[Freesurfer] FS on Fedora Core 5, GLXBadLargeRequest
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 [EMAIL PROTECTED] local]# cd freesurfer_centos_3.0.3/bin/ [EMAIL PROTECTED] bin]# mv tksurfer tksurferorig [EMAIL PROTECTED] 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 :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] tksurfer hemodynamic waveforms for group analysis
If you're still having trouble with the time course loading, can you send me the command line you're using and the data you are trying to load? On Wed, Jun 07, 2006 at 07:35:49PM -0400, Doug Greve wrote: It is definitely possible to display time courses in tksurfer, but I usually load them from the cmd line with -timecourse. I don't think I've ever done it from the gui. Kevin will have to look into that error. If you'd like to try loading from the cmd line then: cd fegroup/bold/ISI1TR_BERT_ERFIRsm5pf5tpefsub/sph You will need to paint the HDRs onto fsaverage: mri_surf2surf --hemi lh --sval h-lh.bhdr --tval h-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape Do the same thing for sig: cd AV-REST mri_surf2surf --hemi lh --sval sig-lh.bhdr --tval sig-lh-fsaverage.mgh --srcsubject ico --trgsubject fsaverage --noreshape This will create: h-lh-fsaverage.mgh You can then: tksurfer fsaverage lh inflated -overlay AV-REST/sig-lh-fsaverage.bhdr -timecourse h-lh-fsaverage.mgh doug [EMAIL PROTECTED] wrote: 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kevin Teich ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FS on Fedora Core 5, GLXBadLargeRequest
Glenn, You are correct in finding that just the tksurfer app is the one binary from the standard centos4_x86_64 stable freesurfer build that does not work on fc5. By coincidence, I have been working with a 32bit FC5 platform, and found that this is true. That is, the standard centos4 stable build works on 32bit FC5, except for tksurfer. It was necessary to update the nvidia driver on the FC5 platform to get rid of 'GLXBadLargeRequest' messages, but it also necessitated a special build of tksurfer (to fix a problem where the glut lib was not initialized). So, in short, I will remove the FC5 x86_64 'dev' build, and post the special tksurfer builds (for fc5 32bit and 64bit), and include a notice that fc5 users should use the centos4 build, but to copy over tksurfer with the special fc5 version. I still recommend updating the nvidia driver (if using that brand of vid card), as it clearly fixes one of the problems. Thanks for pointing this out! Nick On Thu, 2006-06-08 at 14:16 +0200, Glenn Lawyer wrote: 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 [EMAIL PROTECTED] local]# cd freesurfer_centos_3.0.3/bin/ [EMAIL PROTECTED] bin]# mv tksurfer tksurferorig [EMAIL PROTECTED] 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 :) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] center of pial surface in world coordinates
Hi Martijn, we still support COR. I'm at a disadvantage here in that I've not used Neurolens before. I'm not even sure what the problem is. You can show the surfaces in neurolens and in tksurfer, so what's the problem? doug martijn van den heuvel wrote: 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 [EMAIL PROTECTED] 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FSL output overlay
