Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Any Pre-exisiting Public Amazon EC2 AMI with Freesurfer out there?
by Joshua Lee 28 Oct '11

28 Oct '11

Are there any existing Amazon EC2 AMI registered publicly that can be used? I want to analyze a lot of data fast. Thanks, - Joshua Lee

2 1

TRACULA: how to implement DTI repeat sequence?
by Ansgar Furst 28 Oct '11

28 Oct '11

Dear Anastasia and Team FreeSurfer, First of all thanks so much for developing TRACULA. I think it has a lot of potential! Here is my question: I'm trying to modify "dmrirc_single_subject" file in order to reflect our local sequence and wondered how you are dealing with DTI repeat sequences for the same subject. We acquire 5 B0s and 30 directional scans twice in a row. So our *Diffusion bvalue Table would look like this: ================================================================== * 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 Now I wonder how I would modify the below default settings from the tutorial data to reflect this: ===================================================================== set subjlist = (Diff001) set runlist = (1) # Input diffusion DICOMs (file names relative to dcmroot) set dcmroot = /usr/local/freesurfer/TUTORIAL_DATA/diffusion_tutorial/ set dcmlist = (Diff001/orig/6-1.dcm) ===================================================================== Oh also, I noticed that in the wiki you have the following settings: ======================================================================= set trainfile = $TUTORIAL_DATA/diffusion_tutorial/subj,train,difftutorial23.txt =============================================================================================== In the latest version of the freesurfer distribution I counted 33 subjects for the training algorithm and therefore use: "subj,train,difftutorial33.txt" pointing to /usr/local/freesurfer/trctrain/trc001 /usr/local/freesurfer/trctrain/trc002 /usr/local/freesurfer/trctrain/trc003 /usr/local/freesurfer/trctrain/trc004 /usr/local/freesurfer/trctrain/trc005 /usr/local/freesurfer/trctrain/trc006 /usr/local/freesurfer/trctrain/trc007 /usr/local/freesurfer/trctrain/trc008 /usr/local/freesurfer/trctrain/trc009 /usr/local/freesurfer/trctrain/trc010 /usr/local/freesurfer/trctrain/trc011 /usr/local/freesurfer/trctrain/trc012 /usr/local/freesurfer/trctrain/trc013 /usr/local/freesurfer/trctrain/trc014 /usr/local/freesurfer/trctrain/trc015 /usr/local/freesurfer/trctrain/trc016 /usr/local/freesurfer/trctrain/trc017 /usr/local/freesurfer/trctrain/trc018 /usr/local/freesurfer/trctrain/trc019 /usr/local/freesurfer/trctrain/trc020 /usr/local/freesurfer/trctrain/trc021 /usr/local/freesurfer/trctrain/trc022 /usr/local/freesurfer/trctrain/trc023 /usr/local/freesurfer/trctrain/trc024 /usr/local/freesurfer/trctrain/trc025 /usr/local/freesurfer/trctrain/trc026 /usr/local/freesurfer/trctrain/trc027 /usr/local/freesurfer/trctrain/trc028 /usr/local/freesurfer/trctrain/trc029 /usr/local/freesurfer/trctrain/trc030 /usr/local/freesurfer/trctrain/trc031 /usr/local/freesurfer/trctrain/trc032 /usr/local/freesurfer/trctrain/trc033 Does that make sense? Thanks so much for your help! Ansgar

3 7

Do cerebellum, pons, and brain stem need to be in input MRI?
by Andreas Schuh 28 Oct '11

28 Oct '11

Hi FreeSurfers, I just processed a dataset using FreeSurfer (the base created from the norm.mgz volumes of a longitudinal study) and noticed that the labels for the cerebellum are causing an incorrect segmentation towards the inferior of the cortex. Further, labels for cerebellum, brain stem and the fourth ventricle can be found outside the brain mask (see attached screenshot). Note that input was not a full head scan, but an already skull stripped brain only image, i.e., also without cerebellum and brain stem. Does FreeSurfer not work with such input data? Must the cerebellum be present? Thanks, Andreas

1 0

Viewing Control Points
by Matt Glasser 27 Oct '11

27 Oct '11

Hi, Is it possible to view control points (in control.dat), that you already created? If so, how do you do it? Thanks, Matt.

