Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

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

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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 >>> >

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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

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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

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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.

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BRIK and tkregister
by Joongnam Yang 24 May '05

24 May '05

Hi, I am using an old version of Freesurfer where retinotopy-analysis is enabled. If anyone having such experience, please help me. I am having trouble with csurf, and here is what I did. (1) changed Analyze file (*.hdr, *.img) into *.BRIK and *.HEAD using to3d (2) in csurf, under "session tools", I did "setup align/func scan" and it opens a window where I do "align scan dir" and it only accepts AFNI's *.BRIK and *.HEAD file. (that's why I did the conversion above). When I choose "align=>subj" to do the tkregister registration, it gives me the following error window. AFNI BRIK byte order (determined "only" from BYTEORDER_STRING parameter in this HEAD file): /............/bob+orig.HEAD is INTEL (LSB first) not SUN/SGI/MAC (MSB first) Change to MSB first? This error message was followed by either "cancel" or "force BRIK to MSB, Fix HEAD", but neither option worked, meaning the image shown on "tkregister" was all gobbled. The "subj" image is OK, but the "align" image is screwed. Could anyone give me a hint on where I should go from here? Thanks. Nam.

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Talairach help!!
by Fornito, Alexander 23 May '05

23 May '05

Hi all, Sorry to labour this point, but I'm stuck with the MNI tools and am having trouble progressing through my freesurfer analyses. I can't create the talairach.xfm and was hoping for some help. If I run mri_convert in the command line, I get the following: mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ mri_convert -it spm 190/mri/orig/001/1000190_wbc -ot cor 190/mri/orig/ reading from 190/mri/orig/001/1000190_wbc... INFO: analyzeRead(): found 1 files for 190/mri/orig/001/1000190_wbc ----------------------------------------------------------------- INFO: could not find 190/mri/orig/001/1000190_wbc.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default).INFO: if not valid, please provide the information in 190/mri/orig/001/1000190_wbc.mat file ----------------------------------------------------------------- INFO: analyzeRead(): min = 0, max = 211 TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) Original Data has (1, 1, 1) mm size and (250, 250, 250) voxels. Data is conformed to 1 mm size and 256 voxels for all directions Reslicing using trilinear interpolation writing to 190/mri/orig/... Alternatively, if I run it from the GUI after checking the MNI Linear Register option in expert preferences, I get a message saying MNI align not yet implemented. Then, when I run segment_subject, it begins with the following messages: 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' As far as I'm aware, all the MNI tools packaged with Freesurfer have been installed correctly, and the appopriate enviornment variables have been set in the default settings and in my own. Any tips? Thanks, Alex

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wm fill won't work with partial brain
by Bakkour, Akram 23 May '05

23 May '05

Hello, I have a high resolution image covering the back third of the brain obtained from surface coils and wm fill fails, it tells me that it doesn't find the corpus callosum. This makes sense because it is not a full brain. But I was wondering if there was a way around this and have the program continue to make progress rather than fail and stop. Thanks for the help! Akram.

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Re: remote VNC solution
by Daniel Goldenholz 19 May '05

19 May '05

I was just asked this same question twice in a short time, so I guess that is a sign that others might want to know the answer too. The short version of the question is: "How can I get freesurfer to work from a remote VNC setup?" The answer is, thanks to a hint from Paul Raines, very simple. When you set up your vncserver, use this command: vncserver.glx instead of the usual "vncserver". If you do, then the needed software will be included to draw tksurfer images, and then you can freesurf remotely. Happy surfing! Daniel Tommi Raij wrote: >Hi Daniel, > >I saw from the Freesurfer list that you asked Bruce about a year ago how >to use tksurfer scripts from remote VNC. Bruce suggested you use > >setenv renderoffscreen 1 > >before running tksurfer, but also said that the function might be broken. > >I am trying the get some semi-massive visualization scripts to work from >the other end of a VNC connection (on a Windows ME system) and cannot make >this work, and keep receiving the kind of errors that you apparently >encountered: > >surfer: single buffered window >no glx extension! >surfer: failed, trying double buffered window >Xlib: extension "GLX" missing on display "1.0". >Window type not found! >surfer: failed, no suitable display found > >Were you succesful in making this work, and if so, how? > >Thanks, > >Tommi > >

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RE: [Freesurfer] Problem converting IMA files
by Kristine Beate Walhovd 19 May '05

19 May '05

Hi Bruce I tried -it siemens too (based on some list question) and that did't work either, but I see now that hey are named .IMA not .ima Sorry, the FW-disk I got them from likely caused the problem. Thanks, Kristine -----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tue 4/19/2005 12:00 AM To: Kristine Beate Walhovd Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Problem converting IMA files Hi Kristine, mri_convert should handle ima files. Have you tried -it siemens? Are they named .ima? cheers, Bruce On Tue, 19 Apr 2005, Kristine Beate Walhovd wrote: > Hi > > I've tried converting IMA files (taken directly from the Siemens scanner) in Freesurfer with the command > > mri_convert -ot cor <one filename in the sequence> <output file> > > but it doesn't work. Gives an error message "cannot parse..." (see attached error message). > > I'd be grateful for any suggestions. > > Thanks, > > Kristine > >

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