Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30061 discussions

center of pial surface in world coordinates
by martijn van den heuvel 11 Jun '06

11 Jun '06

Dear Bruce, Thanks for your quick reply. I posted this question on the Neurolens-forum as well. I too think it is just a problem of two different coordinate system. Rick (of the Neurolens forum) mentioned that the pial surface coordinate to world coordinate system is stated in a COR.info file. However, I think that the COR.info file is no longer supported by freesurfer, is this correct? Is there an alternative? Sorry, if my question was not totally clear. I will describe what I did: I translated my anatomy file to talairach space (only translation, no scaling, resliced it so there is not .mat file ) and used it (in SPM analyse format) as input for the freesurfer-train (recon-all -autorecon1,2,3). The recon-all dev table suggests that freesurfer uses brain.finalsurfs.mgz (same orientation as T1.mgz) as the input for creating the surface pial files. In my original anatomy file the (0,0,0) coordinate is around the center of the brain (in talairach space). As my input anatomy is already in Talairach space orig.mgz is also in talairach space and there is a minimum translation by freesurfer to create T1.mgz (I checked this and indead talairach.xfm is almost a 1 1 1 matrix). If freesurfer uses this as the input for the surface rendering, should not be the (0,0,0) coordinate in the middle of the pial surface? Using tksurfer this is indead the case, however using Neurolens this is not the case, there is a large shift. There is a small shift from talairach coordinate system to RAS system, but my surface rendering has a much larger shift (in my example around 45 mm in the Z-direction). Maybe this COR.info file is the solution, holding the translation from scanner coordinates <-> RAS, however I don't have an example of this file and therefore do not now what this file looks like and what it does. Hope you can help me with this problem. Really appreciate your time. greetings, martijn > > > > > > On 6/7/06, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu > wrote: > > >> > > >> I think it's probably just displaying them in different coordinate > > >> systems. tksurfer displays in an RAS coordinate system in which > > (0,0,0) > > >> is essentially the center of the volume, whereas Neurolens is > > probably > > >> displaying scanner coordinates. Does it matter to you? Not sure I > > >> understand - is it causing you any problems? > > >> > > >> Bruce > > >> > > >> On Wed, 7 Jun 2006, martijn van den heuvel > > >> wrote: > > >> > > >> > Dear freesurfer-users, > > >> > > > >> > I want to plot the freesurfer surface rendering (xxx.pial) in the > > >> program > > >> > Neurolens. Loading the image gives no problem and Neurolens gives a > > > > >> > beautiful rendering. However, when loading the pial surface in > > tksurfer > > >> I > > >> > see a difference between the two renderings. The surface in > > tksurfer is > > >> > centered to RAS (0,0,0) , like the T1.mgz image (as it supposed to > > do). > > >> Im > > >> > trying to figure out what this translation is, but I cannot find > > the > > >> answer > > >> > on the web, hence this email. Does tksurfer loads in a translation > > file > > >> > (except for the talaraich.xfm, I got this translation covered), or > > does > > >> it > > >> > do a general shift to the RAS centre? Generally, Im looking for the > > >> > translation matrix from RAS to world coordinates, so I can apply > > this > > >> > translation to the surface before loading it in Neurolens. > > >> > > > >> > I hope someone can help me with this question. > > >> > > > >> > Yours sincerely, > > >> > > > >> > Martijn van den Heuvel > > >> > > > >> > > > > > > >

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freesurfer on windows thru ssh
by Gifford, Sheyna 09 Jun '06

09 Jun '06

Dear Freesurfer Community, Freesurfer is running well on Mac OSX and BSD, but one of my users wants to run it on Windows thru ssh. This is the error that is generated when she tries. >GLUT: Fatal Error in tkmedit: OpenGL GLX extension not supported by >display: localhost:14. I am not at all a windows person. I can only imagine that this has to do with lack of OpenGL support on WindowsXP. Has anyone out there in the community successfully been able to run freesurfer on Windows, thru eXceed or any other method? Many thanks for any advice.

