Freesurfer

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30098 discussions

glmfit and glmfit-sim after built monte-carlo simulation (superiortemporal label)
by Pedro Rosa 14 Apr '16

14 Apr '16

Dear list, I want to limit my vertex-wise group analysis to a smaller spatial region, then I ran my own Monte-Carlo simulation on fsaverage for the superior temporal gyrus: mri_mcsim --o lh/superiortemporal --base mc-z --surface /fsaverage lh --nreps 10000 --label superiortemporal After 36 hours, it finished and I pasted the resulting into $FREESURFER_HOME/average/mult-comp-cor/fsaverage, and ran glmfit: mri_glmfit --glmdir glmdir --y lh.thickness.5.mgh --fsgd table.fsgd --C contrast.mtx --surface fsaverage lh --label /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label It seems it ran only on the label, as expected. However I am not able touse this pre-cached simulation in mri_glmfit-sim. I tried: mri_glmfit-sim --glmdir glmdir --sim-sign abs --cache-dir $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/superiortemporal --no-sim mc-z.abs.th13 --cache-label /$FREESURFER_HOME/subjects/fsaverage/label/lh.superiortemporal.label ...but I get an error although the csd files are in /average/mult-comp-cor/fsaverage... path : ERROR: cannot find any csd files I tried several combinations of the text specified after --no-sim, but all I got is the error above. I though I should refer to my own simulation using --cache-dir, but it requires the --no-sim flag. Can anyone help me? Best, Pedro Rosa.

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DLPFC seed
by Raney, Talia L. 14 Apr '16

14 Apr '16

Hi all, I'm trying to do FC connectivity analysis using the dorsalateral prefrontal cortex as a seed. I checked the text file $FREESURFER_HOME/average/colortable_desikan_killiany.txt and it looks like DLPFC is not listed as a possible structure to do the FC analysis. I attempted to use lh-prefrontal and rh-prefrontal but selxavg3-sess fails because there's no volume/label in fsaverage that is associated with it. Any suggestions on what seeds I could use? Would I have to combine or parcellate other existing seeds? Thank you! Best, Talia

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Re: [Freesurfer] Viewing eroded structure after -seg-erode 1
by Elijah Mak 14 Apr '16

14 Apr '16

Thanks Doug. Do you mean loading the structure (i.e. LeftHippocampus2diff.mgz) on the orig.mgz as an overlay? I am able to do that but I can't seem to find an option for thresholding. Sorry if I misunderstood your original email. Best Wishes, Elijah

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Re: [Freesurfer] PET voxelwise
by Elijah Mak 14 Apr '16

14 Apr '16

Hi Doug, One more question about feeding the -reg to mri_vol2surf, please. I am specifying the registration .lta because I have made edits to it, mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5 --hemi lh --reg FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta --trgsubject fsaverage I get the following error: srcvol = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz srcreg = FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume Input reg is LTA type = 0 # LINEAR_VOX_TO_VOX nxforms = 1 mean = 0.0000 0.0000 0.0000 sigma = 1.0000 1 4 4 9.996573328971863e-01 -2.963314531370997e-03 2.600867860019207e-02 -2.005096435546875e+00 1.517883041479706e-18 9.935718178749084e-01 1.132032126188278e-01 -2.398274230957031e+01 -2.617694810032845e-02 -1.131644248962402e-01 9.932314157485962e-01 1.568508148193359e+01 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 src volume info valid = 1 # volume info valid filename = /Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 -2.328306436538696e-10 0.000000000000000e+00 yras = -1.862645149230957e-09 -2.991509973071516e-08 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 1.091393642127514e-10 cras = 1.471549987792969e+00 -1.038517761230469e+01 1.970146179199219e+01 dst volume info valid = 1 # volume info valid filename = /Users/MacPro/Documents/NIMROD_DTI/FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz volume = 256 256 256 voxelsize = 1.000000000000000e+00 1.000000000000000e+00 1.000000000000000e+00 xras = -1.000000000000000e+00 -2.328306436538696e-10 0.000000000000000e+00 yras = -1.862645149230957e-09 -2.991509973071516e-08 -1.000000000000000e+00 zras = 0.000000000000000e+00 1.000000000000000e+00 1.091393642127514e-10 cras = 1.471549987792969e+00 -1.038517761230469e+01 1.970146179199219e+01 fscale 0.150000 ERROR: source volume is neither source nor target of the registration This error does not appear when I use --regheader though? Best Wishes, Elijah

