Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

Re: [Freesurfer] Freesurfer Digest, Vol 73, Issue 64
by Gonzalo Rojas Costa 26 Mar '10

26 Mar '10

Hi Andreas: As far as I know, the complete command is: recon-all -s subjid -skullstrip -no-wsgcaatlas -wsthresh 35 -clean-bm Sincerely, Gonzalo Rojas Costa Laboratory of Medical Imaging Processing Department of Radiology Clínica Las Condes Santiago Chile > Date: Fri, 26 Mar 2010 11:07:01 +0100 > From: Andreas Berger <andreas.berger.01(a)gmail.com> > Subject: [Freesurfer] changing watershed threshold has no effect > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <68f948a91003260307g4fee4b69s9c04624544df29a1(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hello freesurfers, > > we are having a problem with insufficient skull stripping, in 66 out > of 200 subjects this affects the pial surface, as can be seen in the > attached screenshot1. since the problem is somewhat generalized in > location, i tried to change the watershed threshold as suggested by > the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean > -wsthresh n), but even 0 seems to have no effect (it looks different, > but not less skull), see screenshot2. am i doing it wrong?

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Poor Talairach registration and effect on ICV
by Martin Kavec 26 Mar '10

26 Mar '10

Hi, in our population of MCI patients, unfortunately parts of the cerebellum were not completely scanned. I ran the data throught the whole FS-4.5.0 pipeline and I see that the eTIV normalized volumes of the segmented structues have very large variance compared to the eTIV normalized group of independent age matched subjects with the full brain coveage. I assume that this is possibly due to the suboptimal registration to the template, which is used to compute eTIV. In fact, all the subjects with incomplete cerebellum failed to pass the quality check of the registration to Talairach, but on the first glance the registration seemed fine to me so I just used -notal-check flag to complete recon-all -all. I know I could go back, check more carefully and correct the Talairach transform manually, but I hesitate to go this way. Rather I thougt if it would be possible/feasible to remove the cerebellum from each subject AND the template and possibly achieve better registration from these images. Thanks in advance for opinions, Martin

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changing watershed threshold has no effect
by Andreas Berger 26 Mar '10

26 Mar '10

hello freesurfers, we are having a problem with insufficient skull stripping, in 66 out of 200 subjects this affects the pial surface, as can be seen in the attached screenshot1. since the problem is somewhat generalized in location, i tried to change the watershed threshold as suggested by the wiki. i tried the values 20, 15, 10, 5, 0 (recon-all -all -clean -wsthresh n), but even 0 seems to have no effect (it looks different, but not less skull), see screenshot2. am i doing it wrong?

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Skipping time consuming FS parts.
by Mohammed el Morabit 26 Mar '10

26 Mar '10

Dear FS experts, I have a large data set which I want to recon-all, in order to obtain the cortical, sub-cortical parcellations and the corresponding volumes and thicknesses. As the reconstruction is very time-consuming I was wondering which steps I might skip without significant decrease in quality of the cortical segmentation. I noticed for instance that the automated topology fix takes quite long - if I skip this part, how does that change my results? Thanks in advance. Mohammed.

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Current age or Age of onset
by 류철형 25 Mar '10

25 Mar '10

Dear All I'm trying to search for the cortical thickness change associated with the progression of a neurodegenerative disease. Each patient may have current age, age of onset, disease duration, and disease severity score. To find the cortical areas in which cortical thickness is correlated with the disease duration, Which variable do I have to choose as a covariate? Current age or Age of onset? It may be simple question and 'current age' may be the answer. But, because the current age is the sum of duration and age of onset, we can make the regression equation, Y (thickness) = a*A (onset age) + b*B (duration) + e (error). In my study, the result from qdec was better when the onset age was selected as covariate. I'm waiting for your advice. Chul Hyoung Lyoo

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Creating a distance scale bar for a pial surface-render viewed in tksurfer
by Eric Moulton 25 Mar '10

25 Mar '10

I was wondering if freesurfer has a way of generating a scale for distance, similar to what one would see in the legend of a roadmap. I'm thinking of using such a scale for a 3-d pial surface-render of an averaged brain (as generated using make_average_surface). Since it's a 3-d image, I had in mind a sort of 3D Cartesian coordinate scale, with scale bars for the x, y, and z directions. Does freesurfer have some visual representation of a distance scale like I've described, or perhaps some alternative? Eric Moulton PhD Assistant Neuroscientist P.A.I.N. Group Brain Imaging Center McLean Hospital 115 Mill Street Belmont, MA 02478 Phone: 617-855-2604 Fax: 617-855-3772

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Re: [Freesurfer] the thickness of manually selected vertex
by Guang Zeng 25 Mar '10

