Freesurfer July 2012

freesurfer@nmr.mgh.harvard.edu

128 participants
194 discussions

How to register FLAIR to T1?
by Ed Gronenschild 16 Jul '12

16 Jul '12

Hi, I would like to register FLAIR to T1. Specifications FLAIR: axial acquisition, 24 slices, pixel size = 0.45 * 0.45 mm^2 slice thickness = 5.50 mm (no gap). The slices run from the top of the brain to just below the eyes. This is contrary to the T1 scan which covers the full head down to the neck. I have tried bbregiser as follows: bbregister --s 001 --mov 001_FLAIR.mgz \ --reg 001_register.dat --init-fsl --t1 --tol1d 1e-3 and inspected the result with tkregister2 --mov 001_FLAIR.mgz \ --reg 001_register.dat --surf The result looks bad, it is displaced and rotated by about 20 degrees with respect to T1. It makes hardly any difference if instead of --t1 --t2 as contrast setting was used. Is there a better way to do this registration? For instance, should I crop T1 to about the same space as covered by FLAIR? (FreeSurfer v4.5.0, MacOSX 10.5) Cheers, Ed

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Ribbon
by Colin Reveley 16 Jul '12

16 Jul '12

Hi - I need to make a ribbon volume. I have all the necessary surfaces, but I'm lacking an aseg.mgz because the data is monkey. I saw one guy on the list had success by just calling his orig.mgz aseg.mgz. I tried that, and it calculated the left right pial and white distances. Men sadly it segfaulted. The program mri_ribbon will give me separate left and white gm ribbons. I combined those, coloured them 3 and 42 and did my level best to fill the wm with the right values, but some bits are wrong. What I'm actually trying to do is use matt glassers myelin mapping in caret. other things could be wrong than my ribbon estimate. If anyone has an idea how to make a good ribbon without aseg I'd appreciate it. Please bear in mind I may be missing much of what one gets when one runs recon-all. I have thickness, curv, surfaces, filled.mgz, pretesselstion wm.mgz not so much else. The filled.mgz doesn't fill all non cortex the way the bert ribbon does, so it's not that useful. Thanks, Colin

4 3

qdec
by carolina.mr 16 Jul '12

16 Jul '12

3 2

multiple correction
by Meng Li 16 Jul '12

16 Jul '12

Hi, freesurfer expert, I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? Thanks, Meng

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Error compiling FS with GPU
by Akio Yamamoto 16 Jul '12

16 Jul '12

Hi FS experts, My colleague is trying to compile FreeSurfer by configuring with a "--with-cuda" flag. The build process stopped with the error message: ===== em_register_cuda.cu(347): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(350): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(353): error: calling a host function("LinearGenerator::LinearGenerator") from a __device__/__global__ function("TransformLogps") is not allowed em_register_cuda.cu(357): error: calling a host function("TransformGenerator::TransformGenerator") from a __device__/__global__ function("TransformLogps") is not allowed 4 errors detected in the compilation of ... ===== FYI, the build environment is as follows: GeForce GTX 690 CUDA Toolkit 4.2 CentOS 6.2 Are there any specific requirements for building CUDA-enabled FreeSurfer? Any information/help would be appreciated. Thanks, Akio

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Cutting non-cortex
by Sourena Soheilinezhad 15 Jul '12

15 Jul '12

Hi experts, I have two (unrelated) issues. I am seeking a command-line method to remove non-cortex vertices and triangles from a surface. I have seen the manual method with tksurfer, but perhaps this is not suitable for larger datasets? I have tried to use surf2surf for downsampling of the meshes NOT generated by Freesurfer into icosahedron, to no avail, maybe because this command seeks to map the .sulc data which is absent in the alien mesh. Please let me have any advice for this goal if basically possible with available freesurfer tools. Thanks, Sourena Soheili

2 9

MPRAGE intensity variations
by Chris Watson 15 Jul '12

15 Jul '12

Hello, I ran a subject through recon-all both with and without the "-mprage" flag, and naturally got different results. I'm attaching a screenshot of the pial and main surfaces, along with the orig.mgz of the same slice. The image tends to be brighter in the frontal lobe, and there is an intensity change when going through the slices. The scanner is Siemens 3T (Trio, I think), using a 32-channel head coil. The imaging parameters are: (not sure which are most relevant) TR: 1410 TI: 800 TE: 2.2 Matrix: 256x256 FOV: 256 Flip angle: 9 deg ImagingFrequency: 123.259181 Pixel bandwidth: 199 Is there anything I can do to improve the results? Thanks, Chris PS When I didn't use the '-mprage' flag, I used the '-nuintensitycor-3T' flag. So I changed 2 separate things.

3 3

multiple comparisons correction
by Meng Li 14 Jul '12

14 Jul '12

Hi, freesurfer expert, I have three questions about the multiple comparisons correction in Qdec. I performed the statistical analysis between two groups first in left hemisphere, and got some regions which showed different. 1) so if I then do multiple correction, i don't need to run the mri_glmfit-sim command, and just press the button of the monte carlo null-z simulation in the qdec interface, am i right? 2) Whether mri_glmfit-sim --cache command line and the mc-z in qdec get the same results, or not? and as to the option --cwpvalthresh, should i choose 0.05 or 0.025? 3) And what is the difference between fdr and mc-z correction? I also want to find a solution about an ERROR. I tried to run a cortical thickness analysis to look for differences between two groups (patients and controls) with regressing out the gender factor, the patients group have 1 female and 17 male, after analysis, I got the results. But when I add another continuous variable as covariate, I received the message: "ERROR: matrix is ill-conditioned or badly scaled." Then I tried to change the gender composition the patients groups: 2 female/16 male, and the problem was solved. so is it right about what i did, or I need another way to solve this problem? Thanks, Meng

