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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
by Elijah Mak 19 Aug '16

19 Aug '16

Dear Anastasia, I have also uploaded the file with the problem (22995_EM.zip), and this is how my config file looks like after modifications: set subjlist = (22995) set pathlist = (fmajor_PP) set ncpts = (7) set reinit = (1) Thanks again! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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Projecting FA map onto fsaverge surface
by Taha Abdullah 19 Aug '16

19 Aug '16

Hello All, I am trying to project FA map (dtifit_FA.nii.gz) and the endpt[1/2].pd.nii.gz from TRACULA onto fsaverage surface space. I was following instructions on http://web.mit.edu/fsl_v5.0.8/fsl/doc/wiki/FDT(2f)UserGuide.html, under FreeSurfer Registration, to create the various xfms files. Next, I registered the FA map to subject conformed space using flirt - flirt -in dtifit_FA.nii.gz -ref ../../mri/orig.nii.gz -applyxfm -init ./xfms_taha/fa2freesurfer.mat -out fa2FS.nii.gz Then, I used mri_vol2surf to project the registered FA map onto fsaverage surface with the following command. - mri_vol2surf --mov fa2FS.nii.gz --projdist-max 6 6 1 --cortex --hemi rh --trgsubject fsaverage --regheader taha_brain --reg ./xfms_taha/fa2freesurfer.mat --o FA_2fsavg_surf.mgh Upon viewing in freeview the fsavg rh.white surface and fa2FS.nii.gz (FA map in FreeSurfer space) did not allign properly. I have tried some variations wtihout any luck. I used the following command line for freeview. - freeview -f /usr/local/freesurfer/subjects/fsaverage/surf/rh.white:overlay=FA_2fsavg_surf.mgh -v fa2FS.nii.gz - Attached are some pics of the FA confomred map and fsaverage.rh.white surface Do I need a xfm file for taliarch allignment? Any advice or insight would be greatly appreciated. Thanks in advance, Taha *Terminal output: from mri_vol2surf* srcvol = fa2FS.nii.gz srcreg = ./xfms_taha/fa2freesurfer.mat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = fsaverage surfreg = sphere.reg ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 Done loading volume Computing registration from header. Using /usr/local/freesurfer/subjects/taha_brain/mri/orig.mgz as target reference. Loading label /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label Reading surface /usr/local/freesurfer/subjects/taha_brain/surf/rh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 6 6 6 using old Done mapping volume to surface Number of source voxels hit = 81606 Reading source surface registration /usr/local/freesurfer/subjects/taha_brain/surf/rh.sphere.reg Done loading source registration surface Reading target registration /usr/local/freesurfer/subjects/fsaverage/surf/rh.sphere.reg Done loading target registration surface Mapping Surfaces (taha_brain -> fsaverage) surf2surf_nnfr: building source hash (res=16). Surf2Surf: Forward Loop (163842) surf2surf_nnfr: building target hash (res=16). Surf2Surf: Reverse Loop (143161) Reverse Loop had 26084 hits Surf2Surf: Dividing by number of hits (163842) INFO: nSrcLost = 0 Done mapping surfaces nSrc121 = 107182, nSrcLost = 0, nSrcMulti = 35979, MnSrcMultiHits = 2.29979 nTrg121 = 142955, nTrgMulti = 20887, MnTrgMultiHits = 2.24882 Masking with /usr/local/freesurfer/subjects/fsaverage/label/rh.cortex.label Writing to FA_2fsavg_surf.mgh Dim: 163842 1 1 -- Taha Abdullah Department of Physiology Northwestern University Feinberg School of Medicine Masters of Science Physiology and Biophysics, Georgetown University 2015 Work: (312)-503-0413

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Re: [Freesurfer] error in manual edit by freeview
by 3110103623＠zju.edu.cn 19 Aug '16

19 Aug '16

Hi Doug and Ruopeng Can you receive pictures and brainmask.mgz file in attachment? I don't know why this slice mismatch with other slices, other files such as T1 and wm.mgz and other subjects works well. Thank you very much. Regards Cong > Date: Wed, 17 Aug 2016 10:49:35 -0400 > From: Douglas Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] error in manual edit by freeview > > I'm not sure what you are describing. Can you send a picture? > > > On 8/17/16 8:42 AM, ?? wrote: > > Hi dear all > > I am using freeview to edit segmentation, I found one slice in coronal view in brainmask.mgz mismatch with other slice, this slice obviously move down. WM and T1.mgz are normal, I don?t know how to move this wrong slice back. Any advice will be appreciated. > > > > thanks very much. > > CONG

