Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

motion threshold
by Mürner-Lavanchy, Ines 26 Sep '12

26 Sep '12

Dear FreeSurfers, Due to motion I have to exclude participants from my analysis. Is there an objective measure which could serve as a cut off value concerning motion in the scanner? Can I find it in one of the FreeSurfer files generated through the recon-all process? Subjectively, one can see which images are good or good enough for segmentation. But I'd rather like to include or exclude participants based on an objective threshold. Thank you very much in advance, Best regards, Ines

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Reconstructed skull malformations
by Vancelette, Reid Vincent 25 Sep '12

25 Sep '12

Hi group, I recently reconstructed a high-resolution 3D T1-weighted structural MRI using Freesurfer. The subject had non-metallic extensions that were tied to her head through a series of braids. Looking at the MRI in TkMedit, I can noticeably see pieces of the extensions above her scalp. My group performs MR-constrained MEG/EEG analyses and use the outer surface of the scalp as well as the outer and inner surfaces of the skull from the Freesurfer reconstructed MRI to calculate a forward solution. Looking at the scalp, I notice large convolutions and indentations in the reconstructed skull in an MNE program: mne_analyze. My suspicion is that the hair extensions that appear in the reconstructed MRI are causing these indentations in the reconstructed skull. Is there a way to get rid of the artifacts caused by the extensions during the reconstruction process? I am willing to provide whatever information is necessary to resolve this issue. Thanks in advance, Reid

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reference of adult normal volume from cortical parcellation
by tulu 25 Sep '12

25 Sep '12

Dear FS experts, Is there any reference about the volume of cortical gyrus after FS cortical parcellation in normal adult people ? I need the reference value of regional volume base on the cortical parcellation made by FS. Please instruct me the reference paper. Thanks help JLH

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Brain Volume
by Ana Arruda 25 Sep '12

25 Sep '12

Hi, I've been working with Freesurfer and FSL in order to compare the two softwares. However the last one has a tool called "Brain Extraction Tool" (BET) that provides all the brain volume including cerebellum. Is there any option in Freesurfer that makes the same as *BET*? Thank you for your attention, Ana Arruda

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Pooled Structure
by Zsolt Cselényi 25 Sep '12

25 Sep '12

Hi, I would like to find out how to pool parcellation statistics (i.e. ?.aparc.stats table entries) from several areas into a bigger one. For example: how to get the pooled statistics for the area "parietal" which would be made up of "superiorparietal" and "inferiorparietal" cortical structures? Calculating pooled values for things like GrayVol, SurfArea seem rather straightforward (by summing of course) but not so for ThickAvg, ThickStd, MeanCurv, GausCurv, FoldInd and CurvInd. First, should they be pooled using the area or the number of vertices? Second, how should they be pooled? For ThickAvg and MeanCurv I guess it's an area- (or NumVert- ?) weighted mean and for ThickStd maybe a NumVert-weighted pooled SD but not sure whether it's also a (weighted) mean for GausCurv, FoldInd and CurvInd? Please help! Thank you, Zsolt

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manual parcellation
by Linda Douw 25 Sep '12

25 Sep '12

Hi experts, I want to make a new, custom-made parcellation, based on the aparc but with much higher resolution. (I've tried mris_divide_parcellation, which yields strip-shaped instead of isometric labels, and mris_make_face_parcellation, which loses spatial specificity. The wiki describes a way of manually drawing new labels in tksurfer, but I get stuck in the process. I've created a new CLUT, with no. 100-106 being the new subdivisions of the original bankssts label: # Freesurfer LUT information extracted from annotation file: # lh.aparc.annot # 2008-02-29 23:58:32 # This file can be used as the basis for a new LUT file for annotations purposes # which can be loaded into tksurfer using File > Label > Load color table #No. Label Name: R G B A 0 unknown 25 5 25 0 1 bankssts 25 100 40 0 2 caudalanteriorcingulate 125 100 160 0 3 caudalmiddlefrontal 100 25 0 0 4 corpuscallosum 120 70 50 0 5 cuneus 220 20 100 0 6 entorhinal 220 20 10 0 7 fusiform 180 220 140 0 8 inferiorparietal 220 60 220 0 9 inferiortemporal 180 40 120 0 10 isthmuscingulate 140 20 140 0 11 lateraloccipital 20 30 140 0 12 lateralorbitofrontal 35 75 50 0 13 lingual 225 140 140 0 14 medialorbitofrontal 200 35 75 0 15 middletemporal 160 100 50 0 16 parahippocampal 20 220 60 0 17 paracentral 60 220 60 0 18 parsopercularis 220 180 140 0 19 parsorbitalis 20 100 50 0 20 parstriangularis 220 60 20 0 21 pericalcarine 120 100 60 0 22 postcentral 220 20 20 0 23 posteriorcingulate 220 180 220 0 24 precentral 60 20 220 0 25 precuneus 160 140 180 0 26 rostralanteriorcingulate 80 20 140 0 27 rostralmiddlefrontal 75 50 125 0 28 superiorfrontal 20 220 160 0 29 superiorparietal 20 180 140 0 30 superiortemporal 140 220 220 0 31 supramarginal 80 160 20 0 32 frontalpole 100 0 100 0 33 temporalpole 70 70 70 0 34 transversetemporal 150 150 200 0 100 bankssts_1 25 100 41 0 101 bankssts_2 25 100 45 0 102 bankssts_3 25 100 50 0 103 bankssts_4 25 100 55 0 104 bankssts_5 25 100 60 0 105 bankssts_6 25 100 65 0 I load the aparc and the new CLUT into tksurfer, draw points around a new label, close the path, and then custom fill the area. How do I now indicate that this is for instance the new label bankssts_1? The wiki and mailing archive indicate some problems with manually parcellating, but the info seems dated and scattered. So if there is some place I can find this stuff myself, I'd be happy to check it out. Thanks so much, -- Linda Douw, Ph.D. Research fellow

