Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

freesurfer course
by Jayachandra Raghava 12 Feb '14

12 Feb '14

Hello, I am interested in attending a freesurfer course at Martinos Center for Biomedical Imaging in Boston<http://maps.google.com/maps?q=%22114%20Sixteenth%20Street,%20Charlestown,%2…> But, it says that the following lectures are only during spring and fall. 1)Functional analysis (during the Spring course) 2)Diffusion processing (during the Fall course) I would like to attend the course which covers the above topics. Can you please give me the link for the details of the workshop which includes diffusion and functional course. Regards Jay

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distribute dots on the surface
by peng 12 Feb '14

12 Feb '14

Dear Freesurfers, I have run recon-all and got a set of surfaces for the subjects. I wish to distribute N dots about evenly on the surface to cover most gyri and sulci , but I don't how to implement that. One way is to manually put them in the GUI of freeview, but it is not so convenient if N is relative large (say, 200). Can anyone give me a hint which function shall I use? best Peng

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Re: [Freesurfer] Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?
by Bruce Fischl 12 Feb '14

12 Feb '14

Hi Erik yes, those numbers are always estimated from the data unless you specify otherwise. And please remember to cc the list so that others can answer/see the answers in case they are interested in the same type of issue. cheers Bruce On Wed, 12 Feb 2014, Erik Lindberg wrote: > OK Thanks > - I suspected that. What made me a bit confused what that I went in and had > a look at the recon-all log file. And numbers from this file was different > for different subjects at the same batch. > > > > > > > two subjects > setting MIN_GRAY_AT_WHITE_BORDER to 67.9 (was 70) > setting MAX_BORDER_WHITE to 107.3 (was 105) > setting MIN_BORDER_WHITE to 79.0 (was 85) > setting MAX_CSF to 56.7 (was 40) > setting MAX_GRAY to 94.7 (was 95) > setting MAX_GRAY_AT_CSF_BORDER to 73.4 (was 75) > setting MIN_GRAY_AT_CSF_BORDER to 45.6 (was 40) > > > setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) > setting MAX_BORDER_WHITE to 108.1 (was 105) > setting MIN_BORDER_WHITE to 82.0 (was 85) > setting MAX_CSF to 61.0 (was 40) > setting MAX_GRAY to 95.9 (was 95) > setting MAX_GRAY_AT_CSF_BORDER to 76.7 (was 75) > setting MIN_GRAY_AT_CSF_BORDER to 50.5 (was 40) > > > On Wed, Feb 12, 2014 at 2:31 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Erik > > is there a reason not to do it for the whole group? I guess if > the one subject you uploaded had significant motion (which > caused the blurryness) then it might be the case that it needs > separate parameters. In general though it's good to hold this > kind of thing constant as it will definitely bias you to having > greater thickness. Try it on some of the other subjects and see > if the surfaces are at least as accurate as without, and if so > do it uniformly > > cheers > Bruce > > On Wed, 12 Feb 2014, Erik Lindberg wrote: > > Dear Freesufers, > I am trying to understand what happens if I go in > and edit the numbers for > -min_border_white -min_gray_at_white_border in a > single subjects in a > large group. > > Generally we aim to set everything identical when > running a group of > subjects in FS. I went in and had a look at the > recon-all log file and I > can see that the numbers for -min_border_white > -min_gray_at_white_border different for different > subjects. > > Thus - what will happened if I go and edit the > -min_border_white > -min_gray_at_white_border numbers for a single > subjects in a large bach > .... will I still be able compare cortical thickness > with subjects that I > did not edit? > > Or is it necessary to keep the number identical for > all subjects when > editing the min_border_white > -min_gray_at_white_border > > > > > 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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Can -min_border_white and -min_gray_at_white_border be edited for single subject in a large group of subjects?
by Erik Lindberg 12 Feb '14

12 Feb '14

Dear Freesufers, I am trying to understand what happens if I go in and edit the numbers for -min_border_white -min_gray_at_white_border in a single subjects in a large group. Generally we aim to set everything identical when running a group of subjects in FS. I went in and had a look at the recon-all log file and I can see that the numbers for -min_border_white -min_gray_at_white_border different for different subjects. Thus - what will happened if I go and edit the -min_border_white -min_gray_at_white_border numbers for a single subjects in a large bach .... will I still be able compare cortical thickness with subjects that I did not edit? Or is it necessary to keep the number identical for all subjects when editing the min_border_white -min_gray_at_white_border

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Segmentation using Free Surfer.
by Saurabh Thakur 12 Feb '14

12 Feb '14

Hello Free surfer Expert, I have started working on Free surfer. Now i m facing two issues such as : 1. I m trying to use contour ... but it is working as per guidance in website given. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewTools/Voxel… Under heading of Contour Draw....can any tell me pre requisite to draw contour. I have loaded T1 image and then made new volume....after tat ctrl+alt+ left click....not working...? Can any one help me with contour function, how to use in details. 2. I wanted to do segmentation of image into WM,GM and CSF. Please suggest what the best way/ Algorithm to so get MRI image segmentation using Freesurfer. Thanks in advance. cheers Saurabh Thakur,

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Hemispherectomy Surgery
by Kristian Eschenburg 11 Feb '14

