Freesurfer

freesurfer@nmr.mgh.harvard.edu

2 participants
30134 discussions

Mac OS Support and Compatibility
by Mageshwar Selvakumar 13 Oct '16

13 Oct '16

Dear All, I am trying to get started with FreeSurfer. I would like to know if the Mac OS versions (Yosemite, Sierra) are compatible and can run the FreeSurfer, if not please let me know which is the latest Mac OS version that supports FreeSurfer. I tried installing it on Mac OS Sierra but it is not fully functional. I would like to know if the error is caused because of compatibility issues or if I have made a error with the installation. Looking forward for your response. Thanks in Advance, Kind Regards, Mageshwar Selvakumar

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recon-all exited with ERRORS
by Brad Matushewski 13 Oct '16

13 Oct '16

I just tried to run my first recon-all. What now? [Logo] Brad J. Matushewski, M.Sc., R.Kin., CSEP-CEP. Laboratory for Brain & Heart Health School of Kinesiology Western University Room 402, Arthur & Sonia Labatt Health Sciences Building London, ON, Canada, N6A 5B9 Tel: (519) 661-2111 x 89066 Fax: (519) 850-2447

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FreeSurfer Atlas
by AKUDJEDU, THEOPHILUS 13 Oct '16

13 Oct '16

Hi All, Which default atlas does FreeSurfer 5.3 use for the segmentation of subcortical structures? Thanks Theo

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Gamma / Histogram
by Anders Hougaard 13 Oct '16

13 Oct '16

Dear Freesurfers, Please see the attached image. It shows inflated fsaverage surface with gamma.mgh overlaid. Gamma.mgh is from one contrast of a standard group analysis of cortical thickness (two groups A and B, two contrasts A>B and B>A). 1) Is it correct to interpret the gamma values as between-group difference of cortical thickness in mm? 2) I would like to reproduce the histogram in another software. Is it possible to extract the gamma values for each vertex for this purpose? All the best, Anders

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PET/MRI registration failed with bbregister or mri_coreg
by Matthieu Vanhoutte 12 Oct '16

12 Oct '16

Dear Freesurfer's experts, I would like to register PET image onto T1 anatomical. I used bbregister with the following command and it failed : *bbregister --s SUBJID --init-fsl --t2 --mov PET.nii.gz --reg Pet2T1.register.dof6.dat --lta Pet2T1.register.dof6.lta --init-reg-out Pet2T1.init.register.dof6.dat --o rPET.nii.gz * Having heard about mri_coreg solving some bbregister fails, I tested it with the following command : *mri_coreg --s SUBJID --mov PET.nii.gz --reg Pet2T1.register.dof6.mri_coreg.lta --regdat Pet2T1.register.dof6.mri_coreg.dat* But it failed in the same way than bbregister. Do you have any advice on this problem ? Best regards, Matthieu

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Remapping Volume
by Crawford, Anna 12 Oct '16

12 Oct '16

Hi, I am trying to remap a volume. I am using aparc+aseg.mgz volume. I loaded it into Matlab using load_mgh. In Matlab I remap the volume to different values. For example, all original values of 1022 will become 200 and all 1030 values will become 150. (This is just an example, not necessarily these numbers.) I save a new aparc+asegNew.mgz file using save_mgh. I use the same M and mr_parms that I got when I loaded in the original file. I'm not sure what these mean or if I need to change them. Then I use mri_vol2surf to create a new surface overlay onto the inflated hemisphere. When I do this, each region such as post central gyrus is 2 colors spotted together instead of a solid color like in the original. I have attached pictures as an example of what the original and remapped looked like. I didn't change the location of values, just simple gave each value a new one. Why is the one value speckled throughout? Thank you, Anna =================================== Please consider the environment before printing this e-mail Cleveland Clinic is ranked as one of the top hospitals in America by U.S.News & World Report (2015). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Checking Longitudinal Runs
by Tamara Tavares 12 Oct '16

12 Oct '16

Hello Experts, I have a question regarding the outputs to the longitudinal processing stream. I ran my two participant's scans through the Cross, then created a Base and two longitudinal runs. I am primarily interested in looking at ventricular change over time. Other than the aseg output overlaid on the brainmask, should I look at any other outputs to ensure the longitudinal process ran correctly? Thank you in advance for your help, Tamara

1 0

Fdr correction using command line
by neuroimage analyst 12 Oct '16

12 Oct '16

Hi, I was wondering if there is a way to perform fdr correction using command line in freesurfer without using matlab as mri_glmfit-sim only does bonferroni ? Thanks Regards MV

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question about Unpaired T-test group analysis
by kinson li 12 Oct '16

12 Oct '16

*Hello, * *Question 1: I would like to conduct an Unpaired T-test group analysis, I have two group of people, Group A8 age is 8 and Group A9 age is 9, and I to test the* change in thickness with age. But I am little confusion about the matirx and FSGD design. I am appreciated if you can take a look at my FSGD file and Matrix file. Please correct me if I am wrong, Question2 : I am using tksurfer to analysis the brain thickness, and I have a question about setting threshold, for I am not so sure about the relation between threshold and Min. is the equation Min = -log10(threshold) correct?( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Visualization) For example, if I want the threshold to be 0.05, and the Min will be set to 1.3 Please see the image attached in this email, and correct me if I am wrong. Thank you! Jincheng

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Using caudate as a seed
by Raney, Talia L. 12 Oct '16

12 Oct '16

Hi, Is there any way in FSFAST to use caudate as a seed for connectivity analysis? I was checking to see if it had a seg id for which I could run fc-seed-config, but it only had ids for caudate intensity abnormalities. Thank you! Best, Talia

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