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 pixdim00.00 pixdim13.75 pixdim23.75 pixdim34.00 pixdim41.00 pixdim51.00 pixdim61.00 pixdim71.00 vox_offset 352 cal_max0. cal_min0. scl_slope 0.00 scl_inter 0.00 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start0 slice_end 0 slice_duration 0.00 time_offset0.00 intent Unknown intent_code0 intent_name intent_p1 0.00 intent_p2 0.00 intent_p3 0.00 qform_name Unknown qform_code 0 qto_xyz:1 3.75 0.00 0.00 0.00 qto_xyz:2 0.00 3.75 0.00 0.00 qto_xyz:3 0.00 0.00 4.00 0.00 qto_xyz:4 0.00 0.00 0.00 1.00 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Unknown sform_code 0 sto_xyz:1 0.00 0.00 0.00 0.00 sto_xyz:2 0.00 0.00 0.00 0.00 sto_xyz:3 0.00 0.00 0.00 0.00 sto_xyz:4 0.00 0.00 0.00 0.00 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descripFSL3.3 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 pixdim00.00 pixdim10.937500 pixdim20.937500 pixdim31.200477 pixdim41.00 pixdim51.00 pixdim61.00 pixdim71.00 vox_offset 352 cal_max7638. cal_min0. scl_slope 1.00 scl_inter 0.00 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start0 slice_end 0 slice_duration 0.00 time_offset0.00 intent Unknown intent_code0 intent_name intent_p1 0.00 intent_p2 0.00 intent_p3 0.00 qform_name Scanner Anat qform_code 1 qto_xyz:1 -0.937500 0.00 -0.00 131.00 qto_xyz:2 0.00 0.937500 -0.00 -119.197502 qto_xyz:3 0.00 0.00 1.20 -77.393600 qto_xyz:4 0.00 0.00 0.00 1.00 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 0.00 0.00 131.00 sto_xyz:2 0.00 0.937500 0.00 -119.197502 sto_xyz:3 0.00 0.00 1.20 -77.393600 sto_xyz:4 0.00 0.00 0.00 1.00 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descripFSL3.3 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] converting .img to .mgz
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] converting .img to .mgz
that should work. Why do you want another way? Bruce On Thu, 8 Jun 2006, Chacko Cherian wrote: 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FSL output overlay
What do you mean to get proper output from reg-feat2anat? This program produces a freesurfer registration file, which you then check with reg-feat2anat --manual ... doug Vishwadeep Ahluwalia wrote: 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 pixdim00.00 pixdim13.75 pixdim23.75 pixdim34.00 pixdim41.00 pixdim51.00 pixdim61.00 pixdim71.00 vox_offset 352 cal_max0. cal_min0. scl_slope 0.00 scl_inter 0.00 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start0 slice_end 0 slice_duration 0.00 time_offset0.00 intent Unknown intent_code0 intent_name intent_p1 0.00 intent_p2 0.00 intent_p3 0.00 qform_name Unknown qform_code 0 qto_xyz:1 3.75 0.00 0.00 0.00 qto_xyz:2 0.00 3.75 0.00 0.00 qto_xyz:3 0.00 0.00 4.00 0.00 qto_xyz:4 0.00 0.00 0.00 1.00 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Unknown sform_code 0 sto_xyz:1 0.00 0.00 0.00 0.00 sto_xyz:2 0.00 0.00 0.00 0.00 sto_xyz:3 0.00 0.00 0.00 0.00 sto_xyz:4 0.00 0.00 0.00 0.00 sform_xorient Unknown sform_yorient Unknown sform_zorient Unknown file_type NIFTI-1+ file_code 1 descripFSL3.3 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 pixdim00.00 pixdim10.937500 pixdim20.937500 pixdim31.200477 pixdim41.00 pixdim51.00 pixdim61.00 pixdim71.00 vox_offset 352 cal_max7638. cal_min0. scl_slope 1.00 scl_inter 0.00 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start0 slice_end 0 slice_duration 0.00 time_offset0.00 intent Unknown intent_code0 intent_name intent_p1 0.00 intent_p2 0.00 intent_p3 0.00 qform_name Scanner Anat qform_code 1 qto_xyz:1 -0.937500 0.00 -0.00 131.00 qto_xyz:2 0.00 0.937500 -0.00 -119.197502 qto_xyz:3 0.00 0.00 1.20 -77.393600 qto_xyz:4 0.00 0.00 0.00 1.00 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 0.00 0.00 131.00 sto_xyz:2 0.00 0.937500 0.00 -119.197502 sto_xyz:3 0.00 0.00 1.20 -77.393600 sto_xyz:4 0.00 0.00 0.00 1.00 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descripFSL3.3 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
