Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Editing wm.mgz versus correcting intensity normalisation
by Mahinda Yogarajah 04 Dec '11

04 Dec '11

Dear Freesurfer Experts, I am processing some coronally acquired 3T GE FSPGR T1 volumes. I have noticed that on occasion slices pial and white surfaces at the very front of the brain can go very wrong - either frontal slices are excluded all together (present in brainmask.mgz but no pial or wm surfaces derived) or white matter is mistakenly classified as grey matter. In order to correct this am I correct in assuming that the best method would be to use control points to fix the intensity normalisation ? Alternatively, when is it better to edit the wm.mgz volume to include those voxels which are white matter ? - It is not entirely clear to me from the tutorial. Thank you. M

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Error: [Cannot allocate memory] having 16GB of Memory.
by Fidel 04 Dec '11

04 Dec '11

Dear all, I'm having a problem running trac-all -prep. I receive this error (FROM THE TRAC-ALL.LOG WHICH IS ATTACHED): MRIalloc(218, 182, 182): could not allocate 158704 bytes for 25th slice Cannot allocate memory Linux ubuntu 2.6.38-13-generic-pae #52-Ubuntu SMP Tue Nov 8 17:50:45 UTC 2011 i686 i686 i386 GNU/Linux trac-preproc exited with ERRORS at Fri Dec 2 05:02:57 PST 2011 I am using Ubuntu 11.04 (Natty) 32bits and the kernel is 2.6.38-13-generic-pae, that is, it can use more than 4 GB of RAM (In fact, I was running it with 16GB of RAM) so we think memory was not the real cause of the problem. The freesurfer version was: freesurfer-Linux-centos4-stable-pub-v5.1.0 Thanks and best regards. Fidel.

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Transforming Lesion masks to the image space
by Navid Shiee 03 Dec '11

03 Dec '11

Hi, I am using freesurfer to process subjects with WM lesions. My data is axial and my lesion masks are in this space. I wanted to use the lesion mask to correct wm.mgz to improve the cortical surfaces. to perform this I tried to use mri_convert lesion.mgz lesion_FS_spance.mgz --conform It takes the lesion mask to the desired space, however it used linear interpolation, I need nearest neighbor interpolation. I could not find a flag for specifying the interpolation type in mri_convert. Would you please help me with this? Thanks, -- Navid Shiee Ph.D. Candidate Laboratory of MEDical Image Computing (MEDIC) Image Analysis and Communication Laboratory (IACL) Johns Hopkins University

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Brain Volume measures
by Jeff Sadino 02 Dec '11

02 Dec '11

Hello, Thank you Bruce and Doug for your answers to my previous question about a bad talairach.lta file. I am now grabbing volumes using fs5.0.0 and would like to ask for clarification. On the Morphometry Stats page at http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats, it says that the cortex is based on the pial surface. I am wondering what this includes. I loaded up the pial surface in tkmedit along with aseg.mgz. It looks like the following regions are completely outside the pial surface: cerebellum, 4th ventricle, Brain-Stem, optic chiasm. Is it correct that these regions are excluded? And then it looks like the hippocampus, amygdala, and inferior-lateral-ventricle are only halfway outside the pial surface. Is that correct? If it is, then is there a recommended way to exclude the hippocampus, amygdala, and inferior-lateral-ventricle regions in the cortical gray matter? Do these regions get properly accounted for in the subcortical gray calculation? And then for the white matter, the webpage says that it is based on the white surface. Looking at the white surface (lh.white), all of the subcortical gray matter and ventricles are enclosed in the surface. Can someone explain how the subcortical gray gets excluded? Finally, for the SubCortGray reported in aseg.stats file, does that exclude the following areas: Left-Lateral-Ventricle Left-Inf-Lat-Vent 3rd-Ventricle 4th-Ventricle CSF Left-vessel Right-Lateral-Ventricle Right-Inf-Lat-Vent Right-vessel 5th-Ventricle Left-Cerebellum-White-Matter Right-Cerebellum-White-Matter WM-hypointensities What about the brain stem? Why is the cerebellum Gray Matter included? I ask because the only way I can get close to the SubCortGray by using the aseg file is by excluding those regions. Once again, thank you for your invaluable help! Jeff Sadino

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Contrasts in GLM
by Linda Zhang 02 Dec '11

02 Dec '11

Dear all, I have a bit of an amateur question. I've read the slides and tutorial for group analysis, but I'm still confused about the contrasts. I made my fsgd file, which contains two groups: M and F. I also have three continuous variables: Age, MMSE, Education. I would like to test whether thickness is correlated with MMSE scores, after controlling for gender, age, and education. What should my contrast file be in this case? Thanks for the help! Cheers, Linda

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about labels
by LAOUCHEDI MAKHLOUF 02 Dec '11

02 Dec '11

hi everyone i have run recon-all on somme subjects and i want to make build a masque containing somme geri (pre and post central for example) and with some color, to load on a pial surface (as overlay). i tried to understand the commands like mri_annotation2label and mris_label2annot but i didn't succeed to work with. can anyone help me with some example thanks

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Re: [Freesurfer] Error with mri_glmfit-sim \
by Douglas N Greve 02 Dec '11

