Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30085 discussions

unknown error
by Xiantong Zhen 13 Jan '10

13 Jan '10

Hi experts, I run freesurfer to compute the thickness, but I find some subjects failed with error. Would you please tell me how to handle this error. Thank you very much! And the error is as follow: .................................................................................... talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.6987, pval=0.4932 >= threshold=0.0050) awk -f /public/home/users/lzuxucl/freesurfer/bin/extract_talairach_avi_QA.awk /public/home/users/lzuxucl/subjects/S45260/mri/transforms/talairach_avi.log TalAviQA: 0.94844 z-score: -6 ERROR: Talairach QA check failed! z-score = -6 <= -6 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer..nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux node5 2.6.9-55.ELsmp #1 SMP Fri Apr 20 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Mon Jan 11 15:52:39 CST 2010 Best, Xiantong

2 1

(no subject)
by Guang Zeng 12 Jan '10

12 Jan '10

Recently, I sent several emails to ask the same kind of question about building our own template and atlas. Thanks a lot for the quick replies, they helps me a lot. Currently, I still have a question about building our own atlas using mris_ca_train, sorry to bother again. In our lab, we have a labeled surface atlas, we'd like to use this atlas instead of using FS's desikan_killiany.2007-06-20gcs. It is kind of difficult for us to load every subject in our training set to tksurfer, and manually label each ROI based on our ATLAS. >From what I learned from your replies, I did the follwoing steps to creat our own atlas, Step# 1 Select a subject, and then send it to oue ATLAS Toolbox for automatic segmentation and parcellation Step# 2 Sample the volume segmentations onto the surface Step# 3 Convert the sampled segmentations to an annotation file I applied those three steps to 59 subjects seperately, got .annot file for each of them, then I called the mris_train, my command line is: mris_ca_train -n 2 -t /home/freesurfer/ATLASColorLUT.txt lh sphere.reg myatalas.annot $subjects_list lh_myatlas.gcs My results are shown in the attached .ppt file, my question is: If we looked at Fig. 1(b) and Fig. 2 (b). There are no labels around the ventricl areas in my training set, while when the built atlas was loaded to average subject, that area was labled. If there are a way to avoid this problem and improve my atlas? Do I use the wrong command ? Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/196390709/direct/01/

1 0

thickness map from a label
by Ritobrato Datta 12 Jan '10

12 Jan '10

Hello All, I have created some surface labels and want to create corresponding thickness maps (Not stats). Is there a way to do that ? Thanks Ri

2 1

DICOM conversion
by Gergely Orsi 12 Jan '10

12 Jan '10

Dear All, I'm writing this here because I think some of you might be able to help. We're doing presurgical planning and surgical navigation based on fMRI. So far it was simple, but now, the program that we used for such evaluation was not able to evaluate the fmri, because of the poor SNR, so we evaluated with FSL, and got excellent results. Now, at the end, I have (after several conversion, transformation etc) 1 MPRAGE, and 4 coregistered fMRI images (only the tresholded Zstat images, for overlay), all 5 of them as a separate single dicom file. We use a GE machine for the navigation, that requires an MPRAGE (we got it ) and the overlays (4 fMRI in this case), if you have any. The main problem that it accepts only DICOM series (so 5 dicom series would be needed), but we have 5 single dicom files. Is it possible to make a DICOM series from a single dicom file? Any conversion tool? Thx, Gergo

2 1

Paired Analysis, Smoothing Step
by Stidd, Reva (NIH/NIMH) [F] 12 Jan '10

12 Jan '10

Hi there, I've got a sample with T1s and T2s that I'm trying to compare. I did the entire longitudinal stream protocol, and am now doing the paired analysis protocol. I'm stuck on the Spatial Smoothing step: I've only gotten either a ">" or a message reading, "ERROR: Option -sval unknown" Is there any reason why? Thanks, -Reva ----------------------------- CHP-MP6:subjects revastidd$ ls (all *.long.* files, base files and timepoint scans are listed plus the following files/folders:) 12SIB FSGD README Random Output V1_average bert fsaverage lh.paired-diff.thickness.mgh mris_preproc.surface.lh.log mris_preproc.surface.rh.log random rh.paired-diff.thickness.mgh sample-001.mgz sample-002.mgz wmparc.vol.table CHP-MP6:subjects revastidd$ mri_surf2surf --s fsaverage --hemi lh --fwhm 5 \ --sval lh.paired-diff.thickness.mgh \ --tval lh.paired-diff.thickness.sm05mgh ERROR: Option --sval unknown CHP-MP6:subjects revastidd$ mri_surf2surf --s faverage --hemi lh --fwhm 5 \ --sval lh.paired-diff.thickness.mgh \ --tval lh.paired-diff.thickness.sm05.mgh \ > -----------------------------

