Freesurfer July 2009

freesurfer@nmr.mgh.harvard.edu

85 participants
135 discussions

bbregister and surface overlay on EPI
by Praneeth Namburi 25 Jul '09

25 Jul '09

Hello Dr. Greve, I used the bbregister tool to register a BOLD EPI volume to the surface with the --init-fsl option. The result looks good in tkregister2. Using the resulting .dat file, I am trying to express the vertex coordinates of the surface in EPI voxel space (EPI volume: 128 x 128 x 36 matrix, limits: -64 to 64, -64 to 64 and -18 to 18). Given the following 4x4 matrices, vox2ras_epi : vox2ras transformation matrix from the EPI volume header bbregMat : transformation matrix from the .dat file created from bbregister command Given the vertices of the subject's surface (nVert x 4) : srfVert I used the following transformation to express the surface in EPI voxel coordinates: srf_epiVox = srfVert * inv(bbregMat) * inv(vox2ras_epi) When I view the results of this transformation in MATLAB, I can see that the above expression is incorrect. I used imagesc to show one slice of EPI and scatter to plot of all the vertices in that slice. Can you please let me know what the mistake is? Am I applying the transformation in an incorrect coordinate space? Am I missing any transformations? Looking forward for your reply. Thank you. Yours Sincerely, Praneeth

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clusterwise correction for multiple comparison
by Rosa Steimke 24 Jul '09

24 Jul '09

HI! i have a question regarding multiple comparion correction in qdec. can i use a clusterwise correction? i found the following script for glm: mri_glmfit-sim \ --glmdir lh.gender_age.glmdir \ --sim mc-z 5 4 mc-z.negative \ --sim-sign neg \ --overwrite but i dont understand how i should apply it in qdec. what shoudl i use as input directory? rosa -- GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT! Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01

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qdec question
by Prapti Gautam 24 Jul '09

24 Jul '09

Dear Freesurfers, I just have some quick questions regarding qdec: 1. How many covariates does the latest version of qdec allow you to select? I am using FS version 4.3.0 and I cannot select more than 2 continuous variables. I am just wondering if a newer version allows you to select more covariates. 2. Does qdec allow you to choose between study designs DOSS and DODS? I currently do not see this option and I think my current version of qdec defaults to the DODS option. Thank you for your time, Prapti

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mris_expand
by Lars Tjelta Westlye 24 Jul '09

24 Jul '09

Hi, how can I tell mris_expand to expand the surface by a fixed distance rather than by a fraction of the thickness? Thanks, Lars

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Re: [Freesurfer] freesurfer's template for sphere registration
by Zhong Jidan 24 Jul '09

