Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30096 discussions

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

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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

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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 > <><><><><><><><><><><><><><><><><:)

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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.

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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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func2sph-sess target brain setting
by raij＠nmr.mgh.harvard.edu 07 Jun '06

07 Jun '06

Hi, Backround: I am running a fixed effects group analysis with fsaverage (mne305) as the target brain, and merging the activations across subjects on the spherical surface. The individual functional sessions have been co-registered to the individuals' structural brain reconstruction (i.e. the register.dat file inside the bold directory links the functional and structural data within subjects only). Problem: I am not sure how to set the group analysis func2sph-sess and paint-sess "target brain" parameters correctly. Version and environment: I am using the current Martinos Center FreeSurfer standard installation (vs. >3) under nmr-std-env and all the structural reconstructions are new as well. Outline of the analysis (list of commands): preprocessing mkanalysis-sess.new selxavg-sess mkcontrast-sess stxgrinder-sess func2sph-sess <- sphsmooth-sess isxavg-fe-sess stxgrinder-sess paint-sess <- Specific question (with possible answers): *** 1 *** Should I set the target brain already at func2sph-sess: func2sph-sess -analysis XXX -sf sessid -df sesspar -trgsubject fsaverage (if the -trgsubject setting is omitted, then the target appears be the default = ico order 7) *** 2 *** Or is it sufficient (if I ignore the -trgsubject parameter above) to set: paint-sess -analysis XXX -contrast YYY -subject fsaverage -space sph -isxavg fixed -s fegroup -df group.sesspar (here fegroup = the folder where the fixed effects analysis is stored, set at isxavg-fe-sess -s fegroup) *** 3 *** Or must/should I do both 1 and 2 of the above. I am using surf-sess/tksurfer to view the results and set -subject fsaverage even there. I get results that look reasonable either way. I just wonder what is the difference between the methods, and if either method is unambiguously correct. Thanks, 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.

2 3

functional group results on structural data
by Paymon Hosseini 07 Jun '06

07 Jun '06

hi i used the following commands to create a group subjects: func2tal-sess -res 4 -analysis rk_enc2_sm5 -sf sessid -df sesspar isxavg-fe-sess -analysis rk_enc2_sm5 -sf sessid -df sesspar -group Y15ENC2_sm5_grp -space tal stxgrinder-sess -analysis rk_enc2_sm5 -all -space tal -s Y15ENC2_sm5_grp i use this command to view the results: tkmedit-sess -analysis rk_enc2_sm5 -map sig -s Y15ENC2_sm5_grp -space tal -isxavg fixed -c omnibus the output is: -------------------------------------------------------------- tkmedit-sess logfile is /autofs/space/engram_012/users/pman/rk_fmri/code/log/tkmedit-sess.log -------------------------------------------------------------- setenv SUBJECTS_DIR /space/engram/12/users/pman/rk_fmri/STRUCTS INFO: Found session in: ./Y15ENC2_sm5_grp INFO: Y15ENC2_sm5_grp is a group average INFO: Found session in: ./Y15ENC2_sm5_grp INFO: Y15ENC2_sm5_grp is a group average INFO: subject is talairach INFO: subject is talairach INFO: Anatomical directory set to /autofs/space/sake_003/users/inverse/anat_data/talairach/mri/orig ------------------------ SUBJECTS_DIR /space/engram/12/users/pman/rk_fmri/STRUCTS /autofs/space/engram_012/users/pman/rk_fmri/code tkmedit talairach orig -overlay /autofs/space/engram_012/users/pman/rk_fmri/code/Y15ENC2_sm5_grp/bold/rk_enc2_sm5/tal-ffx/omnibus/fsig_000.bfloat -overlay-reg /autofs/space/engram_012/users/pman/rk_fmri/code/Y15ENC2_sm5_grp/bold/rk_enc2_sm5/tal-ffx/register.dat -fthresh 2 -fmid 5 -fslope 1 -aux brain ------------------------ Reading 7 control points... Reading /usr/local/freesurfer/stable/lib/tcl/tkm_common.tcl Reading /usr/local/freesurfer/stable/lib/ the figure looks fine, but, i would like to be able to see the functional maps on an average-subject hi-res structural map. can you please tell me how to do this? i am using "nmrenv" on engram.nmr.mgh. thanks a lot, paymon

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RE: [Freesurfer] Segmentation optimization (fwd)
by Doug Greve 07 Jun '06

07 Jun '06

As far as the orientation goes, mri_convert will assume that the spm .mat file uses an RAS geometry. You should look at the volume in tkmedit and go through each orientation to make sure that each looks correct. ie, for sag the nose should be to the right, for ax the nose should be at the top. For left/right, tkmedit displays in radiological convention, so make sure your fiducial is on the correct side. doug ---------- Forwarded message ---------- Date: Wed, 7 Jun 2006 16:02:06 +0100 From: Joao Pereira <jmsp2(a)wbic.cam.ac.uk> To: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: RE: [Freesurfer] Segmentation optimization Here are the acquisistion parameters and some other data as well (images acquired with 1.5T field): Coronal 3D FSPGR IR GENESIS_SIGNA Sequence: GR Seq Variant: SS\SP\SK Flip Angle: 20 Options: FAST_GEMS\VB_GEMS\EDR_GEMS\PFF TR = 13.9 TI = 650 TE = 4.2 NEX = 1 pixel bandwidth = 81.4 Acq. Matrix = 0\256\224\0 Spatial Resolution = 0.982143 220mmx220mmx174mm (256x256x116) voxel size: 0.86x0.86x1.50mm^3 1.164 pixels per mm Also, another question that need to check: I transform the Analyze images so that they are SPM oriented (RAS). When I the convert them with mri_convert (no other options set), this orientation (neurological) is maintained, right? (At least it seems so, from the ijk matrix). Please let me know if this interpretation is correct. Once more, thank you! Joao -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu]On Behalf Of Bruce Fischl Sent: 06 June 2006 17:50 To: Joao Pereira Cc: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Segmentation optimization what is the resolution of your images? You might as well send us the complete set of acquisition parameters. Bruce On Tue, 6 Jun 2006, Joao Pereira wrote: > Hello again, > > I've been having some problems with FS segmentation, especially around the > temporal lobes, where there is a clear underestimation of the pial surface > (and manual edits are not being too successful). The problem is clearly > related to the poor resolution of the used images. > > Are there any parameters to change in order to optimise the segmentation > process? > > Also, in order to evaluate the segmentation I want to use the grey matter > segmented volume mask. Is it the ?h.ribbon.mgz files or should I consider > something else? > > Thank you again. > > Joao Pereira > > > _______________________________________________ > 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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center of pial surface in world coordinates
by martijn van den heuvel 07 Jun '06

07 Jun '06

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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FSL output overlay
by Vishwadeep Ahluwalia 07 Jun '06

07 Jun '06

Hi, I'm a relatively new FS user. Ive a single subject functional dataset analyzed in FSL. I ran recon-all autorecon1 ,2 and 3 on the subject's SPGR. Everything worked fine. i ran reg-feat2anat to register my functionals to the anatomical but when i hit compare button in tkregister2 , the alignment is all wrong. I tried changing the dof to 12 and maxangle to 180 but the output again looks the same. the functionals are almost inverted compared to the outline of the anatomical. During the processing i saw a warning saying that the 'neither sform or qform in the nifti-1 are valid 'and another warning saying the ' your volume will probably be incorrectly oriented'. which is evident in the output. I thought FSL and FS both use FLIRT for registration. so why are the results different? Please advise. Regards, Vishwadeep A. Grad. Student Medical Physics PhD Program VCU

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