Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Rejoindre mon réseau sur LinkedIn
by Sinem Burcu Erdogan via LinkedIn 26 Dec '13

26 Dec '13

LinkedIn ------------ Sinem Burcu Erdogan souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Sinem Burcu Erdogan http://www.linkedin.com/e/-qq80um-hpoic7zr-14/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir l'invitation de Sinem Burcu Erdogan http://www.linkedin.com/e/-qq80um-hpoic7zr-14/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… ------------------------------------------ Quel est l'intérêt de faire partie du réseau de Sinem Burcu Erdogan ? Le réseau de Sinem Burcu Erdogan développera votre propre réseau : Si vous acceptez l'invitation de Sinem Burcu Erdogan, vous pourrez voir qui vous connaissez dans son réseau et demander à Sinem Burcu Erdogan de vous présenter. Appartenir à un réseau est toujours un plus pour votre carrière. -- (c) 2012, LinkedIn Corporation

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manual edit
by irene saviozzi 26 Dec '13

26 Dec '13

Hello, I'm learning to use freesurfer. I would understand if the tissue that is not brain (i.e. meninges), which is not automatically included in pial, must be deleted with the manual editing or not. I would also like to understand how add cortex manually in the pial surface with tkmedit. I attach two screenshots as examples. Thank you Irene

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fsl & T2pial
by Octavian Lie 24 Dec '13

24 Dec '13

Dear All, I plan starting running the -FLAIRpial flag for pial refinement, after recently upgrading freesurfer to dev (12/19/2013), centos6 86X64 build. I installed the new fs according to the wiki guidelines. I read on the forum that FSL_DIR has to be set up, and FSL has to be installed for bbregister to work. The default wiki installation does not set FSL_DIR. I found a bbregister file dated 12/17/2013 by Doug in freesurfer/bin, so it could be that the above issue has been solved, please confirm. Octavian

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Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations Usage
by Salil Soman 24 Dec '13

24 Dec '13

Hi, Have been able to run kvlQuantifyHippocampalSubfieldSegmentations.sh to get hippocampal subfield segmentation number of voxels. How do I convert these values into volumes? I am guessing the voxel size of the original image is not the correct conversion factor. Also, I have not been able to find any details regarding the doPartialVolumedSegmentation vs doNonPartialVolumedSegmentation options for this code. Can anyone point me to more details of why one would use one method vs the other? Thanks, -Salil

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P-value of interaction term in DODS
by jh kim 23 Dec '13

23 Dec '13

Dear Doug and experts Using DODS model in QDEC, I've found 2 significant clusters in whole-brain cortical thickness analysis between controls and patients (2 group, 1 factor), controlling for the effect of age (one covariate). My question is how can I obtain p value for interaction term (group*age) in each cluster? Is it possible to do that analysis in FreeSurfer pipeline? Or should I extract individual cortical thickness of each cluster and test this interaction term using statistics software (e.g., SPSS)? Thank you in advance for your help. Kim

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Rejoindre mon réseau sur LinkedIn
by Oya Hiroyuki via LinkedIn 23 Dec '13

23 Dec '13

LinkedIn ------------ Oya Hiroyuki souhaite se connecter à vous sur LinkedIn : ------------------------------------------ Je vous invite à faire partie de mon réseau professionnel en ligne sur le site LinkedIn. Accepter l'invitation de Oya Hiroyuki http://www.linkedin.com/e/-qq80um-hpk42h0n-23/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe5… Voir le profil de Oya Hiroyuki http://www.linkedin.com/e/-qq80um-hpk42h0n-23/rso/132163904/4Gcq/name/66471… ------------------------------------------ Vous recevez des invitations par e-mail. Cet e-mail est destiné à Freesurfer List. Découvrez pourquoi nous avons inclus ceci : http://www.linkedin.com/e/-qq80um-hpk42h0n-23/plh/http%3A%2F%2Fhelp%2Elinke… (c) 2012, LinkedIn Corporation. 2029 Stierlin Ct, Mountain View, CA 94043, USA.