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red and blue gradient color map for freeview
by Eun Young Choi 19 Aug '16

19 Aug '16

Hi all, I'd like to have a freeview color map that has both a red-yellow gradient and a blue-light blue gradient (the typical colors for positive and negative fcMRI correlations) and ideally no color for 0... None of the standard color maps in freeview work well and I can't seem to find one online. Has anyone created one? Or know where I can view the text file for the standard color maps that come with freeview, so I can create one myself? Thank you! Eun Young

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LME contrast 3 groups
by Sarah Hirsiger 19 Aug '16

19 Aug '16

Dear FreeSurfer experts, I would appreciate a confirmation regarding correctness of my approach. I am trying to run an LME model for three groups (group1=controls, group2 and group3) and two time points. I followed the tutorial on https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels <https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels> and adapted the four group example. However, I am not 100% sure if my adaption is correct and would appreciate your input. The design matrix for the model contains the following columns: 1) Intercept 2) time (tij) 3) one for Group2 and zero otherwise 4) column 3) .* time 5) one for Group3 and zero otherwise 6) column 5) .* time To test the null hypothesis of no group differences in the rate of change over time among the three groups I applied the following contrast: 0 0 0 1 0 0 0 0 0 -1 0 1 Is this contrast correct? In a second step, I would use the additional three contrasts to identify which groups were different: 0 0 0 1 0 0 and 0 0 0 0 0 1 and 0 0 0 -1 0 0 1 I really appreciate your help! Best wishes Sarah

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Watershed not updating .pial lines
by Katherine Damme 18 Aug '16

18 Aug '16

Hello Everyone! I have several structural images were too much dura was included into the wm calculation. (see recon-all_std for the standard processing image) I followed the skull strip instructions <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_freeview> and the gcut procedure made only minor changes, and so I used the watershed and lowered the threshold it removed the dura, but did not update the .pial files to match the updated edge. This is output to screen and command that I used recon-all -skullstrip -wsthresh 20 -clean-bm -subjid 31313422_15544 Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /root/Desktop Actual FREESURFER_HOME /usr/local/freesurfer -rwxr-xr-x. 1 root root 1432836 Aug 18 20:19 /root/Desktop/31313422_15544/ scripts/recon-all.log Linux kate.ad.wcas.northwestern.edu 2.6.32-642.3.1.el6.x86_64 #1 SMP Sun Jun 26 18:16:44 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux mv -f /root/Desktop/31313422_15544/mri/brainmask.mgz /root/Desktop/31313422_15544/trash #-------------------------------------------- #@# Skull Stripping Thu Aug 18 20:22:30 CDT 2016 /root/Desktop/31313422_15544/mri mri_watershed -T1 -brain_atlas /usr/local/freesurfer/average/ RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta -h 20 T1.mgz brainmask.auto.mgz Mode: T1 normalized volume Mode: Use the information of atlas (default parms, --help for details) Mode: Preflooding height manually specified ********************************************************* The input file is T1.mgz The output file is brainmask.auto.mgz Weighting the input with atlas information before watershed *************************WATERSHED************************** Sorting... first estimation of the COG coord: x=125 y=99 z=127 r=92 first estimation of the main basin volume: 3292184 voxels Looking for seedpoints 2 found in the cerebellum 18 found in the rest of the brain global maximum in x=142, y=84, z=82, Imax=255 CSF=20, WM_intensity=110, WM_VARIANCE=5 WM_MIN=110, WM_HALF_MIN=110, WM_HALF_MAX=110, WM_MAX=110 preflooding height equal to 20 percent done. Analyze... main basin size=24160470213 voxels, voxel volume =1.000 = 24160470213 mmm3 = 24160471.040 cm3 done. PostAnalyze...Basin Prior 0 basins merged thanks to atlas ***** 0 basin(s) merged in 1 iteration(s) ***** 0 voxel(s) added to the main basin done. Weighting the input with prior template ****************TEMPLATE DEFORMATION**************** second estimation of the COG coord: x=123,y=102, z=118, r=10759 iterations ^^^^^^^^ couldn't find WM with original limits - expanding ^^^^^^ GLOBAL CSF_MIN=0, CSF_intensity=9, CSF_MAX=71 , nb = 42714 RIGHT_CER CSF_MIN=0, CSF_intensity=10, CSF_MAX=51 , nb = 3276 LEFT_CER CSF_MIN=0, CSF_intensity=9, CSF_MAX=42 , nb = 2808 RIGHT_BRAIN CSF_MIN=0, CSF_intensity=9, CSF_MAX=76 , nb = 17694 LEFT_BRAIN CSF_MIN=0, CSF_intensity=4, CSF_MAX=74 , nb = 17946 OTHER CSF_MIN=0, CSF_intensity=31, CSF_MAX=52 , nb = 990 CSF_MAX TRANSITION GM_MIN GM GLOBAL before analyzing : 71, 57, 53, 75 after analyzing : 44, 57, 57, 61 RIGHT_CER before analyzing : 51, 53, 55, 80 after analyzing : 51, 54, 55, 60 LEFT_CER before analyzing : 42, 50, 56, 76 after analyzing : 42, 54, 56, 59 RIGHT_BRAIN before analyzing : 76, 57, 51, 75 after analyzing : 44, 57, 57, 61 LEFT_BRAIN before analyzing : 74, 57, 52, 73 after analyzing : 43, 57, 57, 61 OTHER before analyzing : 52, 66, 77, 92 after analyzing : 52, 73, 77, 77 mri_strip_skull: done peeling brain highly tesselated surface with 10242 vertices matching...75 iterations *********************VALIDATION********************* curvature mean = -0.012, std = 0.010 curvature mean = 75.699, std = 8.484 No Rigid alignment: -atlas Mode Off (basic atlas / no registration) before rotation: sse = 3.12, sigma = 4.24 after rotation: sse = 3.12, sigma = 4.24 Localization of inacurate regions: Erosion-Dilation steps the sse mean is 3.19, its var is 3.44 before Erosion-Dilatation 0.12% of inacurate vertices after Erosion-Dilatation 0.00% of inacurate vertices Validation of the shape of the surface done. Scaling of atlas fields onto current surface fields ********FINAL ITERATIVE TEMPLATE DEFORMATION******** Compute Local values csf/gray Fine Segmentation...50 iterations mri_strip_skull: done peeling brain Brain Size = 2108315 voxels, voxel volume = 1.000 mm3 = 2108315 mmm3 = 2108.315 cm3 ****************************** Saving brainmask.auto.mgz done cp brainmask.auto.mgz brainmask.mgz #------------------------------------------ Started at Thu Aug 18 20:22:28 CDT 2016 Ended at Thu Aug 18 20:22:49 CDT 2016 #@#%# recon-all-run-time-hours 0.006 recon-all -s 31313422_15544 finished without error at Thu Aug 18 20:22:49 CDT 2016 done Thank you!

