Freesurfer February 2009

freesurfer@nmr.mgh.harvard.edu

86 participants
126 discussions

ROI
by Kelly Silva 03 Feb '09

03 Feb '09

Hello, I´ sending an image and I need to create a ROI with this results. How can I do that? Thanks and best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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thresholds for segmentation
by Bai Xue 03 Feb '09

03 Feb '09

Hi, What is the different thresholds set in Freesurfer for segmenting white matter, grey matter and CSF? Thanks a lot! Bai

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read_surf/patch issue
by Keller, Corey J. 02 Feb '09

02 Feb '09

Hi Freesurfers, I am having some issues plotting a reconstructed brain in matlab. I have used the read_surf function to load in the pial surface file lh.pial and save the lh_pial.vert and lh_pial.tri. I get the following output: fv.vertices fv.faces] = read_surf('lh.pial') fv = vertices: [140817x3 double] faces: [281630x3 double] h = patch(fv,'FaceColor',[.5 .5 .5]) ??? Error using ==> patch Faces values must be >= 1.0. My first 10 face values are: fv.faces(1:10,1:3) ans = 0 1 5 6 5 1 0 26 1 27 1 26 0 5 26 39 26 5 1 2 6 7 6 2 1 27 28 1 28 2 This seems to be the issue because every other row the faces values are greater than zero. Do you know why all of my recon output pial files look like this and how I can fix the issue. Thanks. Best, Corey

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lGI value aberrantly too high but no topological defect
by Christian Scheel 02 Feb '09

02 Feb '09

Dear all, I have successfully run 'recon-all -lgi' for all my subjects. However the computation process stopped in one of the brains claiming an lGI vertex value was aberrantly too high and giving me the following error message: ##### ... remeasuring lGI value for vertex iV = 32501. It may take a few minutes. WARNING -- Problem for vertex iV = 32501, lGI value is aberrantly high (lGI=40.5282)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface. ERROR: compute_lgi did not create output file '/home/freesurfer/christian/34/surf/tmp-mris_compute_lgi-rh.pial/rh.pial_lgi.asc'! ##### I have already restarted the computation twice without success. The script always crashes at the same vertex. The error message and the wiki page mention such an error in connection with possible topological defects. However when I check the mris_euler_number for the subject's rh.pial it interestingly does not show me any topological defect. Here is the output: ##### [freesurfer@localhost ~/christian]$ mris_euler_number /home/freesurfer/christian/34/surf/rh.pial euler # = v-e+f = 2g-2: 133775 - 401319 + 267546 = 2 --> 0 holes F =2V-4: 267546 = 267550-4 (0) 2E=3F: 802638 = 802638 (0) total defect index = 0 ##### In all other brains the lGI calculation was successful. Does anyone of you have an idea? Any help is greatly appreciated. Best wishes, Christian Scheel --- University of Cologne Department of Psychiatry

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cortical thickness maps
by Feng-Xian 01 Feb '09

01 Feb '09

Hi, Thank you for your help before. I finished the group analysis of cortical thickness with QDEC on FreeSurfer and I would like to get the cortical thickness maps with inflated surface on Windows XP. Would you teach me how can I change the cortical thickness maps from FreeSurfer to Windows XP? Thanks in advance! Feng-Xian ------------------------------------------------- Chang Gung University Mail Server Web Mail system By Chang-Gung University Information Center (http://www.cgu.edu.tw/ic/)

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[Fwd: Re: [Freesurfer] annotation file and labels for fsaverage]
by carl＠nmr.mgh.harvard.edu 31 Jan '09

