Freesurfer June 2014

freesurfer@nmr.mgh.harvard.edu

155 participants
234 discussions

Mean diffusuvuty MD
by Alshikho, Mohamad J. 01 Jul '14

01 Jul '14

Hi Fs Experts, In order to calculate the mean diffusivity MD in my DTI data I did the following: 1. For the Eigvals.nii (the output of dt_recon) I used the following command line: fslmaths eigvals -div 3 md.nii 2. mri_vol2vol -mov md.nii --reg register.dat --fstarg -- interp nearest -- o md.anat.mgh 3. mri_segstats --seg $SUBJECTS_DIR/mri/aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --seg-erode 2 --i md.anat.mgh --sum md.stats is this correct ? I highly appreciate any suggestions and advices Mohamad

2 1

Pons and midbrain segmentation....
by Gonzalo Rojas Costa 01 Jul '14

01 Jul '14

Hi: How can I segment the pons and midbrain using freesurfer ?... or any other segmentation software that do such task ?... Sincerely, Gonzalo Rojas Costa -------------------------------- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Clínica las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

2 1

reading & writing surface files in python
by Alex Kell 30 Jun '14

30 Jun '14

hi freesurfers, i'm looking to read and write freesurfer surface files in python -- like MRIread.m & MRIwrite.m but for surfaces and in python. i'm happy to write the code myself, but it seems like the kind of thing that has been done before and i don't want to reinvent the wheel if i don't have to. i poked around and found pyfsio, which reads but doesn't write surfaces. any suggestions? thanks, alex

2 1

4 groups non-linear effect
by Jacobs H (NP) 30 Jun '14

30 Jun '14

Dear FreeSurfer team, We have processed our T1 data of 4 groups of subjects: controls and patients of varying degrees illness. Now we want to perform : - a F-test to compare the 4 groups (we have one covariate that we want to take into account) - a F test to investigate a differential effect of a blood value across the 4 groups. However, this effect might be non-linear (e.g. inverted U-shape). We have made our fsgd-files, but now we are struggling with the contrast files. Could you help us out on how to create these F-test contrasts? Thanks! Heidi

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Re: [Freesurfer] recon-all CUDA error (Chiu, Bryan (PHTH))
by Chiu, Bryan (PHTH) 30 Jun '14

30 Jun '14

Hi all, I am still working on this problem. Does anyone know if Freesurfer is asking for CUDA 5.0, except that I have CUDA 6.0 installed? My next steps will be to find out if Freesurfer is calling an older version of CUDA that isn't installed, or trying the CUDA samples. I really want to get this to work. -Bryan Date: Fri, 27 Jun 2014 17:59:37 +0000 From: "Chiu, Bryan (PHTH)" <bryan.chiu(a)ubc.ca> Subject: [Freesurfer] recon-all CUDA error To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <680D9B8D5FEAAF40A1A5878265424CA44A594981(a)s-itsv-mbx06p.ead.ubc.ca> Content-Type: text/plain; charset="iso-8859-1" Hi, I'm fairly novice at Linux and I've been trying to setup CUDA for recon-all. I get an error as follows: [TLA@COGMOB-linuxPC ~]$ recon-all -s bert -use-gpu -openmp 8 Testing for CUDA device: /usr/freesurfer/bin/mri_em_register_cuda: error while loading shared libraries: libcudart.so.5.0: cannot open shared object file: No such file or directory Linux COGMOB-linuxPC 2.6.32-431.el6.x86_64 #1 SMP Fri Nov 22 03:15:09 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s bert exited with ERRORS at Fri Jun 27 10:53:29 PDT 2014 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any idea what is going on? I setup CUDA and my Nvidia drivers according to this tutorial (http://aspratyush.wordpress.com/2012/05/06/install-nvidia-cuda-on-centos-6/) With, of course some slight changes to install the latest toolkit. Thanks in advance, - Bryan

1 0

Problem with mris_euler_number
by Jürgen Hänggi 30 Jun '14

30 Jun '14

Dear FS experts I am trying to reconstruct surface-based cortical models with a high resolution (0.5x0.5x0.5mm) using the cm flag. After topology fixing, the function mris_euler_number stops and reports the following error: mrisFindNeighbors: ../surf/lh.orig: face[324829].v[2] = 164499, but face 324829 not in vertex 164499 face list Invalid argument Any idea how to fix this problem? Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

how to generate statistics after segmentation of hippocampal subfields
by kangchengwang0808＠gmail.com 28 Jun '14

28 Jun '14

Hi experts, After segmentation of hippocampal subfields, how to generate statistics of the subfield regions, such as volume? Thank you Wang Kangcheng Faculty of Psychology, Southwest University, China Email: kangchengwang0808(a)gmail.com / wangkangcheng.001(a)163.com Address: No.2 Tiansheng Road, BeiBei District, Chongqing, 400715,P.R.China

1 0

freesurfer lme matlab tools
by melinda dora 27 Jun '14

27 Jun '14

Dear Free-surfer Group, I am currently attempting to use the lme matlab tools for my longitudinal analysis. My dataset consists of two time-points, and I am interested in the group by time interaction for my dataset. I am attempting to follow the wiki instructions, but are finding them hard at times. I have reached the stage where, for the mass-univariate analysis", it says to do [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3); May I just ask if its correct to fit the model with two random effects when I only have two time-points. Furthermore, this command is currently running, and it keeps saying, over and over, Warning: Matrix is close to singular or badly scaled. Results may be inaccurate. RCOND = 7.100165e-19. > In lme_mass_fit_EMinit>(parfor body) at 98 In parallel_function>make_general_channel/channel_general at 907 In remoteParallelFunction at 28 Has anybody else recieved this error? Is there a simpler method whereby to fit my model and the matrix, ie is there actually something wrong with my design matrix? It is as follows: intercept time hr+ 3xtime hr- 5xtime hc 7xtime hrill 9xtime age First column, all ones (intercept) Second column; time third column; group1 fourth column; group1*time fifth column; group 2 sixth column; group2*time seventh column; group three eighth column; group three*time nineth column; group4 tenth column; group4*time eleventh column; age Does this look correct? Can anyone please advise me on the error I am getting? Cheers, Melinda

2 1

Right hemispheric white matter mean FA
by Alshikho, Mohamad J. 27 Jun '14

27 Jun '14

Hi Fs Experts, In order to calculate the right hemispheric white matter mean fractional anisotropy (FA), I did the following: 1. I used " rh.dwhite.ribon.mgz" as input in mri_binaraize to create a binary mask (I did convert mgz to nii and vice versa) 2. I used mri_segstats --seg /aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i fa.anat.mgh -mask <MY BINARY MASK_THE OUTPUT OF MY PREVIOUS STEP>--sum fa.stats to generate the statistics . Is that right? Kindly, Any suggestions or comments? Thanks, Mohamad

2 4

aparc+aseg OR wmparc
by Alshikho, Mohamad J. 27 Jun '14

27 Jun '14

Hi Fs Experts, I am working on FA ROI analysis for my subjects, I did the following: 1. Mri_vol2vol -mov fa.nii -reg register.dat -fstarg -interp nearest -o fa.anat.mgh 2. Mri_segstat wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt -I fa.anat.mgh -sum fa.stats Then I used less fa.stats in order to view the statistics results... my question here is: can I use aparc+aseg.mgz instead of wmparc.mgz in my command line in step 2 in order to exclude the unsegmentedwhite matter in the output stats. Thanks, Mohamad

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Freesurfer June 2014