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Irregularity in white matter vertex spacing (freesurfer 6.0)
by Keith Jamison 14 Apr '16

14 Apr '16

We ran freesurfer 6.0 on some 0.8mm data and we are seeing patches of cortex with very sparse vertex coverage. I'm attaching an example (_fs60.png) showing a patch on the inferior bank of the calcarine sulcus. This particular issue doesn't seem to occur in freesurfer 5.3.0 (_fs530.png), which was run after downsampling anatomy to 1.0mm. Is this a known issue with 6.0? Is there a straightforward way to fix it? Similarly, in both versions we often see small "clumps" of really dense vertices (*_fs60_zoomed.png). Is there anything we can do to clean these up? For our application, we'd really like white-matter vertex spacing to be as "regular" as possible. Thanks! -Keith

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Re: [Freesurfer] mri_surfcluster issues
by Antonin Skoch 14 Apr '16

14 Apr '16

Dear Doug, thank you very much for the support. I am quite confused by this info about correcting of area of fsaverage clusters. Could you please clarify to me the following: How exactly the values of lh.area, lh.white.avg.area.mgh of fsaverage were computed? How the cluster area inside mri_surfcluster (and also mri_glmfit and mri_mcsim) is computed? How the correction for average subject is applied? I assumed that area belonging to particular vertex is computed by summing areas of faces originating in particular vertex divided by 3. The face areas are computed from vertex coordinates by the method (based on cross-product of vectors) http://stackoverflow.com/questions/26312570/calculate-surface-area-of-a-3d-… This is how the vertex area from surface file is computed inside PALM. Is the same method used in freeSurfer? I checked the values of lh.white vertex area computed in PALM and they do NOT correspond neither to lh.area, nor lh.white.area.mgh values. I am listing areas of 3 representative vertices of fsaverage white surface got from lh.white.avg.area, lh.area and computed from lh.white in PALM: vtx 50: lh.white.avg.area 0.4952, lh.area 0.589, PALM 0.5967 vtx 110: lh.white.avg.area 0.5533, lh.area 0.5198, PALM 0.5421 vtx 1000: lh.white.avg.area 0.6193, lh.area 0.3349, PALM 0.4305 Any clues why there is a difference? In cluster summary file, there are flags FixVertexAreaFlag 1 and FixSurfClusterArea 1. What is the significance of these flags? I tried to set --no-fix-vertex-area. The FixVertexAreaFlag got value 0, but the vertex areas produced by mri_surfcluster were the same. Is it possible to turn off also FixSurfClusterArea? I also found flags FixVertexAreaFlag and FixGroupSubjectArea in .csd files. Are there similar corrections applied to cluster size values in .csd files? Thank you in advance for help. Regards, Antonin Skoch > Dear FreeSurfer experts, > > I am using mri_surfcluster to compare results from PALM and FreeSurfer > cluster extent inference. > > I came across several issues in mri_surfcluster I cannot cope with. > > 1. > I observed that --mask option in mri_surfcluster does not prevent > cluster to growing outside the mask. > > When I run > > mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum > summary.txt --subject fsaverage --surf white --hemi lh --thmin 0 --ocn > cluster_summary.mgz --mask ./mask.mgh > > the cluster is growing outside mask and covers all surface including > non-cortical (masked) regions. > > Is this intended behavior? This behavior (allowing clusters leak > outside mask) seems strange to me since it could possibly influence > results of cluster-extent inference in case of mask-constrained analysis. This is happening because you are setting the threshold to 0. > > 2. > How behaves mri_glmfit-sim in permutation-based building > cluster-extent null distribution with mask? Is in this case also > allowed to clusters to leak outside mask? No > > 3. > Another issue is concerning reported cluster area. I tested > mri_surfcluster on data where overlay values > (lh.thickness.fsaverage.mgh) were set to 0 outside cortex mask (they > were non-zero also in some portion of non-cortical vertices). When I > set thmin to non-zero value in mri_surfcluster > > mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum > summary.txt --subject fsaverage --surf white --hemi lh --thmin 0.00001 > --ocn cluster_summary.mgz --mask ./mask.mgh > > I get cluster comprising (almost) all cortex, not leaking to > non-cortical areas. But what is strange, the reported cluster size is > far larger than area of the whole cortical surface. > > number of voxels in search space = 149953 > Done loading source values (nvtxs = 163842) > overall max = 5 at vertex 817 > overall min = 0 at vertex 8 > surface nvertices 163842 > surface area 65417.097656 > surface area 65416.648438 > NOT Adjusting threshold for 1-tailed test > Searching for Clusters ... > thmin=0.000100 (0.000100), thmax=-1.000000 (-1), thsignid=0, > minarea=0.000000 > Found 2 clusters > Max cluster size 76431.562500 > Saving cluster numbers to pok.mgz > > > Here is output of mri_surfcluster: > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ NVtxs > 1 5.000 817 76431.56 -25.8 4.6 -37.5 149874 > 2 2.670 144205 0.53 -15.8 -40.4 -3.8 1 > > How it is possible? The surface area of 65416.648438 has not been corrected for the fact that fsaverage is an average subject. The area in the summary table has been corrected. > > 4. > Does the fsaverage/surf/lh.area correspond to area of particular > vertices on fsaverage/surf/lh.white? I expect yes. The lh.area file does correspond. However, the area measures on the raw fsaverage surface are not accurate because the average surface has much less surface area due to averaging out the individual folding patterns. > > 5. > How it is possible to calculate area of specified vertex of surface? I > tried to do that by creating .label file with particular vertex number > and running > > mri_surfcluster --in lh.thickness.fsaverage_masked.mgh --sum > summary.txt --subject fsaverage --surf white --hemi lh --thmin 0.00001 > --clabel myVertex.label > > I indeed got report of 1 cluster with 1 vertex, with VtxMax value > identical to vertex index in myVertex.label > but the area value in summary.txt is different that value in > fsaverage/surf/lh.area. You can extract it out of ?h.white.avg.area.mgh using mri_segstats with the --slabel function. > > Thank you very much in advance for clarification, > > Antonin Skoch

