Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

aseg.stats volume mismatch
by Gabor Perlaki 06 May '14

06 May '14

Dear all, I've loaded the mri/aseg.mgz in slicer3D and done a label statistics on the image. The left caudate was reported to be 4005 mm^3 and the right caudate to be 4011 mm^3 by Slicer3D. However, these numbers are somewhat different from the values reported in aseg.stats: 3757 mm^3 and 3901 mm^3. Could anyone help me how to resolve these findings? Thanks, Gabor

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Two positions are available @ Queensland Brain Institute
by Yong Liu 06 May '14

06 May '14

Dear all, Two positions are available @ Queensland Brain Institute. *POSITION 1:* Postdoctoral Fellow Position in Neuroimaging and Brain Network Analysis at Queensland Brain Institute The Neuroimaging and Brainnetome Laboratory of Queensland Brain Institute (QBI) and Centre for Advanced Imaging (CAI) at the University of Queensland, Australia, solicits applications for postdoctoral fellow positions in neuroimaging and brain network analysis in healthy and neuropsychiatric diseases. We are looking for an excellent and highly motivated candidate with a PhD degree in neuroimaging, physics, mathematics, computer science, neurobiology, experimental psychology or comparable background. Interest and/or previous experience in/with neuroscience, MRI methods, design and image analysis are a plus. Experience with the LINUX/UNIX operating system is a positive add on. The successful candidate will participate in the multidisciplinary project involves developing algorithms of neuroimage processing and brain network analysis and software and applying them to neurosychiatric diseases. The main focus of this project is twofold: (1) developing new algorithms for structural MRI, functional MRI, DTI, and resting state MRI; (2) the assessment of differences between psychiatric patients and healthy controls in brain functioning, anatomy, default mode and functional connectivity. The postdoctoral fellows will be jointly supervised by Professor Tianzi Jiang and other Professors (QBI) who are experts in neuroscience. As at 30 June 2014, an applicant must not have had more than five years full-time equivalent professional research experience since the award of a PhD. The current salary range for the award is on a four-level scale from A$71,528.60 – A$79,708.50 per annum. Commencing salaries are based strictly on the number of full years’ experience since receiving a doctorate. Salary scales are reviewed from time to time. Please contact Professor Tianzi Jiang on tianzi.jiang(a)uq.edu.au for research plan. To submit an application for these positions, please refer to http://www.uq.edu.au/research/research-management/uq-postdoctoral-research-… . The application deadline is *19 May 2014.* *POSITION 2: * Postdoctoral Position in Imaging Genetics at Queensland Brain Institute The Neuroimaging and Brainnetome Laboratory of Queensland Brain Institute (QBI) and Centre for Advanced Imaging (CAI) at the University of Queensland, Australia, solicits applications for postdoctoral fellow positions in imaging genetics of the human and mice. We are looking for an excellent and highly motivated candidate with a PhD degree in neurobiology, genetics, experimental psychology, and neuroimaging or comparable background. Interest and/or previous experience in/with neuroscience, animal MRI, design and image analysis as well as wet lab experience are a plus. The successful candidate will participate in the multidisciplinary project involves developing transgenic mice model of psychiatric and neurological diseases. The main focus of this project is to address how risky genes of schizophrenia and Alzheimer’s disease affect brain networks in the human and mice. The postdoctoral fellows will be jointly supervised by Professor Tianzi Jiang and other Professors (QBI) who are experts in neuroscience. As at 30 June 2014, an applicant must not have had more than five years full-time equivalent professional research experience since the award of a PhD. The current salary range for the award is on a four-level scale from A$71,528.60 – A$79,708.50 per annum. Commencing salaries are based strictly on the number of full years’ experience since receiving a doctorate. Salary scales are reviewed from time to time. Please contact Professor Tianzi Jiang on tianzi.jiang(a)uq.edu.au for research plan. To submit an application for these positions, please refer to http://www.uq.edu.au/research/research-management/uq-postdoctoral-research-…. The application deadline is *19 May 2014.*

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Viewing functional data on the inflated brain
by Sherryse Corrow 05 May '14

05 May '14

Hi all, Earlier today, I posted the message listed below. However, we discovered part of our issue. When we run reg-feat2anat, there is no anat2exf.register.dat file created. Therefore, we have no registration matrix to use. Before, we were inadvertently using the anat2std file instead. Any suggestions on how to get the anat2exf.register.dat file created? Thanks, Sherryse -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre

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vertex-wise cortical thickness and whole brain labeling
by Caka 05 May '14

05 May '14

Hi Douglas and all, I have used the ‘recon-all’ command to segment the gray matter of 140 subjects. I have three questions: (1) as the segmentation is done in the individual space, how can I register the results into the template brain? The results includes the surface and the vertex. Is it ‘mri_surf2surf’? (2) If the gray matter is registered into the template brain, then same number of vertex in every region would be obtained. Then what information does the value of each vertex stands? Is it the cortical thickness changes? (3) We know that Freesurfer provides two kinds of brain region labeling, 68 regions and 77 regions in the cerebral cortex respectively. I am wondering whether I can use my own labeling, like 1000 regions? How can I do this? Thank you very much! Qiongmin Ma

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Re: [Freesurfer] LOOK FOR HELP
by 刘东博 05 May '14

