Freesurfer

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30099 discussions

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

2 8

recon-all CUDA error
by Chiu, Bryan (PHTH) 27 Jun '14

27 Jun '14

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

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Vertex-wise comparison thickness left and right hemisphere
by Martijn Steenwijk 27 Jun '14

27 Jun '14

Dear all, I would like to vertex-wise compare the left and right hemisphere thickness in a group of subjects. Would it be okay to just substract lh.hickness.0.mgh and rh.thickness.0.mgh (i.e. the files concatenating the thicknesses of all patients), then smooth and then perform a one sample t test? Or does freesurfer include a more sophisticated test to perform such a comparison? Best, Martijn

2 2

Re: [Freesurfer] Question about eTIV estimation
by Zia, Mohammad 26 Jun '14

26 Jun '14

Hi, Thanks for the replies and link. And sorry for the double post. Thanks, --Mohammad This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

1 0

Question about eTIV estimation
by Zia, Mohammad 26 Jun '14

26 Jun '14

Hi, Does the eTIV estimate include the CSF between the dura mater and pia mater? Thanks, --Mohammad This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by e-mail and destroy all copies of the original.

1 0

Question about eTIV estimation
by Zia, Mohammad 26 Jun '14

26 Jun '14

3 2

How to use clusterwise correction for multiple comparisons in Freesurfer
by Miao Wei 26 Jun '14

26 Jun '14

Dear Freesurfer experts, My dataset was processed by Brainsuite, so that after registration they are in .dfs format. Now I wanted to do multiple comparison correction. How do I import the data to freesurfer and do the corrections? Thanks. Miao

2 6

Longitudinal preprocessing troubleshooting
by Chiu, Bryan (PHTH) 26 Jun '14

26 Jun '14

Hi all, I have a set of data with ~75 subjects with up to 4 timepoints of scans. The structure of the data indicates that it would be best processed using a longitudinal design. I have recon-all most of the scans. There are a few scans that I am worried about and wondering how to treat each case. I do one sanity check with freeview using a modified version of bert's command: "freeview -v $SUBJECTS_DIR/bert/mri/brainmask.mgz -v $SUBJECTS_DIR/bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f $SUBJECTS_DIR/bert/surf/lh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/rh.white:edgecolor=yellow -f $SUBJECTS_DIR/bert/surf/lh.pial:annot=aparc:edgecolor=red -f $SUBJECTS_DIR/bert/surf/rh.pial:annot=aparc:edgecolor=red" 1a) Skull strip or underanalysis errors: I have attached one screenshot of a very severe case of an underanalysis. How should I treat this case? I have recently read about Editing a Recon in Freeview, but I'm not sure how to proceed with this. b) Skull strip errors -- Some scans have a very small amount of cerebral cortex labelling into the dura mater/ skull. Does this warrant the manual removal via freeview of the skull? 2) Since I am running this through the longitudinal processing, could I be able to skip #1 hoping that the averaging of the timepoints into a 'base' will remove these issues? 3) I have 2 brains that are completely whited out in Freeview (see attached). However the analysis went through and it looks good to me. Opening the raw Nifti file in mricroGL does not show this at all. What is going on and should I be concerned? 4) I have 2 other brains that failed the recon-all. One of them is a Talairach fail and the other one failed mri_watershed. Looking at these brains in mricroGL shows a dark shadow being cast over the brain running diagonally from the front of the head to the back. I think this is the root of the problem. Is there a way to fix this or should I consider these scans problematic and exclude them? Regards, - Bryan

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