Freesurfer February 2014

freesurfer@nmr.mgh.harvard.edu

128 participants
236 discussions

Running a template through recon-all
by Danielle Sliva 12 Feb '14

12 Feb '14

Dear FreeSurfer experts, I am trying to map volumetric ROIs obtained from VBM to surfaces in 5-6 year old children. I saw in a couple previous posts that it is recommended to run the template brain through recon-all, map the ROIs to the template surface, and then propagate the ROIs to all subjects using either mri_surf2surf, or (after turning the ROIs into labels) using mri_label2label. The problem I have is that we used a custom age-appropriate template that will not pass through recon-all. I have tried using -notalairach & -notal-check. Here is the output from the recon-all.log: register_mri: find_optimal_transform find_optimal_transform: nsamples 3481, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 117 --> 126 resetting gm mean[0]: 74 --> 74 input volume #1 is the most T1-like using real data threshold=24.0 skull bounding box = (128, 99, 138) --> (128, 154, 185) using (128, 117, 162) as brain centroid... mean wm in atlas = 126, using box (128,110,156) --> (127, 123,167) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri->nbins=255, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf Linux rc-twice 3.2.21-mosix #1 SMP Mon Jul 2 08:55:48 EDT 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s TOM_5yr_2 exited with ERRORS at Mon Feb 10 19:11:23 EST 2014 I am using version 5.3. Can you suggest any other options to get this template through recon-all? Thanks in advance, Danielle

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How to avoid tumour from being segmented out
by Melanie Morrison 12 Feb '14

12 Feb '14

Hi there, I am creating surfaces from my volume T1-weight scans so that I can run them in AFNI's SUMA program. Problem is that my tumour has been segmented out because its intensity and the intensity of its surround area is much lower that what is being segmented. How can I avoid this? Or edit this? I need my functional MRI data to be displayed around the tumour region which is now unfortunately cut out. (HELPP!!!) Thanks, Melanie Morrison

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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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Freesurfer February 2014