31 Jan '09

Hi Jeff - read the thread below starting with my Sept 8 2008 email. Bruce - what is the status on the insula label for aparc? carl > Hello all, > > Thank you for your quick replies to my previous posts. One more question. I am wondering what the difference is and if I should be taking average thickness measurements for cortical regions from lh.aparc.a2005s.stats or lh.aparc.stats. I think the main difference is that lh.aparc.a2005s.stats was made with ?h.atlas2005_simple.gcs and lh.aparc.stats was made with ?h.curvature.buckner40.filled.desikan_killiany.2007-06-20gcs. Which one is more accurate? I am using freesurfer 3.0.5. > > Thank you, > Jeff Sadino Bruce Fischl fischl at nmr.mgh.harvard.edu Tue Sep 9 10:03:31 EDT 2008 Previous message: [Freesurfer] annotation file and labels for fsaverage Next message: [Freesurfer] dicom image viewer Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] great, thanks Ron. Bruce On Tue, 9 Sep 2008, Ron Killiany wrote: > I believe Sarah will be over at MGH on friday to begin finalizing this. > > --ron > > On Mon, Sep 8, 2008 at 9:31 PM, Bruce Fischl <fischl at nmr.mgh.harvard.edu>wrote: > >> Hi Dara, >> >> there is an insula label in the works (*lots* of people have asked this >> question). Ron: any updates on the insula label? >> >> thanks >> Bruce >> >> On Mon, 8 Sep 2008, Dara Manoach wrote: >> >> Thanks very much for the detailed info Karl (and Doug and Bruce)! >>> >>> My primary ROI is ACC, so we'll probably use Aparc with the cingulate >>> divisions. I'll have to review the paper to see if the anatomic bases of >>> the divisions are described. I'm surprised, though, that there is not an >>> insula label, and I'm wondering why it would not be possible to use ROI >>> labels from the two annotation schemes to examine activation in group data >>> (i.e., ACC labels from aparc and insula from aparc2005). >>> >>> best, >>> dara >>> >>> On Sep 8, 2008, at 8:18 PM, Bruce Fischl wrote: >>> >>> for what it's worth we label the cc now explicitly in the aseg, which is >>>> certainly more accurate than the aparc used to be. >>>> >>>> Thanks for the detailed answer though Carl! >>>> >>>> Bruce >>>> On Mon, 8 Sep 2008 carl at nmr.mgh.harvard.edu wrote: >>>> >>>> >>>>> Hi Dara, >>>>> >>>>> You can certainly use either one as Doug says, but depending on your >>>>> purposes, one or the other may have some virtues. 2005 consists of >>>>> discrete sulcal and gyral labels with traditional anatomical names so >>>>> there are a lot more labels (which is why Doug describes it as very >>>>> detailed), whereas aparc in general collapses these into summary >>>>> regions. >>>>> >>>>> But it is not a a simple case of lumper vs splitter....For instance it >>>>> seems that >>>>> >>>>> Aparc divides the cingulate into rostral anterior, caudal anterior, >>>>> posterior cingulate whereas in aparc 2005 it is lumped into one >>>>> cingulate >>>>> label >>>>> >>>>> Aparc shows the corpus c. nicely (I think there may even be a >>>>> subparcellation available in development) whereas the cc is lost in the >>>>> medial wall in 2005. >>>>> >>>>> Aparc differentiates the pars orbitalis nicely on the orbital surface >>>>> from >>>>> the rest of the ofc, aparc 2005 does not ? possibly of interest to >>>>> someone >>>>> who is looking at ventrolateral pfc and its neighbors >>>>> >>>>> Aparc includes in its lateral ofc label everything lateral to the rectus >>>>> gyrus, including the central ofc and the (unlabeled) transverse sulcus >>>>> neither of which would be understood as being in the lateral ofc as that >>>>> term is typically used today. >>>>> >>>>> Aparc 2005 shows a view that nicely differentiates the rectus gyrus on >>>>> sagital section from the adjoining, whereas aparc lumps a broad >>>>> territory >>>>> into ?medial OFC? >>>>> >>>>> Aparc 2005 includes parcellation of the Insula, aparc does not and it is >>>>> lost in the unknown medial wall (there has been talk of fixing this but >>>>> is >>>>> this real, Bruce or Doug?) >>>>> >>>>> Perhaps what we need is a ?best of aparc and aparc 2005?. >>>>> >>>>> For surfing purposes you can also ?fool? tksurfer into showing you the >>>>> names of the (typically more more detailed) 2005 parcellations while >>>>> viewing the brain labeled with the aparc labels which at times have more >>>>> detail ? though I have never asked Doug if this will always work >>>>> correctly. >>>>> >>>>> If others have discovered pros and cons in other regions, please share. >>>>> >>>>> Best, >>>>> >>>>> >>>>> Carl >>>>> >>>>>

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Freesurfer February 2009