2 1

SPM conversion to FreeSurfer-style reg matrix
by jswonder 09 Jun '06

09 Jun '06

Hello all, I am looking for a way to convert an SPM .mat to a FreeSurfer registration matrix (register.dat); basically, something like the old spmmat2register command, but not obsolete...any suggestions? Thanks!

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Re: group analysis error
by adam walczak 09 Jun '06

09 Jun '06

never mind...figured out. thx --- adam walczak <xfadam(a)yahoo.com> wrote: > Hello, > > While running group analysis (mri_glmfit step), on > an > admittedly tiny subject group (3). I used two > classes > (male/female) and age. I received the following > error: > > ERROR: DOF = 0 > > I am wondering if three subjects is too small a data > set for this to run or if I am just doing something > wrong. It got through the other preprocessing > steps, > but got stuck here. > > My contrast vector is [0 0 1] like the tutorial. > > Thanks for any help. > > Adam > > adam > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam > protection around > http://mail.yahoo.com > adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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group analysis error
by adam walczak 09 Jun '06

09 Jun '06

Hello, While running group analysis (mri_glmfit step), on an admittedly tiny subject group (3). I used two classes (male/female) and age. I received the following error: ERROR: DOF = 0 I am wondering if three subjects is too small a data set for this to run or if I am just doing something wrong. It got through the other preprocessing steps, but got stuck here. My contrast vector is [0 0 1] like the tutorial. Thanks for any help. Adam adam __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

1 0

converting .img to .mgz
by Chacko Cherian 08 Jun '06

08 Jun '06

Hi everybody, I ve got a small question on converting .img scans(Analyze) TO .mgz... suppose i have a raw.img(and raw.hdr) file and I want to use recon-all for converting this to .mgz do I just need to do recon-all -i raw.img -s <subject_name> Or is there any other way I can directly use .img files instead of converting to the native .mgz format...? Thanks a lot,in advance Chacko. __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

3 3

FSL output overlay
by Vishwadeep Ahluwalia 08 Jun '06

08 Jun '06

Hi, To elaborate my problem a little more ... Running FSL command avwhd gave me : filename spiral.nii.gz sizeof_hdr 348 data_type INT16 dim0 4 dim1 64 dim2 64 dim3 25 dim4 250 dim5 1 dim6 1 dim7 1 vox_units Unknown time_units Unknown datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 3.7500000000 pixdim2 3.7500000000 pixdim3 4.0000000000 pixdim4 1.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 0.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Unknown qform_code 0 qto_xyz:1 3.750000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 3.750000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 4.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Unknown sform_code 0 sto_xyz:1 0.000000 0.000000 0.000000 0.000000 sto_xyz:2 0.000000 0.000000 0.000000 0.000000 sto_xyz:3 0.000000 0.000000 0.000000 0.000000 sto_xyz:4 0.000000 0.000000 0.000000 0.000000 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descrip FSL3.3 aux_file And avwhd on the spgr gave me: filename spgr.nii.gz sizeof_hdr 348 data_type INT16 dim0 3 dim1 256 dim2 256 dim3 124 dim4 1 dim5 1 dim6 1 dim7 1 vox_units mm time_units s datatype 4 nbyper 2 bitpix 16 pixdim0 0.0000000000 pixdim1 0.9375000000 pixdim2 0.9375000000 pixdim3 1.2000000477 pixdim4 1.0000000000 pixdim5 1.0000000000 pixdim6 1.0000000000 pixdim7 1.0000000000 vox_offset 352 cal_max 7638.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Scanner Anat qform_code 1 qto_xyz:1 -0.937500 0.000000 -0.000000 131.000000 qto_xyz:2 0.000000 0.937500 -0.000000 -119.197502 qto_xyz:3 0.000000 0.000000 1.200000 -77.393600 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Right-to-Left qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Scanner Anat sform_code 1 sto_xyz:1 -0.937500 0.000000 0.000000 131.000000 sto_xyz:2 0.000000 0.937500 0.000000 -119.197502 sto_xyz:3 0.000000 0.000000 1.200000 -77.393600 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descrip FSL3.3 aux_file When I analyze the data in FSL I get the expected activation (Left hemisphere activation for right hand movement)so I know that FSL is reading or assuming the orientation correctly for the functional(even though sform and qform are unknown). My question is : after I run the recon-all process on the spgr, what do I need to do to the functional data to get freesurfer to read it correctly inorder to get proper output from reg-feat2anat? Any help is appreciated. Thanks Regards, Vish

