Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

effect of demeaning the age
by amirhossein manzouri 05 Aug '14

05 Aug '14

Hi, I am looking at group differences between patients(20) and controls(n=20). I get significant results when I use Age, while I get no significance using Demeaned age both with DODS, also the pattern of significance is different. Would you please explain why? Best regards, Amirhossein Manzouri

3 5

.label files for subcortical structures
by Krieger, Donald N. 05 Aug '14

05 Aug '14

Hi Everyone, What tool(s) are used to extract the vectors for subcortical labels? What I need are the RAS coordinates for the cerebellum, basal ganglia, etc. Is there something for extracting them from aseg.mgz ? Or is there something for generating a .annot file so that mri_annotation2label may be used? Or is there some other way? Thanks. Don

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Structural analysis
by Silas 05 Aug '14

05 Aug '14

Hi all, I'm currently making a structural analysis on about 60 Parkinson patients and controls, and i would like to investigate specific regions in the brain - which do not seem to be included in the asegstats2table. How do i proceed from here? Best, Silas

2 1

Jacobian mri_cvs_register
by André Ribeiro 05 Aug '14

05 Aug '14

Dear Freesurfer Community, How can I obtain the Jacobian of the deformation field estimated through mri_cvs_register for further use like VBM analysis? Regards, Andre Santos Ribeiro

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new version of mri_label2label
by APRIL CLAUSEN 05 Aug '14

05 Aug '14

I believe there was a bug in the mri_label2label script in the 5.3 install of FreeSurfer for Mac OS Lion (10.7 and up), and that this has been fixed. Can someone provide instructions on how to download and where to (directory) install this script. April Clausen

1 0

uploading a surface in freeview
by carina＠van-vlodrop.de 05 Aug '14

05 Aug '14

2 2

Flaws in my segmentation
by Isaiah C. Smith 04 Aug '14

04 Aug '14

Hello, There is some flaw in my segmentation that is not allowing me to change produce a mesh in MNE. How do I fix the segmentation in freesurfer so that skull surfaces do not overlap? Isaiah (Error Shown Below) Checking that inner skull surface is inside outer skull surface...[failed] Surface inner skull is not completely inside surface outer skull(sum of solid angles = 8.85217e-16 * 4*PI). Could't create the geometry

1 0

merging segmented volumes
by Barnes Anna (UNIVERSITY COLLEGE LONDON HOSPITALS NHS FOUNDATION TRUST - RRV) 04 Aug '14

04 Aug '14

Dear All What is the simplest way to reduce the number of regions that the segmentation code produces. Very best regards Anna Anna Barnes, PhD, CSci, MIPEM Clinical Scientist (PETMRI) UCL Institute of Nuclear Medicine UCL Hospitals NHS Foundation Trust 235 Euston Road | London NW1 2BU | UK anna.p.barnes(a)ucl.ac.uk<mailto:anna.p.barnes@ucl.ac.uk> or anna.barnes1(a)nhs.net<mailto:anna.barnes1@nhs.net> 0203 447 0524 ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ********************************************************************************************************************

2 1

Please need help with mris_convert.
by Tara Miskovich 04 Aug '14

04 Aug '14

Hi all, I am trying to convert a group cluster to GIFTI (.gii) format. I just need some help running mris_convert. The example for a label to GIFTI is mris_convert --label lh.V1.label V1 lh.white lh.V1.label.gii I'm trying to figure out what is required here. I understand I put in the label after label and the output at the end, but in this example I am not sure what the V1 and lh.white are for. Thanks, Tara -- Thank you, Tara

1 0

Freesurfer and MNE
by Isaiah C. Smith 03 Aug '14

03 Aug '14

I have the MRI data, but I am confused as to how to proceed with the mne_setup_mri for the brain, skull and scalp volume conduction models because the brain and T1 are the defaults. Do I need to add some other slices? And does the subject data need to be placed in /freesurfer/subjects for it to be read by MNE? Isaiah

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