05 May '14

Dear Freesurfer: I have some problems with using mri_surf2vol .I'd like to ask if you could help me with this.--volreg Contains the matrix that maps XYZ in the reference anatomical to XYZ in the functional volume. And to get this reg I use bbregister. But the result of bbregister is functional to anatomial volume,so I need to inverse the matrix.When I use convert_xfm in fsl I found the register.dat(which is the reslut of bbregister)is not a 4*4 matrix ,it just like dsub1 1.000000 1.000000 0.150000 9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04 1.634627580642700e-02 -3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04 -4.015868902206421e-02 -3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00 -2.181045338511467e-02 0 0 0 1 round Is there a command I can use to inverse the register.dat?Or if I use convert_xfm which part of the register.dat should I use? Thank you ! Yours Dongbo Liu 2014-05-06 10:22 GMT+08:00 刘东博 <lldbuestc(a)gmail.com>: > Dear Freesurfer: > I have some problems with using mri_surf2vol .I'd like to ask if you > could help me with this.--volreg Contains the matrix that maps XYZ in the > reference anatomical to XYZ in the functional volume. And to get this reg > I use bbregister. But the result of bbregister is functional to anatomial > volume,so I need to inverse the matrix.When I use convert_xfm in fsl I > found the register.dat(which is the reslut of bbregister)is not a 4*4 > matrix ,it just like > dsub1 > 1.000000 > 1.000000 > 0.150000 > 9.999998807907104e-01 3.475215926300734e-04 3.422866575419903e-04 > 1.634627580642700e-02 > -3.475832345429808e-04 9.999999403953552e-01 1.798802986741066e-04 > -4.015868902206421e-02 > -3.422244917601347e-04 -1.799785532057285e-04 1.000000000000000e+00 > -2.181045338511467e-02 > 0 0 0 1 > round > Is there a command I can use to inverse the register.dat?Or if I use > convert_xfm which part of the register.dat should I use? > Thank you ! > > Yours > Dongbo Liu > >

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Registering functional data to inflated brain
by Sherryse Corrow 05 May '14

05 May '14

Dear FreeSurfer community, We are having some issues registering our functional data (or masks) from FSL to an inflated brain in FreeSurfer. Some of our masks, when registered to the inflated brain and viewed in FreeSurfer, are not showing up on the cortical surface. We have followed web-tutorials for registration but are still having the issue. Any suggestions? Sherryse, University of British Columbia -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology & Visual Sciences UBC/VGH Eye Care Centre

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comparing two conditions with disproportionate number of trials
by Eryilmaz, Huseyin Hamdi 05 May '14

05 May '14

Dear FS experts, I have a question about the way contrasts work in an event-related design. I am wondering if freesurfer is doing some sort of weighing when it compares two different conditions with incomparable number of trials. For example condition A is represented by 10 trials in the paradigm file, whereas condition B consists of 80 trials. In that case, for the contrast A>B does freesurfer compensate for the small number of trials in condition A? If so, could it lead to inflated activations? We suspected this as in our results, the condition with fewer trials depicted strong activations. Thanks very much for the tips! Best, Hamdi -- Hamdi Eryilmaz, PhD Massachusetts General Hospital A.A. Martinos Center for Biomedical Imaging Brain Genomics Laboratory 149 13th St, Charlestown, MA 02129 Phone: +1 617 643 7462<tel:%2B1%20617%20643%207462>

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Brain Seg Volumes
by Mayer Kristina 05 May '14

05 May '14

Hi there, I am using freesurfer for datas of two year olds. - Is there a special command to run freesurfer on children's data? - When I checked the seg.stats for volumes, I got a higher value for BrainSegVolNotVentSurf (value: 845377 mm3), than for the BrainSegVol (value: 839497) in one patient. The recon-all -all finished without error. How is this possible? Thanks in advance, Kristina

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When/What to edit?
by O'Shea,Andrew 05 May '14

05 May '14

Hello FS experts, I have had a continuing curiosity regarding when/what to edit in FS cortical reconstructions. The wiki does a good job at showing how to deal with large scale problems, (i.e. invalid tal transformation, white matter not being recognized, large portions of the skull included in the surface) however I have yet to come across much that guides edits besides a "trained eye". How do we know when a problem is "big enough" that it needs attention? Are there any tool boxes/ quantitative guidelines that may help someone determine which scans need edits? I know QA tools outputs info on SNR/white matter intensity and I have looked for outliers here. However, I was wondering how else to automate/guide the decision process. Much of the discussion I have seen on this topic in manuscripts is either vague or nonexistent. Does anyone know of any manuscripts that have compared "raw" FS datasets to "selectively edited" datasets? What sort of effects do edits make in the grand scheme of a study? One could imagine problems with someone editing the data when they are knowledgable of the study's hypotheses and groups. Any additional info or guidance on this topic would be much appreciated. -Andrew

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Fwd: Fwd: Optseq2: ntp
by Conchy PF 05 May '14

05 May '14

Hi everybody, I have a question about optseq2. In order to calculate ntp, I need to know the total time that my run lasts. Thus, I do not know whether I have to include in the total trial time the fixation cross time (500 ms) + event (1000 ms) + variable ISI average (1 s, ranging from 500 to 4000 ms), or not to include the variable ISI, increasing the total run time by 50% at the end. On the other hand, I have the same dilema about the event command (ev) and the duration of the stimulus that I should set. Also, if I use the fixation cross plus event duration, they would add together 1.5 ms, while the tr is 2. According to the program's instructions, the stimulus duration must be a multiple of tr. Then, I guess that I should use to calculate the whole thing the fixation cross (500 ms) + the event (1000) + the variable ISI average (1 s). Am I right? Thank you very much and kind regards, C

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