11 Feb '14

Hi I have a dataset of children who have had hemispherectomy surgery to treat epilepsy. I want to be able to run recon-all on these children. I have masked out the remaining tissue from the excised side so that only tissue from the healthy hemisphere remains, and aligned this single hemisphere to a template. To mimic a whole brain, I have flipped the single hemisphere over the X-axis and added it to the other half. Thus, I have the original hemisphere, and the "mirrored" hemisphere in one scan. This is my input to recon-all. However, as the scans were acquired some time after surgery, the remaining hemisphere was not perfectly aligned at the midline and expanded / grew into to the empty cranial space, and there are gaps and overlap between the mirrored side and the original side. Is there a way to run recon-all on the single hemisphere alone, so that I do not have to mirror the brain? Perhaps by supplying a mask, to apply to the FreeSurfer atlases? Thanks Kristian

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Cortical Thickness values
by Natasha Haris 11 Feb '14

11 Feb '14

Dear Freesurfers, Is there anyway to get a compiled list of all the significant clusters with information about their maximum thickness value, x/y/z vertices, t statistic etc on QDEC? Does this have anything to do with a SaveClusterFile command? All of this information must be stored somewhere for the significant clusters to appear - wondering what's the easiest way to extract this info. Thanks, Natasha

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FreeSurferWiki RecentChanges
by Kaiming Yin 11 Feb '14

11 Feb '14

Dear guys, Is there some way to have a more detailed look of the recent changes on the FreeSurfer Wiki page? I click on the recent changes option but can only see the latest 13 updates within around 10 days. Could I have a check of that from further past days? Thanks a lot, Kaiming

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Program Director job opening at the NINDS (fwd)
by Bruce Fischl 11 Feb '14

11 Feb '14

FYI ---------- Forwarded message ---------- Date: Tue, 11 Feb 2014 16:50:15 +0000 From: "Babcock, Debra (NIH/NINDS) [E]" <dbabcock(a)ninds.nih.gov> To: "Babcock, Debra (NIH/NINDS) [E]" <dbabcock(a)ninds.nih.gov> Subject: Program Director job opening at the NINDS Dear Colleagues, The NINDS is currently seeking to hire several program directors. In particular, we are searching for a motivated and energetic PhD or MD with a background in cognitive neuroscience or a related field to administer our Behavioral and Cognitive Neuroscience program. Familiarity with neuroimaging science is a plus, but not required. Applications will be accepted through USAJOBS starting on February 14, 2014 and closing on February 23, 2014. There will be a separate job ad specifically for a similar Medical Officer (MD) position to follow this one; however, both MDs and PhDs may apply to the ad opening on Feb. 14. For more details, please see: http://jobs.sciencecareers.org/job/324934/health-scientist-administrator/ If you know of anyone who might be interested in this position, please forward this information to them. I’m happy to answer questions about the position or the application process. Thanks for your assistance, Deb Babcock Debra J. Babcock, Ph.D., M.D. Program Director, Behavioral & Cognitive Neuroscience NINDS/NIH 6001 Executive Blvd., Room 2108, MSC 9521 Bethesda, MD 20892-9521 Rockville, MD 20852 (for UPS, FedEx, etc.) Phone: 301-496-9964 Fax: 301-402-2060 Email: dbabcock(a)ninds.nih.gov

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Re: [Freesurfer] creating specific files
by Borzello, Mia 11 Feb '14

11 Feb '14

woops- sorry meant to include everyone. The name of the file I use to plot is "lh.pial-outer-smoothed." So I either want to create this file or figure out another way to plot. Do i need lh.pial to make lh.pial-outer-smoothed? ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: Tuesday, February 11, 2014 10:51 AM To: Borzello, Mia Subject: Re: [Freesurfer] creating specific files Hi Mia can you keep ccing the list? I don't know what the "outer smoothed pial surface" is. Is this something we create? I don't think so Bruce On Tue, 11 Feb 2014, Borzello, Mia wrote: > Plotting the electrodes on the surface using matlab. I usually use the outer smoothed pial surface- do I first need the normal pial surface to create this? > > > >> On Feb 11, 2014, at 10:42 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >> >> what kind of plotting do you mean? >>> On Tue, 11 Feb 2014, Borzello, Mia wrote: >>> >>> Okay and is there a way to check if the files I currently have are sufficient to plot with? >>> >>> Thanks, >>> m >>> >>> >>> >>>> On Feb 11, 2014, at 9:58 AM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>>> >>>> if they are zero length there is nothing there now >>>>> On Tue, 11 Feb 2014, Borzello, Mia wrote: >>>>> >>>>> Is this okay to do even if I've done a coregistration, nothing will be deleted? Also, are the pial surfaces necessary for plotting? I'm wondering if I can just use the files that I have to create a plot without having to rerun anything. >>>>> >>>>> Thanks, >>>>> Mia >>>>> >>>>> >>>>> >>>>> >>>>> >>>>>> On Feb 10, 2014, at 4:31 PM, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>>>>> >>>>>> Hi Mia >>>>>> >>>>>> delete the 0 length files and run recon-all -make all -s <subject> >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>>> On Mon, 10 Feb 2014, Borzello, Mia wrote: >>>>>>> >>>>>>> Hi Freesurfers, >>>>>>> I was wondering if there was a way to kind of fill in the blanks for a >>>>>>> Surfer Output folder. I am working with an old data set, and it seem that >>>>>>> some of the files are empty (0 bytes), "rh.pial" for example. Is there a way >>>>>>> to pass the SurferOutput folder in and recreate what's missing? >>>>>>> Thanks, >>>>>>> Mia >>>>> >>>>> _______________________________________________ >>>>> Freesurfer mailing list >>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> > > >

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