Freesurfer August 2011

freesurfer@nmr.mgh.harvard.edu

124 participants
212 discussions

Re: [Freesurfer] register data to the surface
by Douglas N Greve 22 Aug '11

22 Aug '11

This is not the correct procedure. Try looking at the multi-modal integration tutorial on our web site. Basically you should not register the difference image. Instead, register the middle time point of the raw data of the fMRI to the anatomical. Motion correct the time series to the middle time point. When you analyze the data in whatever way you are using, analyze the motion corrected data. You can then use the registration computed from the raw data for anything derived from the motion corrected data. doug francesca strappini wrote: > Yes, It's a whole brain acquisition and the functional and the > anatomical data come from the same subject. > I try to explain all the story. I acquired 12 runs of polarangle per > subject in two different days. I have 3 conditions and 4 runs for > every condition. In each day the subjects did all the conditions (6 > runs per day). > I calculated a sort of subtraction between these conditions, > unfortunately it's not a simple subtraction and for this reason I > didn't use fscalc. What I tried to do is to register this subtraction > to the surface but the process failed probably because the result of > the subtraction is as very small activation only in the occipital > cortex (in fact the conditions are slightly different). > Do you think that is there something else that I can try? > > Thanks! > > > Francesca > -- 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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FW: Occipital Flattening
by Tax, C.M.W. 22 Aug '11

22 Aug '11

Dear all, I tried to cut the occiput surface with Freesurfer. When I follow the manual on the Wikipage and description found here http://www.alivelearn.net/?cat=10 (Line cut trough the calcarine sulcus, surface cut placing 2 points on the medial side, 1 on the lateral side and a fourth point to specify which part I want to keep) I get the following error when clicking the 'cut surface' button: surfer: poffset = 205895.000000, sign = 165453.718750, n = {-703.239014,-3109.317627,-1290.049561} % tksurfer.bin: tnl/t_vertex.c:407: update_input_ptrs: Assertion `a[j].inputstride == vptr->stride' failed. Aborted Please could you help me with this problem? Thank you in advance, Kind regards, Chantal

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Re: [Freesurfer] DOSS or DODS
by Tetiana Dadakova 22 Aug '11

22 Aug '11

Hello Douglas, I did as you suggested and I got the results, but I still have difficulty understanding how exactly the choice of Design Matrix Type influences the analysis, so I have several questions: 1. When I look at thickness difference between two groups and choose age as nuisance parameter, doesn't it mean that calculation take into account the difference in slopes already (as I correct for age)? So therefore, when I also choose DODS or DOSS I do kind of double correction (matrix type + nuisance), don't I? 2. When I choose e.g. DODS and do the analysis, can I see the slopes (or the values of slopes) for two groups somehow? In which file this output is? 3. Can you recommend me anything to read regarding mathematics of how the analysis is done with either matrix type? 4. Just in case you know: how is this step implemented in SPM? It also uses glm, but it doesn't ask for the DODS vs DOSS choice. Thank you, I appreciate you time and help, Tanja. On Wed, Aug 17, 2011 at 6:19 PM, Tetiana Dadakova <tetiana.d(a)gmail.com> wrote: > Thank you, Douglas. > > On Wed, Aug 17, 2011 at 5:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu> wrote: >> >> Hi Tanja, you should use DODS and test for a difference between the age >> slopes of the groups (ie, an interaction between group and age). If there >> are no significant interactions, you should then use DOSS to test for the >> difference between thicknesses. >> doug >> >> Tetiana Dadakova wrote: >>> >>> Dear all, >>> >>> I have two groups of subjects, and I want to see a difference in >>> thickness between them controlling for age. >>> I couldn't find any information in the literature on how the subject's >>> brains in my groups develop with age. Therefore I can't tell whether >>> thickness as a function of age for both groups has the same slope or >>> different. >>> >>> My question is if in this case I should use DODS? >>> >>> Thank you, >>> Tanja. >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> >> >> -- >> 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 >> >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >

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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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Freesurfer August 2011