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recon-all error while data's FOV>256
by bin.lv 25 Sep '12

25 Sep '12

Dear all, I met a problem while running the recon-all. I have a data with FOV= 300>256, so I add the flag -cw256 with reon-all. Then when I check the converted data raw.mgz, I find the brain image is imperfect while some region at the top of head is cut off. My question is, could I choose to cut the part of neck which locates at the button of head? Thank you very much in advance！ Bin Lv

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intracranial volume and dicom
by Knut J Bjuland 25 Sep '12

25 Sep '12

Hi, I have calculated relative volume by dividing each volume by the intracranial volume and multiply it with 100. When I add the relative volume of total gray matter, cortical white matter, lateral ventricle, 3rd centricle, 4th ventricle and ventral DC, I get 82-86 %. Can this be caused by the fact that the intracranial volume is much larger than the brain? In which way can motion correction affect volume if I have series where some subjects have to dicom and other just have one dicom serie? Knut J

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Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer
by Fabian Schrumpf 25 Sep '12

25 Sep '12

Hi bruce, At first I want to build a voxel-based FEM-Model based on the surfaces freesurfer creates. For finally creating the models I want to use the MATLAB toolbox iso2mesh. But I would also be interested in building BEM models as a second approach. best regards Fabian ----- Ursprüngliche Mail ----- Von: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> An: "Fabian Schrumpf" <schrumpf(a)cbs.mpg.de> CC: "Matti Hamalainen" <msh(a)nmr.mgh.harvard.edu> Gesendet: Dienstag, 25. September 2012 15:36:50 Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer Hi Fabian can you cc the list so others can answer? Do you want a voxel-based head model? We generate surface models for BEM analysis that Matti (ccd) can tell you about if you are interested. You could generate a volume by fillin the interior of the various surfaces with mris_fill if you prefer. cheers Bruce On Tue, 25 Sep 2012, Fabian Schrumpf wrote: > Hi Bruce, > > thank you for your reply. I'm new to freesurfer. What I'm trying to do is to build a head model für MEG source localization. Therefore I have to divide the human brain in white matter, gray matter and CSF. After doing WM segmentation and cut/fill freesurfer comes up with a good segmentation of the brain in aseg.mgz. Unfortunately, this segmentation also contains many sub-cortical structures that I don't want to take into account for my head model. I'm trying to find a way to do a segmentation that only considers WM, GM and CSF. Additionally, reducing diversity of segmented tissue should perhaps reduce computation time? > > Best regards > > > Fabian > > ----- Ursprüngliche Mail ----- > Von: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > An: "Fabian Schrumpf" <schrumpf(a)cbs.mpg.de> > CC: freesurfer(a)nmr.mgh.harvard.edu > Gesendet: Dienstag, 25. September 2012 15:08:11 > Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer > > Hi Fabian > > What are you trying to achieve? The easiest thing to do is to run recon-all > with the -all flag so we generate an aseg, then that can be collapsed into > different measures. > > cheers > Bruce > > > On Tue, 25 Sep 2012, Fabian Schrumpf wrote: > >> Hi folks, >> >> I successfully managed to do a brain segmentation using freesurfer. But the result after mri_fill has too much detail. I'd like to do a segmentation only dividing the brain into white matter, gray matter and csf. I suppose that I have to alter some options when registering and aligning the volume to the gca atlas. But i don't know which option that would be. On the other hand, is there any way to edit the atlas itself so that it just contains the regions I am interested in? Thanks in advance for your help. >> >> Best regards >> >> >> Fabian >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > 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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Brain segmentation (gray, white, csf) using freesurfer
by Fabian Schrumpf 25 Sep '12

25 Sep '12

Hi folks, I successfully managed to do a brain segmentation using freesurfer. But the result after mri_fill has too much detail. I'd like to do a segmentation only dividing the brain into white matter, gray matter and csf. I suppose that I have to alter some options when registering and aligning the volume to the gca atlas. But i don't know which option that would be. On the other hand, is there any way to edit the atlas itself so that it just contains the regions I am interested in? Thanks in advance for your help. Best regards Fabian

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