24 Jul '09

Hi Bruce, Thanks for your reply. I'm not clear about two points you mentioned. ->To represent a folded surface we either (1) map to an individual subject, or (2) use a volume transform such as tal and the vertex correspondence from the sphere.reg to find the average coordinate of a vertex. This is how we build the fsaverage and average7 surfaces. For the (2) point, what do you exactly mean? I‘m confused. I thought your fsaverage is derived by averaging 40 subjects' volume image and then reconstruct the surface based on that. How can I use a volume transform such as tal and the vertex correspondence from the sphere.reg to find the average coordinate of a vertex? I'm totally lost with this sentence.. ->You can use the mapping to paint the geometry of one subject onto another folded surface if you want to visualize the geometric mapping (e.g. the curv of one subject on the white surface of another). For this one, I think you mean that, I can use one white surface as a base. Then paint the curvature information on the white surface to see the geometry. But this is not I want... To be specific, if I have a lh.sphere, lh.sphere.reg, they share the curvature information, and the only difference is the spherical coordinates. Then it is non sense to paint the curvature information to another white surface to see the geometry because there is only one .curv file. Another problem is, this lh.sphere may have different number of points with the white surface. ... Not sure whether I understand it correctly, hope for your suggestion. Thanks, Jidan On Tue, Jul 21, 2009 at 8:26 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Jidan, > > the atlas only exists in spherical coords. To represent a folded surface we > either (1) map to an individual subject, or (2) use a volume transform such > as tal and the vertex correspondence from the sphere.reg to find the average > coordinate of a vertex. This is how we build the fsaverage and average7 > surfaces (we know this is a hack, but it's easy and a good visualization > tool). > > You can use the mapping to paint the geometry of one subject onto another > folded surface if you want to visualize the geometric mapping (e.g. the curv > of one subject on the white surface of another). > > > cheers, > Bruce > > > > On Tue, 21 Jul 2009, Zhong Jidan wrote: > > Hi Freesurfer experts, >> >> I asked this question previously, but I found it problematic when >> displayed >> in your mailist. I'm sorry that the question still not solved and I feel >> sorry to trouble you again. >> >> In your sphere registration in freesurfer, the procedure is like: >> creating >> the template.tif by mris_make_template. The template you use in >> Freesurferis created by iterative registration of 40 subjects, >> >> according to >> "High-resolution inter-subject averaging and a coordinate system for the >> cortical surface, Fischl, B., Sereno, M.I., Tootell, R.B.H., and Dale, >> A.M., >> (1999). Human Brain Mapping, 8:272-284(1999)". >> So, after the template generation process, you will get a .tif file which >> include the necessary infomation (like the means and variances of curv, >> sul >> from the aligned spheres). But,do you have the other information of this >> final template, such as the sphere representation, folded surface >> representation of this template? I know that under >> */subjects/fsaverage/surf, there are some surface representations of the >> average of the 40 subjects, but to my knowledge, they are just used for >> visulazation and are not the surface representation of the template.tif >> you >> used, am I right? >> >> 2, subjects' sphere registration to the template sphere >> In this process, we can get the deformed subjects spheres( *.reg ), >> which >> have a one-to-one correspondance to the original subject surfaces. Except >> the .reg sphere with the cuvature information, do you have any other form >> of >> representation of the deformed sphere? You know that there are other >> kinds >> of surface mapping methods, like Miller's Large Defformation deffeomrphic >> surface mapping, they just do surface mapping using the folded surfaces. >> After surface mapping, they will get the deformed folded surface which >> would >> be aligned with the template folded surface. With the deformed subject >> and >> template folded surfaces, they can tell directly which sulcus or gyrus is >> aligned well. So, for your mapping, when I get the deformed sphere, do >> you >> have any command or method to put the sphere back to the folded surface so >> I >> can see the suci and gyri directly? If you also have the surface >> representation of the template, then i can superimpose them to see how >> good >> the alignment is. >> >> If you think I didn't state this problem clearly, please refer to an >> example >> in the following: >> >> I found one reference using your sphere registration method. "Simpliÿÿed >> Intersubject Averaging on the Cortical Surface Using SUMA"Brenna D. >> Argall, >> Ziad S. Saad,and Michael S. Beauchamp"Human Brain Mapping 27:14 >> ÿÿ27(2006)" >> You may see the attachment in : >> >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-May/010558.html >> >> >> In "Spherical Morphing" section, They mentioned that " Using the >> mris_register [Fischl et al., 1999b] routine, each individual subjectÿÿs >> surface was registered to the FreeSurfer average7 template prior to node >> number standardization. Standardization and averaging were then performed >> on >> the surfaces as described above" (using SUMA FYI). >> ---- From this part, I assume that all the deformed surfaces are in >> spherical representation. >> >> Then in the result part, in section "Intersubject Averaging of Functional >> Data: Different Surface Methods", they mentioned they " in order to >> compare >> the ACÿÿPC method to these more complex algorithms, the FreeSurfer program >> >> mris_register [used in Fischl et al., 1999b] was used to morph the >> cortical >> surface models to a predeÿÿned template, and these morphed surface models >> were then used to create a morphed surface average." >> >> In Fig7C ÿÿAverage surface created by averaging the same 28 subjects using >> >> mris_register standardization. You can see that they show the average >> surface in a folded surface representation, not a sphere. >> >> Could you give me a hint that how they do this since you only have a >> sphere >> representation of the aligned surface? >> >> >> -- Regards, Jidan

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Three classes and GLM
by Georg Homola 23 Jul '09