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a confused problem about the GroupAnalysisClusterSummary
by charujing 23 Dec '13

23 Dec '13

Hi all, I learned the tutorial in the website: http://freesurfer.net/fswiki/FsTutorial/GroupAnalysisClusterSummary, and a problem I cannot deal with. In the 9th "CWP - clusterwise p-value. This is the p-value of the cluster", and "Eg, the 13th cluster has a pvalue of p<.006." What I saw in the file is " 13 -5.981 101953 361.51 -45.3 -44.5 -14.5 0.20000 0.00000 0.40000 536 -2401.60 inferiortemporal ". I didnot find any "0.006". Can anyone help me? Thanks. All the best. rujing Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com

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convert FSL .mat matrix to TkReg-RAS space
by Martin Luessi 23 Dec '13

23 Dec '13

Hi, I'm using FSL's mcflirt for motion correction with the "-mats" option to store a registration matrix for each time point. In my application, I would like to use a one-step interpolation process to sample points from the freesurfer surfaces (e.g. white) from the 4D fMRI data. I tried to convert the FSL .mat matrix to "TkReg-RAS space", which, as I understand it, is the space the surface coordinates in "lh.white" etc. are stored in. What I did: 1) Obtain the .mat matrix file using mcflirt: mcflirt -in bold.nii.gz -out bold_mcflirt.nii.gz \ -reffile bold_ref.nii.gz -mats this creates a directory "bold_mcflirt.nii.gz.mat", where the registration matrix files for each time point are stored (MAT_0000, MAT_0001...). As I understand it, the FSL matrix is the transform from bold to bold_ref in mm space. I.e., to get the transform in voxel coordinates, one would use: M_vox = A1 * M * inv(A2) where A1 and A2 are the affine matrices from the headers in bold_ref and bold, resp. The matrix M is the affine matrix computed by mcflirt. 2) Convert the matrix to TkReg-RAS space. The matrix bold->bold_ref matrix in this space is given by M_ras = vox2ras1 * M_vox * inv(vox2ras2) where vox2ras1 and vox2ras2 are obtained using "mri_info --vox2ras-tkr" for bold_ref and bold, resp. Is this correct? I have tried it and for some reason the translated points don't seem to be at the correct locations in the "bold space". What I did is create an all-zero nifti file with the same size as "bold" and then fill-in the points corresponding to the white surface. For later time points (when the subject movement relative to bold_ref is larger), the surface is increasingly misaligned. This tells me that either a) the transform is computed incorrectly or b) MCFLIRT stores something different than the bold -> bold_ref transform for each time point. Any help is appreciated. Best, Martin

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analyzing fMRI data across runs with slightly different slice prescriptions
by Rosa Lafer-Sousa 23 Dec '13

23 Dec '13

freesurfers, we've acquired fMRI data from [slightly different] slice prescriptions, all partial brain slices. we want to analyze this data all together, but we also want to have the best registration possible [i.e., use bbregister]. what's the best way to do this? here are the ideas we have: 1. analyze these data on the individual subject's surface with selxavg3-sess. the one problem is that we don't see how to pass the registration file for each run. [there are different registrations for distortion-corrected or not] 2. run glms for each run independently and then combine the subject's data together with a FFX analysis. what's the easiest way to run a FFX analysis with fsfast? 3. upsample these functional data to the subject's anatomy [either volume or surface] and then run the analysis there. however, this will take a good chunk of memory and compute time. what's the best thing to do here? thanks in advance, rosa -- 210-325-3185 rlaferso(a)wellesley.edu

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Units for Aparcstats2table for thickness and curvature
by Salil Soman 23 Dec '13

23 Dec '13

Hi, I am writing to confirm the units for aparcstats2table for thickness and thicknessSTD are mm, and curvature is radians. It would be a great help if this could be confirmed. Thank you. Salil

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Freesurfer December 2013