Freesurfer May 2005

freesurfer@nmr.mgh.harvard.edu

26 participants
53 discussions

Question
by Wan Park 26 Sep '06

26 Sep '06

Hello, my name is Wan Park and I am working at Columbia University. After converting General Electric DIACOM files into COR, I go to the Setup Structural Scans. There I set the Structural Scan Dir and then Convert/Average. After that, Start the Process Volume, but it seems that there is a problem when it tries to strip the skull. i receive this message: Images (brain): /Users/../Volumes/ste/freesurfer/subjects/scott/mri/brain/COR-001.. not found ... strip skull first So I go to see the logs and I find this: /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_normalize /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 reading from /Users/../Volumes/stem/freesurfer/subjects/scott/mri/orig... normalizing image... 3d normalization pass 1 of 2 building Voronoi diagram... performing soap bubble smoothing... 3d normalization pass 2 of 2 building Voronoi diagram... performing soap bubble smoothing... writing output to /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 3D bias adjustment took 3 minutes and 23 seconds. Command Finished /Users/wanpark/Desktop/FreeSurfer/freesurfer/bin/Darwin/mri_watershed /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain ************************************************************ The input file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/T1 The output file is /Users/../Volumes/stem/freesurfer/subjects/scott/mri/brain If this is incorrect, please exit quickly the program (Ctl-C) *************************WATERSHED************************** preflooding height equal to 25 percent Sorting... first estimation of the COG coord: x=125 y=148 z=132 r=54 first estimation of the main basin volume: 693155 voxels ******************************************************** ******************************************************** ******************************************************** White matter intensity 0 is lower than CSF intensity 26. Please examine input images. Will terminate ... ******************************************************** ******************************************************** ******************************************************** ************************************************************** MRIstipSkull failed. ************************************************************** Command Finished Could you tell me what's wrong? Thanks, Wan Park

4 3

can left and right surfaces be flipped?
by peggy christidis 09 Jun '05

09 Jun '05

Hi there, I just finished creating a surface (with lots of time consuming manual editing) for someone who just informed me that he got the right-left orientation wrong on the volume I was given, and that it needs to be reversed (grrrrr....) Is there any way to do this in FreeSurfer without having to redo the surfaces? Thanks again, Peggy

4 6

Missing libraries?
by Fornito, Alexander 03 Jun '05

03 Jun '05

Hi, We're really stuck on this one... We are running a linux kernel 2.4.26 debian 3.0 (woody). We've installed the freesurfer and the packaged MINC tools in the apporpriate directories and set the appropriate environment variables. We can't get the MNI tools to work through freesurfer, and only some limited MINC tools work if we try to run them on their own (eg., we can use MINC display, but can't do anyting with the images). It seems like there are some libraries missing (see below). Can you tell us why the MINC tools that came packaged with fressurfer aren't working? Is there something else that needs to be installed? If I try to run mri_convert from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. If I run segment_subject I get : segment_subject 190 cp: cannot stat `/data/flanders/work/alex/freesurfer/subjects/scripts/brain.dat' : No such file or directory /data/flanders/work/alex/freesurfer/subjects/190/scripts /data/flanders/work/ale x/freesurfer/subjects registering 190 mri_convert orig orig/orig.mnc reading from orig... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to orig/orig.mnc... mincinfo: error while loading shared libraries: libvolume_io.so.0: cannot open shared object file: No such file or directory Error executing mincinfo on orig/orig.mnc Error: could not open file "/data/flanders/work/alex/freesurfer/subjects/190/mr i/transforms/talairach.xfm". System message: No such file or directory mri_add_xform_to_header: could not read xform file '/data/flanders/work/alex/fre esurfer/subjects/190/mri/transforms/talairach.xfm' Any help would be much appreciated!!! Thanks, Alex

4 5

pictures of MRI image segmentation
by Bagnato, Francesca (NIH/NINDS) 01 Jun '05

01 Jun '05

Hi: I am having troubles in preparing a picture showing MR image segmentation in the coronal, axial and sagittal planes. Any light on that? Thanks, --francesca Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2005 1:50 PM To: Wan Park Cc: free surfer Subject: [Freesurfer] Re: Gray Volume question Hi Wan, they haven't been normalized. Typically you would normalize by the total intracranial volume, which can be a bit tricky to get from only a T1. If you normalize by total brain volume, that should be a bit more conservative, as it would normalize out total atrophy. cheers, Bruce On Tue, 31 May 2005, Wan Park wrote: > Hi, I have a question. I am getting the gray volume for a standard area > (G_subcallosal) in different brains (male and female) with different > conditions. > > If I want to compare these volumes, should I normalize them with the total > brain (or hemisphere) volume or can I use these results directly? I > understand that the FS fills the volume from a particular brain into a > standard brain. So, are the volumes already normalized? Thanks, > > Wan > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

3 5

occipatal cuts
by Joongnam Yang 31 May '05

31 May '05

Hi all, I did the occipital cut for the right brain and flattened it. When I opened it with Tksurfer of csurf, the flattened surface showed up on the right edge of the display window of Tksurfer, instead of being in the center of the window. (The left flattened surface came out in the center, and I did similarly for the left and right brains.). Has anyone had this problem? or how can I fix it? Thanks always for the great help that I get from this listing. Nam.