23 Jul '09

Hi all, I'm having some problems getting a second level fixed effects analysis started on my subjects. There are three runs (dofsum = 884) in each case I'd like to compare. OSGM works fine so far, but when I apply a matrix like this: 1 0 0 0 1 0 0 0 1 To a contrast like that: 0.5 0.5 -1 mri_glmfit tells me: ERROR DOF = 0. I also tried it with an FSGD file, so my approach was the same as for the Fsgdf3G0V example (http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) That makes no difference. When I divide the three runs into two classes, everything works fine again. But why the error with three classes? Any ideas? Thanks, Georg $ mri_glmfit --surf 01 lh --y 01/gender.lh.cope1.sm05.mgz --yffxvar 01/gender.lh.varcope1.sm05.mgz --ffxdof 884 --glmdir 01/results/gender.sm05.lh --X xmat.mat --C test.mat --label $SUBJECTS_DIR/01/label/lh.cortex.label Reading source surface /data/freesurfer/01/surf/lh.white Number of vertices 149696 Number of faces 299388 Total area 96879.085938 AvgVtxArea 0.647172 AvgVtxDist 0.880017 StdVtxDist 0.256396 $Id: mri_glmfit.c,v 1.138.2.10 2009/05/18 15:41:44 greve Exp $ cwd /data/freesurfer/higher/highest/fixed cmdline mri_glmfit --surf 01 lh --y 01/gender.lh.cope1.sm05.mgz --yffxvar 01/gender.lh.varcope1.sm05.mgz --ffxdof 884 --glmdir 01/results/gender.sm05.lh --X xmat.mat --C test.mat --label /data/freesurfer/01/label/lh.cortex.label sysname Darwin FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /data/freesurfer/higher/highest/fixed/01/gender.lh.cope1.sm05.mgz logyflag 0 X xmat.mat usedti 0 labelmask /data/freesurfer/01/label/lh.cortex.label maskinv 0 glmdir 01/results/gender.sm05.lh IllCondOK 0 DoFFx 1 FFxDOF 884 yFFxVar /data/freesurfer/higher/highest/fixed/01/gender.lh.varcope1.sm05.mgz Creating output directory 01/results/gender.sm05.lh Loading y from /data/freesurfer/higher/highest/fixed/01/gender.lh.cope1.sm05.mgz Loading yffxvar from /data/freesurfer/higher/highest/fixed/01/gender.lh.varcope1.sm05.mgz Saving design matrix to 01/results/gender.sm05.lh/Xg.dat Matrix condition is 1 /data/freesurfer/01/label/lh.cortex.label /data/freesurfer/01/label/lh.cortex.label Found 141245 points in label. Pruning voxels by thr: 0.000000 Found 141245 voxels in mask Saving mask to 01/results/gender.sm05.lh/mask.mgh search space = 91409.8 DOF = 0 ERROR: DOF = 0

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problems with qdec
by Paula Diniz 23 Jul '09

23 Jul '09

Hello I`m problems with the levels files. The error is : Loading data table /Users/paula/Freesurfer_ELT_primeiro_trabalho/qdec/qdec.table.dat... Number of columns: 5 fsid column: 1 Number of factors: 4 Number of subjects: 52 Reading discrete factor levels from config file /Users/paula/Freesurfer_ELT_primeiro_trabalho/qdec/gender.levels 'Female', done ERROR: 0xbfffa334 is invalid. Must have at least two levels. Error loading the data table. where is the problem? What I have to do? Thanks -- ================================== Paula Rejane Beserra Diniz Bacharel em Informática Biomédica Mestre em Neurociências Doutoranda em Neurociências Universidade de São Paulo Hospital das Clínicas - Ribeirão Preto ==================================

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Cluster correction for multiple comparisons using mri_glmfit-sim
by Devdutta W 23 Jul '09

23 Jul '09

Hi, I just ran the mri_glmfit-sim command on our data and there were a couple of things I did not understand. We had previously ran the same command on fewer subjects and it had taken about 10 days to run. This time around it only took 2 days even though we had more subjects (there don't seem to be any errors; it just finished sooner). Another thing I noticed was that previously the command wrote several folders (ones that measured thickness, sulc, area, etc. both average and difference between the subject groups) into the output folder we specified in the "glmdir" option. This time it only wrote one (just the average thickness). As far as I can tell, I followed the command exactly as before (copied and pasted the command) with the same number of interations. I also followed the Group Analysis tutorial from the wiki. Can anybody shed some light on this? Why this discrepancy between the two? Thank you, Devdutta

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declaring spherical ROIs centered at common Talairach coord.
by Stephen Towler 23 Jul '09

23 Jul '09

We want to extract a spherical ROI of cortical thickness values centered at the same Talairach coordinate for each brain in a study. Any suggestions? In the 2007 archives there is an instructive thread about declaring spherical ROIs on a volume, but I'm not clear about how we would place the initial point at the same Talairach coordinate in every participant. Thanks, Stephen

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Customised color bar in tksurfer
by 류철형 23 Jul '09

23 Jul '09

Dear all 1. I would like to display average thickness on surface model in tksurfer. The basic color bar included the tksurfer seems to be insufficient for displaying thickness difference (e.g. red to yellow etc.). I'd like to use rainbow color table in displaying the thickness result. How can I make this in tksurfer? or Should I use another utility for displaying purpose (e.g. surfstat)? 2. The y.mgh file contains thickness data of all subjects, I guess. Then, when the y.mgh file is imported and overlayed on the surface in tksurfer, does the displayed color represent the average thickness in y.mgh file subjects? Best Wishes >From Lyoo

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Freesurfer July 2009