Freesurfer

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30132 discussions

Transforming freesurfer meshes to FSL coordinates
by Todd Krieg 22 Aug '11

22 Aug '11

I am trying to use the output meshes from freesurfer (lh/rh.pial and lh/rh.white converted to .stl) with the BET meshes from FSL. They seem to be in different coordinate systems and have to be moved and scaled to match correctly. Is there an easy transform that can do this. I have tried several with no success. ---Todd Krieg Illinois Institute of Technology

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V1 on fsaverage
by Ritobrato Datta 22 Aug '11

22 Aug '11

Hi Is it possible to estimate the V1 boundary on fsaverage using Hinds method ? Thanks Ri

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Re: [Freesurfer] Avg.Thickness in a cluster
by Douglas N Greve 22 Aug '11

22 Aug '11

Does cluster cover the exact same region in the group map as in the individual? Even if you choose the same nominal region (eg, posterior cingulate) you will not get the same exact number when you do it in fsaverage space as when it is done in the native space. doug Antonella Kis wrote: > Dear Doug, > > I just checked my results for the average thickness from each subject > generated in the csdbase.y.ocn.dat file in different clusters (e.g. I > have 5 clusters for p<0.05). For cluster #1 - posteriorcingulate, the > average thickness for subject 1 is different from the average > thickness value in the same region-posteriorcingulate, in the > lh.aparc.stats for the same subject. I thought it should be the same. > Why they are different? Is this right? > > > MANY THANKS! > Antonella > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Coordinate transformations from orig/001.mgz to T1.mgz
by raij＠nmr.mgh.harvard.edu 22 Aug '11

22 Aug '11

Hi, We (Aapo Nummenmaa and I) are developing cross-platform software that would allow translating third-party coordinates back and forth with Freesurfer segmentations. Our example structural image is MEMPRAGE_4e_p2_1mm_iso (1 mm isotropic, 192 sagittal slices, T1 weighting). Our third-party system (TMS-navigator Nexstim NBS) uses DICOM/nifti with origin (0,0,0) at right posterior inferior corner of the stack with x=R-L y=I-S z=P-A. Our goal is to relate the Nexstim NBS coordinates to these two images: 1. $SUBJECTS_DIR/$SUBJECT/mri/orig/001.mgz (not altered by recon-all) 2. $SUBJECTS_DIR/$SUBJECT/mri/T1.mgz (altered by recon-all) For (1) above, "Volume Index" in tkmedit looks like this: origin (0,0,0) is at right anterior superior corner of the stack with x=A-P y=S-I z=R-L. Max values in tkmedit display were (255,243,191). The acquisition had 192 sagittal slices so the last number makes sense - not sure why the second figure is not 255 (perhaps just a display thing). The orig/001.mgz stack should be exactly the same stack as in the Nexstim NBS image (which is just the plain DICOM), without any resampling or other processing, just the axes have been reshuffled a bit. For (2) above, "Volume Index" in tkmedit looks like this: origin (0,0,0) is at right posterior superior corner of the stack with x=R-L y=S-I z=P-A. Max values in tkmedit display were (255,255,255). This makes things difficult, as we do not know what exactly recon-all did to orig/001.mgz when it converted it into T1.mgz. Our question is this: Is there a deterministic way to go from orig/001.mgz to T1.mgz Volume Index coordinates? It seems that recon-all has at least added sagittal slices to make the T1.mgz stack into a cube (looking at lateral shift between 001.mgz and T1.mgz, I would guess that 32 1-mm slices on both sides (2*32+192=256) were added)... Further, it is not clear if the orig/001.mgz volume has been shifted, rotated, or resampled by recon-all when turning it into T1.mgz. Thank you for the advice! Bests, Tommi & Aapo

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cortical thickness in freesurfer 3.02 vs 4.5
by Rune X 22 Aug '11

22 Aug '11

Hi, We are concerned about differences of cortical thickness when we process the same scans in freesurfer 4.5 and 3.02. We have attached an excel spreadsheet of the differences in thickness between 4.5 and 3.02 using the mean thickness of parcellations of both versions in both hemispheres. The difference in the paracellations vary from 3-11% between the versions. Are these findings reliable and explainable in choosing freesurfer 4.5 as our final version. Any comment are greatly appreciated, Thanks! Rune

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pial and WM missing after reunning skullstrip
by Julia Hill 22 Aug '11