2 1

ANN - SVM, Alzheimer's Disease and FreeSurfer
by Pedro Paulo de Magalhães Oliveira Junior 12 Jan '10

12 Jan '10

Hi, We have published another paper using FreeSurfer, maybe you can add it to the Article page in the Wiki http://iospress.metapress.com/content/r1533322r7481q35/?p=2cecbdd44e114a5fb… <http://iospress.metapress.com/content/r1533322r7481q35/?p=2cecbdd44e114a5fb…> *Use of SVM Methods with Surface-Based Cortical and Volumetric Subcortical Measurements to Detect Alzheimer's Disease* Authors Pedro Paulo de Magalhães Oliveira Jr.1, Ricardo Nitrini2, Geraldo Busatto3, Carlos Buchpiguel4, João Ricardo Sato1, Edson Amaro Jr.1 1NIF – Neuroimagem Funcional, Departamento de Radiologia da Faculdade de Medicina do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil 2Departamento de Neurologia da Faculdade de Medicina do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil 3LIM21, Instituto de Psiquiatria da Faculdade de Medicina do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil 4Medicina Nuclear, Departamento de Radiologia da Faculdade de Medicina do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Brazil Abstract: Here, we examine morphological changes in cortical thickness of patients with Alzheimer's disease (AD) using image analysis algorithms for brain structure segmentation and study automatic classification of AD patients using cortical and volumetric data. Cortical thickness of AD patients (n=14) was measured using MRI cortical surface-based analysis and compared with healthy subjects (n=20). Data was analyzed using an automated algorithm for tissue segmentation and classification. A Support Vector Machine (SVM) was applied over the volumetric measurements of subcortical and cortical structures to separate AD patients from controls. The group analysis showed cortical thickness reduction in the superior temporal lobe, parahippocampal gyrus, and enthorhinal cortex in both hemispheres. We also found cortical thinning in the isthmus of cingulate gyrus and middle temporal gyrus at the right hemisphere, as well as a reduction of the cortical mantle in areas previously shown to be associated with AD. We also confirmed that automatic classification algorithms (SVM) could be helpful to distinguish AD patients from healthy controls. Moreover, the same areas implicated in the pathogenesis of AD were the main parameters driving the classification algorithm. While the patient sample used in this study was relatively small, we expect that using a database of regional volumes derived from MRI scans of a large number of subjects will increase the SVM power of AD patient identification. Keywords: Alzheimer's disease, FreeSurfer, magnetic resonance imaging, support vector machine, surface based methods ----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.2 www.Netfilter.com.br --- Novo Netfilter Small Business

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modification of tksurfer and tkmedit palette...
by Gonzalo Rojas Costa 12 Jan '10

12 Jan '10

Hi: I want to modify the color palette that tksurfer uses to display overlay data... How can i modify it ?... the same question for tkmedit... Sincerely, Gonzalo Rojas Costa

1 0

RAS to Vertex Index
by Oya, Hiroyuki 12 Jan '10

12 Jan '10

Dear EXPERTS, I have a coordinate set (RAS) in a volume and would like to map those coordinates in a surface of same subjects. Is there a good way to convert Volume RAS to vertex index directly rather than searching with mouse? Thank you. Hiroyuki

2 1

combining multiple labels to a single label
by Ritobrato Datta 11 Jan '10

11 Jan '10

Hi all, Is there a way / program to specify and combine multiple labels to create a single label ? Please let me know. Thanks a lot Ri

3 2

manually labeled subjects used for building the desikan_killiany gcs file
by Guang Zeng 11 Jan '10

11 Jan '10

Hello, there, If it possible that I can view or download the manually labeled subjects you used for building the desikan_killiany gcs file from somewhere in the wiki? Thanks! Guang _________________________________________________________________ Hotmail: Powerful Free email with security by Microsoft. http://clk.atdmt.com/GBL/go/196390710/direct/01/

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Freesurfer