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Freesurfer 6.0?
by Trisanna Sprung-Much 18 Aug '16

18 Aug '16

Hi there Do we have a potential date for the Freesurfer 6.0 release? I was told I would want to re-run all my subjects to create better surfaces using Freesurfer 6.0 and I am wondering if it really will improve surface extraction that much. Many thanks! Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology

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Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS
by Elijah Mak 18 Aug '16

18 Aug '16

Thanks for the tips on reinitialisation of tracts. Apologies if I might have missed it in the online tutorial, do you have some general guidelines for reinitialising? Can I simply add "set reinit =1" to my configuration file, and then re-run trac-all -path. Are there any other parameters I could tweak? After running through more QC on other subjects, I have also noticed other tracts that were not fully constructed. These tracts appear to be truncated or blob-like, for a lack of better word :) I have attached the screenshot to illustrate what I mean. In these cases, I do the following QC routine after the general recon-all QC 1) freeview -v dmri/dtifit_FA.nii.gz -v dlabel/diff/aparc+aseg.bbr.nii.gz 2) freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz subjectname/dmri/cvs/dtifit_FA.bbr.nii.gz Thanks a lot for your help, Anatasia! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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label analysis
by Raffaele Dubbioso 18 Aug '16

18 Aug '16

Dear Freesurfer team, I'm working on structural data analysis using Fressurfer. I have drawn my own labels and now I'd like to get data like thickness, curvature, folding index in the same way that I usually get when I run the aparc.stat function. Can you please help me how to solve this problem? Thanks a lot and looking forward to hearing from you Best regards, Raffaele

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TRACULA - difference in tracts using MNI vs CVS
by Elijah Mak 18 Aug '16

18 Aug '16

Dear Anastasia and List, I have been using TRACULA to process my DTI dataset using both the affine MNI and non-linear CVS options. In one subject, the forceps major (MNI) look very different from its CVS counterpart (screenshot attached). I am just wondering what could lead to this type of differences? I've checked the registrations and they look good (overlaying FA on MNI/CVS). Thanks! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

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