Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30088 discussions

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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Recon-all exits with errors for a patient with TBI
by Emad Ahmadi 23 Dec '13

23 Dec '13

Hello, I'm analyzing some images of patients with TBI. There's one of them having abnormalities in T1 images (skull fracture, epidural/intracranial hemorrhage, shifts) that can trouble image registration; when I run recon-all for this patient, it exits with errors. I wonder if it has anything to do with the abnormalities troubling the registration of T1 images. I've attached the log file, and some axial sections of the T1 images can be viewed here: https://drive.google.com/folderview?id=0B4AFmHFjy_bsbkotd2QyZjZ6dW8&usp=sha… Thank you and Merry Christmas! Emad

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Freesurfer installation error
by Octavian Lie 22 Dec '13

22 Dec '13

Dear All, I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version (12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf libraries missing in my distro, here is fs home directory: FREESURFER_HOME /usr/local/fs5.3/freesurfer FSFAST_HOME /usr/local/fs5.3/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/fs5.3/freesurfer/subjects MNI_DIR /usr/local/fs5.3/freesurfer/mni Testing using the commands on the testing page went OK, however, if I close the terminal, open another one, commands are not recognized, and I have to reset freesurfer home every time I open a terminal with setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh I thought this is a sudo issue, however if I use sudo setenv FREESURFER_HOME /usr/local/fs5.3/freesurfer, it tells me: sudo: setenv: command not found I mention I changed the default shell from bash to tcsh recently, Please advise, Octavian

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Freesurfer dev install/ testing error
by Octavian Lie 22 Dec '13

22 Dec '13

Dear All, I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version of Freesurfer (I used previously version 5.1). Installation was uneventful, including getting the return to command > source $FREESURFER_HOME/SetUpFreeSurfer.csh FREESURFER_HOME /usr/local/fs5.3/freesurfer FSFAST_HOME /usr/local/fs5.3/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/fs5.3/freesurfer/subjects MNI_DIR /usr/local/fs5.3/freesurfer/mni When testing Freesurfer with freeview or tkmedit bert commands, I get invariably the following error 'error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory' Can you advise what I should do, including syntax (Gari has a similar problem, and he solved it "after reinstalling netCDF and updating the links (and some 64 bit packages missing too)"). Please let me know what else I should add/ modify after sudo apt-get install libnetcdf6 and what other packages and links have to be installed/ fixed Many thanks, Octavian

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jpeg compressed dicom mri convert error
by Octavian Lie 22 Dec '13

22 Dec '13

Dear all, I tried to run a subject's T1 starting with the dicom convert step (until now, I used .nii volumes as imput, after dicom conversion in spm; I would like to be able to use the dicom convert in freesurfer, since I have a -T2pial step to refine pias afterwards, and it's easier this way). I get the following mri_convert error about jpeg compression (this is the only dicom output processed at our facility): recon-all -s subj -i /home/ovl/Desktop/freesurferdicom/subj/T1/51129 Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer Linux Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/fs5.3/freesurfer/subjects/subj mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129 /usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129 /usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz $Id: mri_convert.c,v 1.206 2013/11/12 03:15:51 greve Exp $ reading from /home/ovl/Desktop/freesurferdicom/subj/T1/51129... Starting DICOMRead2() dcmfile = /home/ovl/Desktop/freesurferdicom/subj/T1/51129 dcmdir = /home/ovl/Desktop/freesurferdicom/subj/T1 Ref Series No = 302 Found 167 files, checking for dicoms Found 165 dicom files in series. First Sorting Computing Slice Direction Vs: -0.999557 0.0285859 -0.00787544 Vs: -0.99956 0.028586 -0.00787546 Second Sorting Counting frames nframes = 1 nslices = 165 ndcmfiles = 165 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.4.70-- ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) jpegUID: --1.2.840.10008.1.2.4-- Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj exited with ERRORS at Sun Dec 22 21:22:11 CST 2013 For more details, see the log file /usr/local/fs5.3/freesurfer/subjects/subj/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Is there a workaround in freesurfer? Thank you, Octavian

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Freesurfer installation testing tksurfer error
by Octavian Lie 22 Dec '13

22 Dec '13

Dear All, I have recently upgraded freesurfer (dev version 12/19/2013 centos6, 86X64) on my ubuntu 12.04 box, I previously used v 5.1(centos 4). I fixed all other issues that I posted about (libnetcdf missing,.tcshrc editing), now all seems to go well, including testing, except when I load tksurfer bert rh pial, I see it well, and I can use tksurfer tools well, as expected; however, if I want to close the window displaying surfaces (either before or after closing tksurfer tools gui), I cannot; the only way to kill the process and exit tksurfer is to close the terminal. Also, if I try to maximize the same window, I get the following error: surfer: Error sending tcl command MoveToolWindow 65 656: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed I loaded other subjects previously processed with v5.1 version, and I have the same issue. All other guis, including tkmedit, freeview and qdec work well. Please advise, Octavian

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