25 Mar '10

Thanks! Yeah, I forgot this. Now, the results look right now. > Date: Thu, 25 Mar 2010 16:17:33 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: freesurfer_zg(a)hotmail.com > Subject: RE: [Freesurfer] the thickness of manually selected vertex > > are you sure you are using 1-based indices in matlab? Also, please post > these to the list so that others can answer! > On Thu, 25 Mar 2010, Guang Zeng > wrote: > > > > > Using mris_anatomical_stats, I got > > > > table columns are: > > number of vertices > > total surface area (mm^2) > > total gray matter volume (mm^3) > > average cortical thickness +- standard deviation (mm) > > integrated rectified mean curvature > > integrated rectified Gaussian curvature > > folding index > > intrinsic curvature index > > structure name > > 537 372 892 2.248 0.455 0.110 0.026 4 0.6 lh.mynew.label > > > > I also calculate the average thickness of the vertices by loading the label file and thickness file into MATLAB, I got some numbers as: > > average cortical thickness: 2.2670 > > standard deviation: 0.5476 > > > > These numbers looks very close, are the difference caused by the partial volume? > > > > Thanks! > > Guang > > > >> Date: Thu, 25 Mar 2010 15:52:34 -0400 > >> From: fischl(a)nmr.mgh.harvard.edu > >> To: freesurfer_zg(a)hotmail.com > >> CC: freesurfer(a)nmr.mgh.harvard.edu > >> Subject: RE: [Freesurfer] the thickness of manually selected vertex > >> > >> nope, mris_anatomical_stats will take either (with -l or -a I think) > >> On Thu, > >> 25 Mar 2010, Guang Zeng wrote: > >> > >>> > >>> Do I need convert the .label file to an annotation file before I run mris_anatomical_stats? > >>> > >>> Could I get the same results if I do something like this: > >>> > >>> 1. create the label file, and load it using MATLAB, > >>> 2. find the corresponding ID of vertices I clicked. > >>> 3. load .thickness file using matlab > >>> 4. find the corresponding thickness value of these vertice > >>> 5. compute the mean > >>> > >>> Thanks! > >>> > >>> Thank! > >>> Guang > >>> > >>>> Date: Wed, 24 Mar 2010 16:15:35 -0400 > >>>> From: fischl(a)nmr.mgh.harvard.edu > >>>> To: freesurfer_zg(a)hotmail.com > >>>> CC: freesurfer(a)nmr.mgh.harvard.edu > >>>> Subject: Re: [Freesurfer] the thickness of manually selected vertex > >>>> > >>>> Q1: yes. > >>>> Q2: do you want each of them individually or the average? You can save a > >>>> label file of the 4 vertices and use mris_anatomical_stats to get the > >>>> average > >>>> > >>>> cheers > >>>> Bruce > >>>> > >>>> On Wed, 24 Mar 2010, Guang Zeng wrote: > >>>> > >>>>> > >>>>> Hi, there, > >>>>> > >>>>> I have two questions about the ?h.thickness file. > >>>>> > >>>>> If I load a subject's surface ?h.inflated using tksurfer, then I load its thickness file ?h.thickness, > >>>>> > >>>>> By clicking mouse on the surface, I can read the corresponding curvature value of a specific vertex. > >>>>> > >>>>> Q1, Here, the value next to 'Curvature' is actually its thickness value, right? > >>>>> Q2, If I select four vertexes on the surface, is there a way that I can save the thickness values of these four vertexes into a txt file? > >>>>> > >>>>> > >>>>> Thanks! > >>>>> Guang > >>>>> > >>>>> _________________________________________________________________ > >>>>> Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. > >>>>> http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:… > >>>> _______________________________________________ > >>>> 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. > >>>> > >>> > >>> _________________________________________________________________ > >>> Hotmail: Trusted email with Microsoft?s powerful SPAM protection. > >>> http://clk.atdmt.com/GBL/go/210850552/direct/01/ > > > > _________________________________________________________________ > > Hotmail: Trusted email with Microsoft?s powerful SPAM protection. > > http://clk.atdmt.com/GBL/go/210850552/direct/01/ _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/210850552/direct/01/

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the thickness of manually selected vertex
by Guang Zeng 25 Mar '10

25 Mar '10

Hi, there, I have two questions about the ?h.thickness file. If I load a subject's surface ?h.inflated using tksurfer, then I load its thickness file ?h.thickness, By clicking mouse on the surface, I can read the corresponding curvature value of a specific vertex. Q1, Here, the value next to 'Curvature' is actually its thickness value, right? Q2, If I select four vertexes on the surface, is there a way that I can save the thickness values of these four vertexes into a txt file? Thanks! Guang _________________________________________________________________ Hotmail is redefining busy with tools for the New Busy. Get more from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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definition of some aseg.stats measures...
by Gonzalo Rojas Costa 25 Mar '10

25 Mar '10

Hi: What is the definition of the following measures that appears at the beginning of "aseg.stats" file: "Brain Mask Volume", "Brain Segmentation Volume Without Ventricles" (BrainSegVolNotVent), "Brain Segmentation Volume" (BrainSegVol), "Intracranial Volume" (IntraCranialVol, ICV) ?... The cerebelum is included in the ICV ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Clínica Las Condes

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Longitudinal processing edits
by Pierson, Ronald K 24 Mar '10

24 Mar '10

I apologize if this has been covered before, but I wanted to make sure I understand the best way to edit at the appropriate times during the longitudinal stream. 1) Run recon-all -all on each scan 2) If needed, control points are chosen on the individual scans, and recon-all using the -cp option 3) Run the -base processing for the subject 4) WM and brain (pial) edits are done on the base, rerun as needed 5) Final longitudinal processing of each scan I assume the final processing of the individual scans should need very little manual intervention, since the control points and edits will be carried through to that stage. Is this correct, or have I oversimplified or missed something? Ronald Pierson Administrative Chair of Imaging, PREDICT-HD Manager, Research and Development Department of Psychiatry, Carver College of Medicine W-278 GH, 200 Hawkins Dr Iowa City, IA 52242

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Freesurfer March 2010