2 3

white matter volume in a ROI
by dolphinede＠aol.com 27 Oct '11

27 Oct '11

Dear FreeSurfer experts, i have created a ROI in qdec , where i have found a significant correlation between lgi and age. I mapped this ROI to all subjects. I am interested to compare in this ROI the pial-surface area, the grey matter volume and if possible the white matter volume for this specific region and i am not sure how to do this? Best regards Daniel Klein

5 4

Segmentation error?
by Gergely Orsi 27 Oct '11

27 Oct '11

Dear Freesurfers!! I've encountered two strange segmentation "errors", if they are errors at all. Please see the attached fs.png: You can see that there are excess pial tissues on the superior part of the brain. The pial surface is defined correctly and the excess pial tissue is outside the red line yet it is coloured pink. My question, is : Does this have any impact on the results? The second is related to the hippocampus. Please see the attached fs2.png: The pial surface around the hippocampus looks a bit weird. It actually discards 1/3 of the hippocampus (it is outside the red line). Do you have any suggestions regarding the two problems. I'm using FS 4.5 on several 64bit linux distributions. -- Gergely Orsi biologist - research associate Diagnostic Center of Pécs H-7623 Pécs, Rét str. 2. Tel.: 0036-70-3174676 E-mail: gergo.orsi(a)gmail.com

3 12

Changing labels of aseg.mgz to {BG, CSF, GM, WM}
by Andreas Schuh 26 Oct '11

26 Oct '11

Hi FreeSurfers, The results of FreeSurfer include a subcortical segmentation and a segmentation of white matter only. However, there is no segmentation of (background), cerebrospinal fluid, gray matter, and white matter only as produced by other tools. Such segmentation is often (as in our case) required for an evaluation study. Thus, relabeling the subcortical segmentation (mri/aseg.mgz) should be an option. Find attached a C++ implementation of such program, depending only on the nifticlib library. Questions: a) Does this mapping of FreeSurfer labels to the classes BG, CSF, GM, and WM look correct? Note that it is mainly based on Table 41 on page 71 of the master thesis of Kowkabzadeh found on the web [1]. b) Is there already such tool in the FreeSurfer package actually? I have seen mentioning of mri_compute_volume_fractions on this mailing list but could not figure how to use it. (A more meaningful help output of the tools would be nice... in particular what [options] are available). Thanks, Andreas [1] K. Kowkabzadeh, Evaluations of Tissue Segmentation of brain MR Images, Master of Science Thesis in Biomedical Engineering, Department of Signals and Systems, Division of Biomedical Engineering, Chalmers University of Technology, Göteborg, Sweden, 2010 Report No. EX048/2010, http://publications.lib.chalmers.se/records/fulltext/125991.pdf

1 0

Remote tkmedit/qdec segmentation fault
by Martijn Steenwijk 26 Oct '11

26 Oct '11

Dear all, I would like to use Freesurfer's (5.1.0, 64bit) gui interfaces remotely to inspect Freesurfer's results produced on a server. I used two setups in an attempt to realize this: 1. PuTTy with X11 forwarding and Xming 2. TightVNC with VirtualGL In both configurations, entering for example the command 'tkmedit' or 'qdec' (or in case 2 'vglrun cmd') results in a segmentation fault. In another thread I found the suggestion to 'setev QDEC_DONT_USE_HISTOGRAM_EDITOR 1', but unfortunately this doesn't help. Do you have any ideas to fix this? Thanks in advance, Martijn

2 3

gray scale inflated surf rendering prob
by Gregory Kirk 26 Oct '11

26 Oct '11

send a question that martina asked before and we have not solved the prob. on macs when we run tksurfer xxx lh inflated for example the surf comes up looking smoother,low resolution rendered. if we load something like curvature that displays in color the surface looks fine, so the problem is only with the grayscale surfaces. this occurs on all the macs in a psychiatry dept. lab,other macs at other labs around the surfs always appear normal, i have never seen this problem before, the machines used to display the surfs normally and then all of a sudden it started happening all the time on this one group of macs, seems it must be associated with some config change or upgrade,but i am not much of a mac uses, i use linux. anybody out in freesurfer land seen something like this and can give me a clue ? thanks greg

2 1

-notalcheck question
by Christopher McCarthy 26 Oct '11

26 Oct '11

Freesurfer Experts, I am having lots of success, and making progress, with FreeSurfer thus far. I have been able to load DICOMS into Slicer3 to reorient, and resample them, after using FSL to extract the brain. Loading these brains into FreeSurfer is straight forward, and I've run them through the entire process. However, I am still hoping to use brains that have been previously skull stripped but are unfortunately saved in analyze (.img, .hdr) format. All of the things that I've tried have led to a talairach error, and the brain being incorrectly oriented when loaded in tkmedit. Using slicer3, however, I was able to load the .img file and put the brain in ACPC space using the ACPC registration module included. It still gives me a talaraich error, but if I run recon1 with -notalcheck, the process runs without error and the brain is correctly oriented in tkmedit. Is this data usable? If I run it with notalcheck will I be unable to use volumetric analysis reliably? Thanks for your help and patience! Chris McCarthy

2 1

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