Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30130 discussions

Running flame on mris_preproc output
by Luetcke, Henry 06 Dec '06

06 Dec '06

Hi all, I used mris_preproc to generate a surface file from 4 feat directories, as described in the tutorial: mris_preproc --out lh.cope1.nii.gz --target fsaverage --hemi lh \ --iv fbert1.feat/stats/cope1.nii.gz fbert1.feat/reg/freesurfer/anat2exf.register.dat --iv fbert2.feat/stats/cope1.nii.gz fbert2.feat/reg/freesurfer/anat2exf.register.dat --iv fbert3.feat/stats/cope1.nii.gz fbert3.feat/reg/freesurfer/anat2exf.register.dat --iv fbert4.feat/stats/cope1.nii.gz fbert4.feat/reg/freesurfer/anat2exf.register.dat I would now like to feed the resulting lh.cope1.nii.gz into fixed-effects analysis with flame and tried the following: flame -cope=lh.cope1.nii.gz -dm=design.mat -cs=design.grp -tc=design.con -fe However, flame complains that not all compulsory arguments have been provided. I guess I need a varcope file and a mask file. How can I generate these, given that I am dealing with a surface format file? Thanks very much in advance for your help. Best regards, Henry ________________________________ Henry Lütcke Biomedizinische NMR Forschungs GmbH am Max-Planck Institut für Biophysikalische Chemie Am Fassberg 11 37077 Göttingen Germany Phone: +49-(0)551-201 1735 Mobile: +49-(0)176-20808069 Mail: hluetck(a)gwdg.de

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Icosahedron nodes
by Emily Cooper 05 Dec '06

05 Dec '06

Dear FreeSurfer gurus, We are trying to conduct a simple group analysis, employing freesurfer. However, our aim is to use the software only up to the point where the functional data is projected to a common space, and from that point on export the data to a text file and conduct the analysis using an external mathematical package (R, http://www.r-project.org) We have received very useful information from this message board in the last 2 weeks assisting us in this endeavor, but are still stumped by part of the workflow. At this point, we have succeeded in projecting our functional files (AFNI format) to the FreeSurfer surface representation so that each individual functional data is project to the individual registered surface. Given that each individual surface has a different number of surface nodes, we reasoned that to conduct a group analysis, it would be necessary to project the functional data not to the individual surface of each participant, but instead, to the registered icosahedron representation. The documentation of mri_vol2surf states that using the "icoorder" option, will result in mapping to an icosahedron with *prespecified* sizes. Specifically, we have tried projecting to an ico with order 7 (documentation states 163842 nodes in this reprsentation). However, when using this option and outputting to a "paint" (.w) file, we do not get this number of nodes for the icosahedron. Instead, different subjects' icosahedrons have different numbers of nodes. This is evident when the paint file is converted to and ".asc" file via mris_convert. Before we continue, we would like to know if this is a bug in mri_vol2surf, in mris_convert, or perhaps not a bug at all (i.e., different icosahedrons may indeed have different number of nodes by design). Now that we find ourselves with no way to equate the number of nodes in each participants' surface representation we are faced with a quandary: How do we conduct the group analysis? It has been suggested to us that we use the surf2surf utility. The documentation of that utility mentions that both the src and target surfaces may be icosahedrons. If we do indeed need to use this utility, should we map data between icosahedrons, or would it be better to cut down one stage of interpolation and just directly project the surfaces of all subjects to one reference subject (e.g., subject b -> subject a, subject c ->subject a, and so on). Thanks for any assistance, Emily

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(no subject)
by Lichen Liang 05 Dec '06

05 Dec '06

Dear All, I tried to extract a surface from a MRI scan (T1, 1.5T) using Freesurfer 3.0.3 on a Linux computer. I just run "recon-all" script for the same scan 6 times (same computer, no human interaction). To my supprise, I got 6 different results ( different #triangles, #vertices). Go back to check the intermediate results, all T1.mgz, WM.mgz are identical, but lh.origdifferent. Can someone tell me why my results are not consistent? Thanks very much for your help. Li-Chen

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mri_vol2surf warnings
by Joongnam Yang 04 Dec '06

04 Dec '06

Hi all, When I ran mri_vol2surf to turn FSL output to a paint file that Freesurfer can read, I got the following error. WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented But the command ran through and paint files were produced. My question is, "Do I just ignore the warnings or are they serious?" Nam.