2 1

FS on Fedora Core 5, GLXBadLargeRequest
by Glenn Lawyer 08 Jun '06

08 Jun '06

Hi, Around the 25th of April there was a brief discussion regarding running FreeSurfer on a FC5 machine. Some users were having a problem with tksurfer not displaying and an error with the X server (GLXBadLargeRequest). I just installed the centos _x64 3.0.3 verson of FreeSurfer on a FC5 machine, nvidia graphics card, and experienced the same error. However, Nick mentioned that a FC5 build of FreeSurfer is available at ftp://surfer.nmr.mgh.harvard.edu/pub/dist named freesurfer-Linux-fc5-x86_64-dev20060426.tar.gz I installed this build on my machine, and this version of tksurfer displays properly (at least a first test, fsaverage + curvature + aparc.anot + wireframe) Nick went on to say "This is a 'dev' version, meaning its built from a codebase that is slightly ahead of date with the stable version, but none-the-less should behave identically to stable. This FC5 build won't be updated on a regular basis, since it is not one of our standard platforms (it was built offsite)." Just for kicks, I linked the FC5 tksurfer into my freesurfer_centos bin, and that also seems to work. Thus I can use the centos_3.0.3 version of everything except tksurfer, for which I use the FC5 version [root@localhost local]# cd freesurfer_centos_3.0.3/bin/ [root@localhost bin]# mv tksurfer tksurferorig [root@localhost bin]# ln -s ../../freesurfer_fc5_3/bin/tksurfer . -- -------------------------------------- I'm only in it for the glory. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

2 1

tksurfer hemodynamic waveforms for group analysis
by raij＠nmr.mgh.harvard.edu 08 Jun '06

08 Jun '06

Dear Fellow Freesurfers, I am trying to display HDR waveforms (time courses) for group level FIR analyses in tksurfer. When opening the group analysis data with tkmedit and a functional overlay, obviously some sort of time course data is loaded, because I can scroll back and forth between the different time points/frames of the functional overlay (for the specific contrast that I loaded). However the load timecourse function does not seem to be working. When attempting to load a hemodynamic waveform, I receive either an error (func_load_timecourse: error in FunD_New) without opening the HDR window, or then the time course volume is "interpreted as encoded scalar volume" and only one time point, of only one contrast, is shown in the HDR window. I have tried downloading all possible and impossible files related to the group analysis (.hdr/.bhdr/.bfloat/.dat/.mat/.w) from both within the specific contrast directory or the one higher level, but they all fail in either of the two ways above. The wiki, in this case, was not very helpful in trying to discover which file to load: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial_2fVisualization Is this function currently functional? If so, which file should I load? Details: group brain = fsaverage STUDY_DIR = /space/cognito/21/users/raij/avml_fmri_mctogether/ SUBJECTS_DIR = /space/cognito/5/users/raij/subjects_mri/ environment = nmr-std-env on machine ai (FreeSurfer vs >3) group analysis name = fegroup, analysis = ISI1TR_BERT_ERFIRsm5pf5tpefsub example contrast: AV-REST Thanks for your help! Tommi --- Tommi Raij, M.D., Ph.D. MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging Bldg 149, 13th St Charlestown, MA 02129 U.S.A.

3 2

GLM model
by Antao Du 07 Jun '06

07 Jun '06

I want to test the difference of cortical thickness in two groups and age is accounted for as a covariate. Should I use "different offset, same slope" or "different offset, different slope" in GLM model? Thanks, Antao

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