Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30093 discussions

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

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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?

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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

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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

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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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Edits to aseg
by Tamara Tavares 20 Jan '17

20 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

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'nuisance factors adjusted' values
by hiroki.sato＠med.tohoku.ac.jp 19 Jan '17

19 Jan '17

Dear experts, I have some questions. I did Qdec group analysis with three nuisance factors. And one region remained after FDR correction. Then I did 'mri_surfcluster' specifying the FDR-determined voxel-wise threshold as the --thmin. After that I ran 'mri_segstats' and got the values. 1)Are these values 'nuisance factors adjusted' values? 2)If not, is there a way to get 'nuisance factors adjusted' values using FreeSurfer? Best Regards, Hiroki

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Feature requests/bug reports in FS 6
by Chris Adamson 19 Jan '17

19 Jan '17

Freesurfer devs, I have a few issues to report for FS6. Bugs: defect-seg needs to use white.preaparc rather than white. My fixes were to change the mris_seg2annot call on line 114 to include -surf white.preaparc and comment out the mri_segstats call on line 122 Feature requests: Freeview It really needs a 3D brush. What would be nice for segmentation images is the ability to double click on a label on the list on the left and have the viewer automatically centre on voxels having that label in the image. Thanks in advance, Chris. Dr Chris Adamson Senior Research Officer Developmental Imaging, Clinical Sciences Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road, Parkville, VIC 3052 Australia E chris.adamson(a)mcri.edu.au<mailto:chris.adamson@mcri.edu.au> www.mcri.edu.au<http://www.mcri.edu.au/> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. P Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________

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aparc stats file output
by Marianna Riello 19 Jan '17

19 Jan '17

Dear Freesurfer users, I have a question on the 'aparc.stats' file output: Which of your label corresponds to: Ventro and Dorso Lateral Prefrontal Cortex? Supplementary motor areas? Putamen? Angular Gyrus? Thank you for your help Sincerely, Marianna

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