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new Intel Mac freesurfer distribution
by Nick Schmansky 04 Dec '06

04 Dec '06

Intel Mac owners, A distribution of Freesurfer is now available for the new Intel- processor Macs. It can be downloaded here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ Look for the file: freesurfer-Darwin-apple-i686-dev3-20061004.tar.gz To install it, copy it to /Applications, and then: tar zxvf freesurfer-Darwin-apple-i686-dev3-20061004.tar.gz To setup: setenv FREESURFER_HOME /Applications/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh This distribution is from our 'dev' (development) code base, so it is slightly different from the normal publicly distributed 'stable' release. A stable build release of this Intel Mac distribution (with associated install GUI) will coincide with the next stable build release (next month, hopefully). Nick

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regarding .plt files
by Chacko Cherian 04 Dec '06

04 Dec '06

Hello users, I am using the latest stable version of FreeSurfer and there are two files wm.plt and gm.plt which are created after the recon-all process.What do these signify and how do I open them? Thanks in advance Chacko. ____________________________________________________________________________________ Need a quick answer? Get one in minutes from people who know. Ask your question on www.Answers.yahoo.com

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error message during Fix Topology lh in 3T data
by Bum Seok Jeong 04 Dec '06

04 Dec '06

During Fix topology, error message showed. Would you please let me know what happened? Thanks for advance #-------------------------------------------- #@# Fix Topology lh Fri Dec 1 22:06:19 EST 2006 cp ../surf/lh.orig.nofix ../surf/lh.orig cp ../surf/lh.inflated.nofix ../surf/lh.inflated /gr/caseD00916/scripts mris_fix_topology -mgz -sphere qsphere.nofix -ga caseD00916 lh reading spherical homeomorphism from 'qsphere.nofix' using genetic algorithm with optimized parameters ************************************************************* Topology Correction Parameters retessellation mode: genetic search number of patches/generation : 10 number of generations : 10 surface mri loglikelihood coefficient : 1.0 volume mri loglikelihood coefficient : 10.0 normal dot loglikelihood coefficient : 1.0 quadratic curvature loglikelihood coefficient : 1.0 volume resolution : 2 eliminate vertices during search : 1 initial patch selection : 1 select all defect vertices : 0 ordering dependant retessellation: 0 use precomputed edge table : 0 smooth retessellated patch : 2 match retessellated patch : 1 verbose mode : 0 ************************************************************* INFO: assuming .mgz format $Id: mris_fix_topology.c,v 1.41 2006/02/06 19:41:59 nicks Exp $ $Id: mrisurf.c,v 1.453 2006/04/21 17:14:26 segonne Exp $ before topology correction, eno=-974 (nv=172934, nf=347844, ne=521752, g=488) using quasi-homeomorphic spherical map to tessellate cortical surface... Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 12 iterations marking ambiguous vertices... Too many intersected faces for face 142725 (71953, 71952, 70394) reading input surface /gr/caseD00916/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Linux b2_tm128.bwh.harvard.edu 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22:53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Dec 1 22:07:15 EST 2006 <210> /gr% ls 3T_spgr.nii caseD00916/ <211> gr% cat caseD0091 6/scripts/recon-all-status.log status file for recon-all Thu Nov 30 14:50:29 EST 2006 #@# MotionCor Thu Nov 30 14:51:05 EST 2006 #@# Nu Intensity Correction Thu Nov 30 14:51:55 EST 2006 #@# Talairach Thu Nov 30 14:53:33 EST 2006 #@# Intensity Normalization Thu Nov 30 14:54:02 EST 2006 #@# Skull Stripping Thu Nov 30 14:57:30 EST 2006 recon-all finished without error at Thu Nov 30 14:58:57 EST 2006 New invocation of recon-all status file for recon-all Thu Nov 30 15:04:52 EST 2006 #@# EM Registration Thu Nov 30 15:04:52 EST 2006 #@# CA Normalize Thu Nov 30 15:09:12 EST 2006 #@# CA Reg Thu Nov 30 15:10:26 EST 2006 #@# CA Reg Inv Fri Dec 1 00:12:14 EST 2006 #@# Remove Neck Fri Dec 1 00:13:14 EST 2006 #@# SkullLTA Fri Dec 1 00:14:49 EST 2006 #@# SubCort Seg Fri Dec 1 00:22:05 EST 2006 #@# ASeg Stats Fri Dec 1 01:06:04 EST 2006 #@# Intensity Normalization2 Fri Dec 1 01:19:19 EST 2006 #@# Mask BFS Fri Dec 1 01:24:25 EST 2006 #@# WM Segmentation Fri Dec 1 01:24:31 EST 2006 #@# Fill Fri Dec 1 01:32:10 EST 2006 #@# Tessellate lh Fri Dec 1 01:33:53 EST 2006 #@# Smooth1 lh Fri Dec 1 01:34:00 EST 2006 #@# Inflation1 lh Fri Dec 1 01:34:13 EST 2006 #@# QSphere lh Fri Dec 1 01:38:05 EST 2006 #@# Fix Topology lh Fri Dec 1 02:08:50 EST 2006 Linux 2.6.17-1.2157_FC5 #1 SMP Tue Jul 11 22 :53:56 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Dec 1 02:09:39 EST 2006