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mri_vol2surf misaligment
by Francesca Strappini 14 Apr '16

14 Apr '16

Dear Freesurfers, I run the preprocessing step of some functional data with preproc-sess, then the Fourier analysis with matlab. Now, I'm trying to plot this data on the surface: mri_vol2surf --mov Katkov_OT_45.nii.gz --trgsubject MishaK --hemi lh --reg register.dof6.dat --o Katkov_OT_45_LH.nii.gz I used as registration matrix the one produced by the preprocessing step but when I try to visualize the map on the surface it looks like completely misaligned. Thank you Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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FSFAST (seed based correlation analysis)
by Alshikho, Mohamad J. 14 Apr '16

14 Apr '16

Hi Freesurfers, How can I perform seed based correlation analysis using PET images? In other words how can I use the same approach of FSFAST, but by including PET images instead of fmri images, to study the correlation between PET signal within a seed mask ( e.g precentral gyrus ) and the whole brain regions? What is the best approach to run this analysis? Best, Mohamad

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SNR calculation
by BAUTISTA-PERPINYA Maximilià 14 Apr '16

14 Apr '16

Hi experts, I wish to calculate signal-to-noise ratio (SNR) of my T1 MRI images. Do you know if I can use freesurfer for this? SNR = mean signal at ROI / standard dev. of background noise. The mean signal at ROI I can obtain from the aseg.stats table, but I cannot seem to find a value describing the standard dev. of the background noise. Does anybody know if freesurfer can output this? Otherwise, how would you recommend to calculate it? Thank you for your help. Best, Max

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Flipping Surface .mgh file to opposite hemisphere via fsav_sym
by Bastian Cheng 14 Apr '16

14 Apr '16

Dear Freesurfer-Experts, I am trying to flip surface files (.mgh) from right to left. I have read your instructions concerning xhemi and performed registration to fsaverage_sym: foreach subject (subjectlist) surfreg --s $subject --t fsaverage_sym --lh surfreg --s $subject --t fsaverage_sym --lh --xhemi end I would now like to flip surfaces containing fMRI-values (initally on the right hemisphere) to the left hemisphere for statistics in a common space. How do I achieve this? I have tried using mri_surf2surf with different side (--srchemi rh --trghemi lh) using the fsaverage_sym as subject. However would I not need a registration file rh.lh.sphere.reg for that? It doesn't work with using the left side as targed either (results are shifted and do not match the location on the original hemisphere) What am I doing wrong? I dont want to compare the right with the left hemisphere (I simply want to have all affected surfaces on one side of the brain). any help would be appreciated! Bastian

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