Freesurfer January 2017

freesurfer@nmr.mgh.harvard.edu

123 participants
215 discussions

qdec on LGI data
by André Schmidt 23 Jan '17

23 Jan '17

Dear FS experts I want to perform a 2-sample test on my LGI data using qdec (whole brain analysis with potential covariates). I already ran the recon-all -s my_subject_id -qcache -measure pail_lgi command for each of the subjects and included pial_lgi as measure in the QDEC Design tab. However, it is not clear to me how I need to create the qdec.table.dat file with the output from recon-all -s my_subject_id -qcache -measure pail_lgi. Do I need the lh/rh.pial_lgi.fsaverage.mgh files, and if yes, how can I extract the information from these files? Many thanks for your help! Best wishes André

2 1

Edits to aseg [repost]
by Tamara Tavares 23 Jan '17

23 Jan '17

Hello, After I make edits to my aseg output in the longitudinal stream, do I just run the following command to recreate the final volumes: recon-long -autorecon2-noaseg -subjid <Subj_ID> I assume the -subjid is the name of the edited time point and <Subj_ID> is the name of the recreated volumes? Thank you, Tamara

1 0

Generating intermediate surfaces?
by Souheil Inati 22 Jan '17

22 Jan '17

Hi All, I would like to generate some surfaces a bit below the white surface (in the white matter) and at several locations between the white and pial surfaces. Having trouble finding enough on the wiki - I’m guessing it’s some combination of mris_make_surfaces and mris_inflate? Any help would be greatly appreciated. Thanks, Souheil

2 2

Regarding: Habenula ROI
by Dr Sampada Sinha 22 Jan '17

22 Jan '17

Dear freesurfer experts, Is it possible to create Habenula as region of interest from fsaverage (orig.mgz images) using tkmedit? I will be using following links to guide me for creating Habenular region of interest https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurfe… Thanks for your help. Kind regards, Sampada -- Sampada Research medical scientist (B) Department of Geriatric Mental Health (DGMH) King George Medical University Lucknow-226003 , Uttar Pradesh India

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Covariates / rmANOVA
by Gracien, Rene-Maxime 20 Jan '17

20 Jan '17

Hello, we are trying to use covariates while calculating a rmANOVA as described in https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. Is this technically possible with freesurfer? Thank you, best regards, René

2 1

27th Annual RRI conference: Neural Dynamics and Brain Health
by Rosanna Olsen 20 Jan '17

20 Jan '17

We are happy to invite you to Toronto for the 27th Annual Rotman Research Institute conference entitled, "Neural Dynamics and Brain Health.” The conference will take place March 20-22, 2017 at the Metro Toronto Convention Centre. Visit the conference website for the complete program and venue information: http://research.baycrest.org/conference Join us for this unique opportunity that brings together researchers with basic and translational scientific expertise. Our conference will present cutting-edge research on basic neural mechanisms informed by structural and functional neuroimaging. Sessions will cover: * Comprehensive descriptions of neural dynamics across the lifespan in health and disease * Exclusive insight into how brain simulation of brain damage caused by disorders, such as epilepsy or stroke, can guide treatment * Avenues for healthy brain aging: the effect of exercise and music on the brain. Deadlines to note: Poster submission deadline: January 31, 2017 Early bird registration deadline: January 31, 2017 *Pre-Registration deadline: February 28, 2017* We look forward to welcoming you at the Rotman Research Institute Conference in Toronto! If you have any questions, please direct inquiries to Paula Ferreira, Centre for Education at conference(a)baycrest.org or call 416-785-2500 ext. 2363. -- Rosanna Olsen, Ph.D. Scientist, Rotman Research Institute, Baycrest Assistant Professor, University of Toronto rolsen(a)research.baycrest.org http://research.baycrest.org/rolsen <http://research.baycrest.org/rolsen> <http://goog_639572707> <http://research.baycrest.org/conference>

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Re: [Freesurfer] Registration Checking Problems
by Anderson Napolitano 20 Jan '17

20 Jan '17

Good Morning Dr. Greve, Thank you for your rapid response. I've attached the output of the command: tkregisterfv --debug --mov template.nii.gz --reg template.reg.lta --surfs below. Please let me know if I can provide you with any further information and I will get to it as soon as I can. Thank you, Anderson Napolitano?

1 0

ROI with precise coordinates
by Lisa Delalande 20 Jan '17

20 Jan '17

Dear all, I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10,-15,-5. Does a command line exists for that ? It is possible without drawing the label ? Thanks in advance for your help, Best regards. And I wish you a Happy New Year 2017 ! Lisa

2 4

Question
by N Saf 20 Jan '17

20 Jan '17

Dear FreeSurfers, I have a question about aseg file. I load the aseg file of bert subject in itk-snap and read the volume for 17 and 53 label but it is a bit larger of the volume in bert stats file. I do the same for some of my subjects too and I see the same result .I don't know why it is like that ?would you please clear the reason for me.because I need to compare the FreeSurfer result and I should use of aseg file labels but I'm afraid the comparison I'm doing is not valid. Sincerely yours, Nazanin

2 6

Freesurfer 6.0rc and Cuda library version
by Parzer, Peter 20 Jan '17

20 Jan '17

Would it be possible for the developers to provide the *_cuda binaries linked to different version of CUDA, as for example is done for bedpostx_gpu by FSL? The *_cuda binaries distributed with Freesurfer 6.0 are linked to CUDA 5.0. It not possible to install such an old CUDA version on a current Linux System.

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Freesurfer January 2017