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Transforming a surface-based volume back to the 3D surface render
by Eric Moulton 04 Dec '06

04 Dec '06

Can I transform a surface-based volume back into its corresponding surface rendering using the transformation matrix used to create the surface-based volume to begin with? I'm using Freesurfer to register individual statistics generated by FSL onto the surface-map of an average brain, and then transforming these maps into mni305.cor.mgz space. At this point, I now have individual statistical surface maps in MNI space that have the benefit of Freesurfer's surface-based registration. From these MNI maps, I conducted a group analysis with FSL, resulting in a group zstat map I would like to transform back onto the average brain surface-map that I initially used to register the individuals. So basically, I need help transforming a volume in mni305.cor.gz space back onto its surface-based map. I was thinking of running mri_vol2surf, but I would need a register.dat file that contained the exact inverse parameters to go from surf->mni305. I could use tkregister2 to create a serviceable register.dat, but I'm certain that a perfect transformation is necessary for these surface-mapped volumes. How would I create this register.dat from mni305->surf, or is there a more direct way to accomplish this? Thanks, Eric Eric Moulton PhD Research Fellow P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2475 Fax: 617-855-3772 Any information, including protected health information (PHI), transmitted in this email is intended only for the person or entity to which it is addressed and may contain information that is privileged, confidential and or exempt from disclosure under applicable Federal or State law. Any review, retransmission, dissemination or other use of or taking of any action in reliance upon, protected health information (PHI) by persons or entities other than the intended recipient is prohibited. If you received this email in error, please contact the sender and delete the material from any computer.

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common space nodes
by Emily Cooper 01 Dec '06

01 Dec '06

hi, i'm trying to map the functional data from each of my subjects into a common space on the surface. i have moved my volume functionals into icosahedron space for two subjects and then converted to a .asc text file but the text files show that the two datasets have a different number of nodes (163519 and 163798). i did the same thing without the icosahedron as a trgsubject on vol2surf (presumably in sphere.reg space, then) and also got different numbers for different subjects. is there a way to map the functional data from different subjects on to the same number of nodes (ie. a common space)? and if so, would a particular node on one subject correspond to the same place on another subject? mri_vol2surf --src 003/bold/03.trim_action.100.intval.resam+orig.BRIK --src_type afni --srcreg 003/bold/register.dat --hemi rh --projfrac-avg 0 1 10 --trgsubject ico --icoorder 7 --out 003/surf/trim_action.100.intval.ico7.preconvert -out_type paint mris_convert trim_action.100.intval.ico7.preconvert.w trim_action.100.intval.ico7.asc s003:163519 nodes mri_vol2surf --src 002/bold/02.action.intval.resam+orig.BRIK --src_type afni --srcreg 002/bold/register.dat --hemi rh --projfrac-avg 0 1 10 --trgsubject ico --icoorder 7 --out 002/surf/02.action.intval.ico7 -out_type paint mris_convert 02.action.intval.ico7.w 02.action.intval.ico7.asc s002:163798 thanks, emily

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Talairach problem
by Akram Bakkour 01 Dec '06

01 Dec '06

Hi, I'm running everything on thigpen. setenv SUBJECTS_DIR /space/thigpen/8/users/akram/ADNI_processing I'm having trouble fixing the talairach of these 4 subjects: 005_S_0572 023_S_0030 116_S_0382 126_S_0405 I've tried: mri_convert brainmask.mgz brainmask.mnc mritotal -protocol icbm brainmask.mnc brainmask.xfm cp brainmask.xfm transforms/talairach.xfm This worked for a few other subjects which had similar talairach problems, but didn't work for these four. I tried loading them in tkregister2: tkregister2 --mgz --s $subject --fstal but the volume won't load. Any suggestions how to fix these talairachs? Thanks! Akram.

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