Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

results that are difficult to explain, difference in correlation
by Knut J Bjuland 05 Dec '11

05 Dec '11

I have subject proceed with Freesurfer 4.30 and Freesurfer 5.1. The subjects proceed with Freesurfer 5.1 appears to have thicker cortex than in Freesurfer 4.30. When I correlate the cortical thickness against continuous variables like IQ, I get a difference. Is this expected since I get a correlation on the different side with Freesurfer 4.30 and Freesurfer 5.1.? Can part of the explanation be that Freesurfer 5.1 does not use mri_gcut, and that the registration transformation is changed in Freesurfer 5.1? I get different ras_vox matrix transformation and different flip angle. Knut J

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Freesurfer and Civet
by gcorbetta＠fatebenefratelli.it 05 Dec '11

05 Dec '11

Hi everyone, I am pretty new with Freesurfer and I'd be very grateful if some of you could help me out with the following issue. I have a subject which has been processed both with Freesurfer and Civet-CLASP, and I would love to compare the two output cortical thickness maps. I have resampled the Freesurfer map onto an ico-order 6 template, in order to have the same number of vertex (40962) as the Civet standard output. If I'm not wrong, the Civet algorithm works with the ICBM 152 template whereas Freesurfer with the MNI 305. These two templates are in the same space as the ICBM 152 is spatially registered to the MNI 305, aren't they? This means that I dont need any further spatial registration to one another and that I can compare vertex-per-vertex my FS an Civet maps? I bet it's not as naive as it seems to me right now, but a lot trickier.. Does anyone have an idea about how I could perform this comparison? Thanks in advance! Gabriele Corbetta MSc Lenitem Lab IRCSS Fatebenefratelli , Brescia - Italy

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Re: [Freesurfer] tcl script question: labl_set_color
by Justin Baker 04 Dec '11

04 Dec '11

I am trying to use tksurfer to script overlay of a label + functional map onto an fsaverage5 surface. In particular, I want to set the label to "fill" and color it red. I have: set labelstyle 0 labl_set_color 0 255 0 0 As you can see below, the output of label_print_list shows that the color of the label should be "255 0 0 " but it looks white in the output image. Am I missing something? Thanks ------------ subject is fsaverage5 hemi is lh surface is inflated Label 0 Name: lh.17Networks_LH_ContB_PFClv.label, 109 vertices Structure: -1 Color: 255 0 0 Visible: 1 Bounds: x -20.879234 12.792567 y -4.000000 109.853737 z -4.033233 4.040778

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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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Freesurfer December 2011