1 0

Neuroimaging Postdoc opportunity Melbourne, Australia
by David Abbott 13 Jul '12

13 Jul '12

Research Scientist - Neuroimaging Analysis Level depending upon qualifications and experience: Research Officer / Senior Research Officer / Research Fellow / Senior Research Fellow. · 2 positions available - Structural & Functional Neuroimaging Analysis (both positions requiring methods development and application) · Medical research based at the Florey Neuroscience Institutes, Melbourne, Australia. The Florey Neuroscience Institutes employs more than 400 people who are passionately committed to researching the way the brain works. We are internationally renowned for our discoveries and research on the central nervous system and associated brain disorders. Key areas of interest include addiction, Alzheimer’s disease, cardiovascular disease, depression, epilepsy, Huntington’s disease, motor neuron disease, multiple sclerosis, Parkinson’s disease, schizophrenia, stroke and traumatic and spinal cord injury. An excellent opportunity is available for two Research Scientists to work on projects investigating brain disorders (in particular epilepsy) using brain imaging methods within the Brain Research Institute at our Austin facility in Melbourne, Australia. Successful applicants will assist in the implementation and development of MRI analysis techniques within the Institute. This includes development, implementation and advancement of structural and functional MRI techniques for use in research and clinical environments. - The first position has an initial requirement that the candidate performs analysis and solves problems related to the implementation of structural MRI analysis methods including quantitative morphometric methods such as voxel based morphometry and cortical thickness analyses. - The second position has an initial requirement that the candidate performs analysis and solves problems related to the implementation of functional MRI analysis methods including conventional functional MRI (fMRI), functional connectivity, and simultaneous electroencephalography (EEG) and fMRI. Each Research Scientist will also be expected to assist with aspects of MRI quality control, software development, and participate in general research activities of the Institute including submission of research grants, publication of peer reviewed papers, and publication of software. For more information or to obtain a position description please visit our web site at www.florey.edu.au/careers -- David Abbott, PhD Senior Research Fellow (Physics & Neuroinformatics), Brain Research Institute, Florey Neuroscience Institutes. Honorary Senior Fellow, Department of Medicine, The University of Melbourne. Address: Melbourne Brain Centre, 245 Burgundy Street Heidelberg, Victoria, 3084, Australia.

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Fwd: Register ROI5.nii to fsaverage in tutorial "Cortical Thickness of a Volume-defined ROI"?
by Garikoitz Lerma Usabiaga 13 Jul '12

13 Jul '12

Begin forwarded message: *From:* Garikoitz Lerma Usabiaga <garikoitz(a)gmail.com> *To:* Louis Nicholas Vinke <vinke(a)nmr.mgh.harvard.edu> *Subject:* *Re: [Freesurfer] Register ROI5.nii to fsaverage in tutorial "Cortical Thickness of a Volume-defined ROI"?* Thanks for your answer Louis, I think I'm using it, the steps were: 1- Correct visualization of ROI with: tkmedit -f TT_avg152T1.nii -overlay ROI45.nii -fthresh 0.5 2- I execute spmregister: spmregister --s fsaverage --mov ../../ROI2/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat 3.-Incorrect visualization when I execute: tkmedit fsaverage T1.mgz -overlay ../../ROI2/ROI45.nii -overlay-reg TT_avg152T1_to_fsaverage.dat -fthresh 0.5 -surface lh.white -aux-surface rh.white What I understand is that the .dat is a transformation matrix between TT_avg152T1 and fsaverage, so when I am asking to overlay ROI45.nii, I am asking tkmedit to transform it to fsaverage by the .dat file. Is that correct? What do you think that could be the error? I am attaching the images just in case... Thanks again, Gari PS This is the TT_avg152T1_to_fsaverage.dat: fsaverage 2.000000 2.000000 0.150000 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 -1.000000000000000e+00 0.000000000000000e+00 0.000000000000000e+00 0 0 0 1 round On 2012-07-12, at 17:56, Louis Nicholas Vinke wrote: Hi Gari, When you view the ROI5.nii on fsaverage make sure you include '-overlay-reg TT_avg152T1_to_fsaverage.dat'. TT_avg152T1_to_fsaverage.dat is the transformation computed in the previous step which you need to apply. Nothing was resampled in step 2. -Louis On Thu, 12 Jul 2012, Garikoitz Lerma Usabiaga wrote: Dear All, I am trying to automate ROI creation in freesurfer following the VolumeRoiCorticalThickness tutorial, based on the AAL defined ROI-s from MarsBar. QUESTION ROI5.nii was originally in the same space as TT_avg152T1.nii (see MORE INFO below). I understand that after Step 2 (when TT_avg152T1.nii is registered to fsaverage with spmregister), TT_avg152T1 will be in fsaverage space. But, we didn't transform or register ROI5.nii, so I understand that it will continue in the same original space. When I visualize ROI5 over the original TT_avg152T1 it is ok, but when I visualize it over the fsaveraged one, it is not. Shouldn't we need to register or normalize ROI5.nii to fsaverage as well prior to the mri_vol2surface mapping? MORE INFO: 1.- I created the ROI5.nii in MarsBar: "ROI definition" > "Export" > "Export ROI to image" (select: MNI_Frontal_Inf_Tri_L_roi.mat) > from image (select: avg152T1.nii) > Save it (name: ROI45.nii) 2.- I follow exactly the same steps as the tutorial, but in step 3) when I check the ROI in the inflated surface, it is clearly out of place... Thank you very much in advance, Gari Garikoitz Lerma Usabiaga Predoctoral Researcher www.bcbl.eu 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.

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Freesurfer July 2012