22 Aug '11

Hi Bruce I am new to freesurfer and im having a few issues with a number of my scans. The cerebellum and sections of the occipital lobe seems to be cut off on a number of subjects, so i went in and altered the skull stripping by increasing the watershed threshold to 35 and using -no-wsgcaatlas. When i review the scans afterwards, the pial and WM surfaces haven't included the original missing sections of the scans. How do i go back and include these missing sections? I have attached a screenshots. Thank you kindly Julia Julia Hill Research Assistant School of Psychiatry University of New South Wales Previously Prince of Wales Medical Research Institute www.NeuRA.edu.au Barker Street Randwick Sydney NSW 2031 Australia PO Box 1165 Randwick Sydney NSW 2031 Australia T +61 2 9399 1268

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recon-all error messages
by Catherine Wan 19 Aug '11

19 Aug '11

Dear List, I've been encountering a series of error messages when I did recon-all on a number of subjects, using Freesurfer v5.1 Below are the error messages for 3 different subjects (all with lesions). I tried them using both dicom and nifti, and on various computers, but the same messages appeared. Any advice would be much appreciated. Many thanks! Catherine *SUBJECT 1* Correction of the Topology Finding true center and radius of Spherical Surface...done Surface centered at (0,0,0) with radius 100.0 in 15 iterations marking ambiguous vertices... 188852 ambiguous faces found in tessellation segmenting defects... 1 defects found, arbitrating ambiguous regions... analyzing neighboring defects... 1 defects to be corrected 0 vertices coincident reading input surface /mnt/nfs/hippo1/freesurfer5/freesurfer/subjects/Aphasia_MIT/DMAR_pre1_nii/surf/lh.qsphere.nofix... reading brain volume from brain... reading wm segmentation from wm... Computing Initial Surface Statistics -face loglikelihood: -10.1436 (-5.0718) -vertex loglikelihood: -8.7336 (-4.3668) -normal dot loglikelihood: -3.6140 (-3.6140) -quad curv loglikelihood: -7.5212 (-3.7606) Total Loglikelihood : -30.0124 CORRECTING DEFECT 0 (vertices=98583, convex hull=1425) Excessive topologic defect encountered: could not allocate 1019599903 edges for retessellation Cannot allocate memory *SUBJECT 2* mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated avg radius = 51.9 mm, total surface area = 58524 mm^2 writing inflated surface to ../surf/lh.inflated writing sulcal depths to ../surf/lh.sulc step 060: RMS=0.039 (target=0.015) inflation complete. inflation took 0.3 minutes mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 ../surf/lh.inflated normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm Segmentation fault *SUBJECT 3 *(stuck on this step for > 48 hrs) CORRECTING DEFECT 0 (vertices=130, convex hull=179) After retessellation of defect 0, euler #=-30 (62919,184624,121675) : difference with theory (-51) = -21 CORRECTING DEFECT 1 (vertices=46, convex hull=64) After retessellation of defect 1, euler #=-29 (62936,184700,121735) : difference with theory (-50) = -21 CORRECTING DEFECT 2 (vertices=75, convex hull=105) After retessellation of defect 2, euler #=-28 (62974,184859,121857) : difference with theory (-49) = -21 CORRECTING DEFECT 3 (vertices=54486, convex hull=3968)

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bug report tracula stage 2
by Knut J Bjuland 19 Aug '11

19 Aug '11

Hi I have started to run tracula on my own data. However when I run the second stage I get this erros bedpostx_seychelles: line 260: /media/Elements/freesurfer/dti/1/dtsave/1/dmri.bedpostX/monitor: Permission denied. I have tried running is as root as well but it did not help. Is there anything I can do to bypass thiss error. I am using Fedora 15. Knut J

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qdec: Measure: area vs area.pial
by Tetiana Dadakova 19 Aug '11

19 Aug '11

Dear list, In qdec in "Measure" option I can choose either area or area.pial. What is the difference between them? Thank you, Tanja.

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Talairach error
by Ahmed, F, Me <fahmed＠sun.ac.za> 19 Aug '11

19 Aug '11

Hello Freesurfers, I got this error on my processing and wondered what the problem may be: Talairach Failure Detection Mon Aug 15 16:26:35 SAST 2011 /mnt/hgfs/VBM/freesurfer_EONCS/EONCS/NN117/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Linux localhost.localdomain 2.6.18-8.1.8.el5 #1 SMP Tue Jul 10 06:50:22 EDT 2007 i686 i686 i386 GNU/Linux recon-all exited with ERRORS at Mon Aug 15 16:26:35 SAST 2011 Any help would be greatly appreciated! Kind regards, Fatima

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