1 0

Gray Volume question
by Wan Park 31 May '05

31 May '05

Hi, I have a question. I am getting the gray volume for a standard area (G_subcallosal) in different brains (male and female) with different conditions. If I want to compare these volumes, should I normalize them with the total brain (or hemisphere) volume or can I use these results directly? I understand that the FS fills the volume from a particular brain into a standard brain. So, are the volumes already normalized? Thanks, Wan

2 1

RE: [Freesurfer] questions on check_subject
by Bruce Fischl 31 May '05

31 May '05

is this only on Tiger? And does it happen with all your subjects now that you have upgraded? On Tue, 31 May 2005, Jia Liu wrote: > Hi, Bruce- > > Thanks for your reply. I re-did morph for the right hemisphere, and the > problem persists. > > CHECKING SUBJECT ttt > WARN: time for rh.orig is older than rh.qsphere > WARN: file rh.sphere.reg is not equal in size to rh.smoothwm > > -rw-rw-r-- 1 jliu jliu 4853285 May 31 12:45 rh.sphere.reg > -rwxrwxr-x 1 jliu jliu 4853068 May 31 09:43 rh.smoothwm > -rwxrwxr-x 1 jliu jliu 4853068 May 31 09:43 rh.orig > > The log file is attached. What should I do to correct this problem? Thanks > again for your help! > > Best, > > jia > >> -----Original Message----- >> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >> Sent: Sunday, May 29, 2005 9:42 PM >> To: Jia Liu >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Subject: RE: [Freesurfer] questions on check_subject >> >> you will need to rerun the morph. >> On Sun, 29 May 2005, Jia Liu wrote: >> >>> Hi, Bruce- >>> >>> No, the ?h.sphere.reg files are slightly larger than the orig files. > Below >>> is the list of files in the surf directory. >>> >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.inflated >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.orig >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.pial >>> -rw-rw-r-- 1 app app 4858721 Mar 16 23:46 lh.rh.sphere.reg >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.smoothwm >>> -rw-rw-r-- 1 app app 4858504 Mar 16 20:35 lh.sphere >>> -rw-rw-r-- 1 app app 4858721 Mar 16 22:14 lh.sphere.reg >>> -rwxrwxrwx 1 app app 4858504 Mar 8 2004 lh.white >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.inflated >>> -rw-rw-r-- 1 app app 4853285 Mar 16 18:54 rh.lh.sphere.reg >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.orig >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.pial >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.smoothwm >>> -rw-rw-r-- 1 app app 4853068 Mar 16 15:17 rh.sphere >>> -rw-rw-r-- 1 app app 4853285 Mar 16 16:59 rh.sphere.reg >>> -rwxrwxrwx 1 app app 4853068 Mar 8 2004 rh.white >>> >>> Will this affect the surface-based group analysis? >>> >>> Thanks again for your help! >>> >>> Best, >>> >>> jia >>> >>>> -----Original Message----- >>>> From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] >>>> Sent: Friday, May 27, 2005 8:10 PM >>>> To: Jia Liu >>>> Cc: freesurfer(a)nmr.mgh.harvard.edu >>>> Subject: Re: [Freesurfer] questions on check_subject >>>> >>>> not sure why the smoothwm would be different size. Is it the same size > as >>>> the orig? How about the rest of the surfaces for each hemis (sphere, >>> white, >>>> pial) >>>> >>>> On Fri, 27 May 2005, Jia >>>> Liu wrote: >>>> >>>>> Hi, >>>>> >>>>> I used check_subject and found following error message on all my >>> subjects: >>>>> >>>>> Zion:/nfs/home/Subjects> check_subject subKL >>>>> CHECKING SUBJECT subKL >>>>> WARN: file rh.sphere.reg is not equal in size to rh.smoothwm >>>>> WARN: file lh.sphere.reg is not equal in size to lh.smoothwm >>>>> WARN: file lh.rh.sphere.reg is not equal in size to lh.smoothwm >>>>> Exit 3 >>>>> >>>>> However, I looked through recon-all log files and found no error >>> messages. >>>>> So what does the error message above mean? How to correct this > problem? >>> Is >>>>> there any document on check_subject? Thanks a lot for your help! >>>>> >>>>> Best, >>>>> >>>>> Jia >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>> >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >

2 4

mesh decimation
by Alex Wade 26 May '05

26 May '05

I am trying to reduce the number of vertices in a freesurfer mesh. I am having some difficulty when I go through matlab using the 'reducepatch' command : some of the surface normals end up being scrambled resulting in strange transparent holes in the mesh. I wonder if there is some command-line routine that will directly take, say, rh.pial , decimate it and write out another mesh, say, rh.pial_dec I see that tksurfer has a write_decimation option and this works in that it generates a file but I don't know what format the output is. It doesn't seem to be a valid surface file and tksurfer will crash when I try to load it. Thanks in advance for your help Alex A.R. Wade Ph.D. Associate Scientist Brain Imaging Center The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115 tel. 415 345 2083 fax. 309 416 6533

2 1

parcellated areas
by Wan Park 26 May '05

26 May '05

Hi, when I do parcellate_subject, I received this message with one of my brains: 2816 1563 3354 2.147 +- 0.645 0.190 0.071 58.221 6.689 ** annotation 003c148c 1449 858 2052 2.369 +- 0.688 0.191 0.055 26.557 2.772 ** annotation 003cdc14 1996 1206 2429 2.019 +- 0.567 0.221 0.085 48.606 6.389 ** annotation 001414b4 Instead of showing the area names, it shows "annotation ..." Do you know where the problem is? Thanks, Wan

2 1

running Freesurfer on a Linux cluster
by Renat Yakupov 26 May '05

26 May '05

Hello. Does Freesurfer run on Linux cluster really taking advantage of it? Is it, what it is called, cluster-aware? What about running on a multi-processor workstation? Up to how many CPU's can it handle? Thank you. Regards, Renat.

3 2

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer May 2005