02 Dec '11

Is this volume data? If so, then use --grf with mri_glmfit-sim instead of --cache. doug Antonella Kis wrote: > Dear Doug, > > Can you please advise me how I can do a multiple comparison for my DTI > group analysis? > > I tried and I ran: > > mri_glmfit --y group-fa-tal.nii > --fsgd DTI_group_analysis.fsgd dods --cwpvalthresh .99 \ --C > contrast.mtx --glmdir group_analysis-0.99.glmdir > > but I got: > > ERROR: Option --cwpvalthresh unknown > so I really don't know how I can do the multiple comparison in this > case: the DTI data. > > Also, I tried to run the: > > > mri_glmfit-sim \ > --glmdir group_analysis.glmdir \ > --cache 2 neg \ > --cwpvalthresh .99 \ > --overwrite > > but I got another ERROE: > > ERROR: cannot find > /usr/local/freesurfer//average/mult-comp-cor///cortex/fwhm04/neg/th20/mc-z.csd > > Thank you very much! > Antonella > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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how to make lh.curv lh.sulc visible
by Maria Felber 02 Dec '11

02 Dec '11

Dear all, in the process of understanding freesurfer I like to see/inspect the created transforms visually. However, so far I am not able to see all the data that is stored in the transforms folder. So is it possible to see files like /transforms/lh.curv or /transfroms/lh.sulc? And if yes, what is the programm and command order? So far, I only figured out how to see data like /transforms/lh.pial lh.orig lh.inflated and so on. Thanks a lot, Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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Computing Volume of Segmentation Label Above or Below a User-Defined Plane
by Joshua Lee 01 Dec '11

01 Dec '11

Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh

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Re: [Freesurfer] Four Groups (Two Factors/Two Levels), One Covariate with very strange results
by Douglas N Greve 01 Dec '11

01 Dec '11

For thickness studies, if you have just one group, then the only thing to test is the slope, and it should not matter (but you might need DeMean to make it well conditioned). doug Knut J Bjuland wrote: > Hi > > Should i also add demean flag if I had just one group an one continus > variable like iq. I get in this case significant findings on the other > side of the brain in Fs 5.1 than in Fs 4.30 > > Thank you for you time > Knut j > > > Date: Thu, 1 Dec 2011 12:09:52 -0500 > > From: greve(a)nmr.mgh.harvard.edu > > To: knutjbj(a)hotmail.com > > Subject: Re: [Freesurfer] Four Groups (Two Factors/Two Levels), One > Covariate with very strange results > > > > I think the problem is just a scaling issue with the ages being 20x > more > > than the offset (which is 1). The next version will handle this > > internally, but you can go ahead and use the DeMean flag in the > FSGD. If > > your goal is to test for a difference in covariate slope across the > > groups, then adding the DeMean flag will not affect the results. > > However, if the continuous variables (covariates) are nuisance > > variables, then you should first test your contrast of interest on the > > slopes (using the DODS model). If there is no difference, then you > > should re-run the analysis with DOSS. > > doug > > > > Knut J Bjuland wrote: > > > Hi Nick > > > > > > Thank for the replay. > > > > > > > > > I have one group with premature that I compares to a group with term > > > born controls. However when I control for gender and age I get this > > > error message. > > > > > > ERROR: matrix is ill-conditioned or badly scaled, condno = 11065.5 > > > -------------------------------- > > > Possible problem with experimental design: > > > Check for duplicate entries and/or lack of range of > > > continuous variables within a class. > > > If you seek help with this problem, make sure to send: > > > 1. Your command line: > > > mri_glmfit --y lh.60.mgh --fsgd group_diff_gender_age_old.fsgd --C > > > Controls_VLBW.intercept.mtx --cortex --glmdir new --surf fsaverage lh > > > 2. The FSGD file (if using one) > > > 3. And the design matrix above > > > > > > > > > But when I added those subject that are commented I am able to run > > > mrl_glm fit without problems. I have checked for the usual errors and > > > there are none duplicated entries. The variables are 4 fixed > > > variables and one continuous variable named age in years. When I add > > > the subjects that are commented out I am able to produce an design > > > matrix. Having said that I am able to produce an matrix that works by > > > adding demean flag, but I am uncertain if it will is good idea. Could > > > you please take a look at my fsgd file and error message. > > > > > > I know that there is difference between Freesurfer versions in > > > results. But should the difference be huge or small. I am able to > > > reproduce results in previous Freesurfer when using group difference > > > in thickness, but not when I am adding continues variables for > > > instance in correlation analysis. I am enclosing two jpg files of the > > > results. > > > > > > > > > Best regards > > > Knut J > > > > > > > > > > > > > > > > ------------------------------------------------------------------------ > > > > > > > ------------------------------------------------------------------------ > > > > > > > -- > > Douglas N. Greve, Ph.D. > > MGH-NMR Center > > greve(a)nmr.mgh.harvard.edu > > Phone Number: 617-724-2358 > > Fax: 617-726-7422 > > > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > > > > The information in this e-mail is intended only for the person to > whom it is > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > > but does not contain patient information, please contact the sender > and properly > > dispose of the e-mail. > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Freesurfer