turn BRIK files to nifti format > which FreeSurfer can read fine. > > cheers, > ziad > > On Nov 24, 2009, at 3:28 PM, Bruce Fischl wrote: > > > These are not the standard .BRIK files? Ziad (ccd) will know. > > > > Bruce > > > > > > On Tue, 24 Nov 2009, Jesse Bledsoe wrote: > > > >> Hello, > >> > >> So far I have had no problems running recon-all with .mnc files but > >> could > >> use some guidance converting/reconstructing brains processed with > >> AFNI > >> (MRDC). > >> > >> There are 120 MRDC files in the T1 directory. > >> > >> I believe I need to run mri_convert on these MRDC files but am > >> unsure of > >> what the correct command would be? > >> > >> Thanks in advance, > >> > >> Jesse > >> > > -- Jesse Bledsoe, M.A. Clinical Psychology Assistant Director, Center for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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recon-all exited error
by Jesse Bledsoe 29 Nov '09

29 Nov '09

Hello Experts, I am getting the following error: mri_watershed Error: GLOBAL region of the brain empty ! Linux circ.psy.msu.edu 2.6.9-67.0.4.ELsmp #1 SMP Fri Jan 18 05:00:58 EST 2008 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Sat Nov 28 13:29:41 EST 2009 I do not seem to be getting this error with the other files. Any suggestions? Thanks so much, Jesse

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a question about the output template by make_average_subject
by Guang Zeng 29 Nov '09

29 Nov '09

hi, there, I called FS command make_average_subject to create an average subjects using 10 subjects. After the process finished, I found that there are two output template file, "lh.reg.template.tif" and "rh.reg.template.tif". How are these two templates different from the template I built by following the steps described in FS WIKI, The Surface Registration Process; Templates,http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates Thanks a lot! Guang _________________________________________________________________ Bing brings you maps, menus, and reviews organized in one place. http://www.bing.com/search?q=restaurants&form=MFESRP&publ=WLHMTAG&crea=TEXT…

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skull strip errors ?...
by Gonzalo Rojas Costa 28 Nov '09

28 Nov '09

Hi: I am sending attached two images with some skull strip errors that I got in a study... Will I got any error as a result of that skull strip algorithm errors, or I must adjust the parameters of the watershed algorithm ?... Sincerely, Gonzalo Rojas Costa --

2 1

mris_anatomical_stats - how do output measures relate to each other ?
by Samantha Clark 28 Nov '09

28 Nov '09

Hi All, I have a very basic question. Could you please point me to a publication or relevant material that describes the relationship of the various parameters that mris_anatomical_stats outputs. To be precise, I wanted to know how measures like thickness, volume, area, curvature are related. Also, would these measures vary when done on a volume based level in comparison to a surface based approach ? Thank you, Sam

2 1

skull strip errors ?...
by Gonzalo Rojas Costa 27 Nov '09

27 Nov '09

Hi: I am sending attached to images with some skull strip errors that I got in a study... Will I got any error as a result of that skull strip algorithm errors, or I must adjust the parameters of the watershed algorithm ?... Sincerely, Gonzalo Rojas Costa

1 0

problems on virtual machine
by liyari5018 27 Nov '09

27 Nov '09

Dear freesurfer users: I don't know how to read my data in virtual system. When I tried to mount the local disk into virtual system, it asked for root authentication. Do you guys know about the password for root? LJ

2 2

Problem with recon-all on the tutorial data (bert)
by L 27 Nov '09

27 Nov '09

Dear Freesurfers, I have had a problem when running recon-all on your tutorial data (bert). Please find following the content of recon-all.log: *$Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $* * $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $* *MRISread(../surf/lh.inflated): could not open file* *No such file or directory* *mris_sphere: could not read surface file ../surf/lh.inflated* *No such file or directory* *Linux freesurfer-virtual 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux* * * *recon-all exited with ERRORS at Fri Nov 20 17:32:05 EST 2009* I suspected that the problem occurred at “mri_ca_register” and reran it as following: *mri_ca_register -align-after -nobigventricles -mask brainmask.mgz -T transforms/talairach.lta norm.mgz $FREESURFER_HOME/average/RB_all_2007-08-08.gca transforms/talairach.m3z* * * It said the following at the end of the process and “talairach.m3z” could not be found in dir “transforms/” *…* *0621: dt=0.056000, rms=0.414 (0.016%), neg=0, invalid=3625* *0622: dt=0.056000, rms=0.414 (0.020%), neg=0, invalid=3625* *0623: dt=0.056000, rms=0.414 (0.005%), neg=0, invalid=3625* ** *writing output transformation to transforms/talairach.m3z...* *Segmentation fault* * * Here is what given by “bugr” command: *FREESURFER_HOME: /usr/local/freesurfer* *Build stamp: freesurfer-Linux-centos4-stable-pub-v4.5.0* *Debian version: 5.0 * *Kernel info: Linux 2.6.28-11-generic i686* I am running the VirtualBox Ubuntu version. I have looked at previous posts but have not been able to figure out an appropriate answer to my problem. Any of your help would be highly appreciated. Thank you. Kind regards, Long

3 2

script to check multiple cases with tksurfer
by Mehul Sampat 25 Nov '09

25 Nov '09

Hi Folks, I would like to visually check the cortical parcellation for a large number of patients (>200) using tksurfer. Is there a script to which I could submit a list of subject id's and get it to launch tksurfer and display the parcellation data for each subject sequentially ? Thanks Mehul

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