Freesurfer

freesurfer@nmr.mgh.harvard.edu

30132 discussions

rotated surfs
by Colin Reveley 13 Jul '13

13 Jul '13

I (still) need to rotate some surfaces so that they enclose MR data that is sliced the same angle as data from the same brain was sliced on a microtome. Transforming surfaces once made is a bit tricky. Is there any reliance on the midline being on the y axis past the point of mri_fill/pretess? (for: mris_fix_topology -mgz subject rh -orig orig -inflated inflated -sphere qsphere -ga -noaseg -noaparc mris_make_surfaces -noaseg -noaparc) what I'd do is take the results from an ACPC aligned set, and apply a transform to T1,wm,filled,filled-pretess and so on. then run the surface making script as normal. the brain's midline is pretty rotated in Z the way I want it. It takes ages to run this so I'm wondering if there is any issue before I go ahead and try it. best, Colin

1 0

Pial surface missing grey matter
by ye tian 13 Jul '13

13 Jul '13

Dear Freesurfers, I would like the pial surface in the circled region in the attachment to extend a little bit more to follow closely the boundary of the grey matter (green line in the second attachment). Is there a way to do so? Thank you very much! Sincerely, Ye

1 0

Inflated surface smooth but white matter surface has holes
by ye tian 13 Jul '13

13 Jul '13

Dear Freesurfers, My inflated surface looks smooth in tksurfer, but white matter surface has holes in it. Is this an indication of topological defects? Thank you very much! Sincerely, Ye

2 2

Freesurfer surface circle of pre-defined size
by sarahp＠nmr.mgh.harvard.edu 12 Jul '13

12 Jul '13

I'd like to make a circle of a pre-defined size on the freesurfer surface, with RAS coordinates as the center of the circle. What would be the best way to do this?

2 1

combining lh.annot and rh.annot files
by Jeff Eriksen 12 Jul '13

12 Jul '13

Is it possible to combine the lh and rh annotation files into a single annotation file? How? -Jeff

2 1

AC/PC positions and other questions
by François Tadel 12 Jul '13

12 Jul '13

Dear freesurfers, I'm working on a function to import automatically the segmentation folder into a Brainstorm database. I have a few questions: - Is there a way to read/get the position of the anterior and posterior commissures (AC/PC)? - What file should I read to get the labels corresponding to the aseg.mgz file? - Is there an easy way to generate surfaces for all the regions defined in aseg.mgz? - How do you create a mesh from a volume mask? Thanks, Francois

2 1

Xhemi results
by amirhossein manzouri 12 Jul '13

12 Jul '13

Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) 4) Is there any way to look at the results through the brain per slice and also the whole brain? -- Best regards, Amirhossein Manzouri

3 8

large SD of aparc in one group
by L. Koenders 12 Jul '13

12 Jul '13

Dear FreeSurfer experts, We have a question regarding the aparc output from the stats files, and hopefulle you can help us. We have 4 independent groups, of about 30 subjects per group, all scanned using the same protocal on the same MRI scanner. We ran the cross sectional FreeSurfer (5.2.0, Linux centos4_x86_64) pipeline, and extracted the volume information per person from the .stat files using Matlab. We transfered the volume information into SPSS, to calculate the Means and Standard Deviations per group. We are interested in a couple of regions of interest (anterior + posterior cingulate, OFC, parahippocamus and insula). What strange is though, it that the means and standard deviations of 3 groups are comparable across all regions, but the SDs of 1 group are very (very!) large. This is not a group in which we expect brain atrophy or anything like that. Below you see the SD values of all groups, with SD values up to four times bigger in group 1! 1 2 3 4 caudal ACC 618 516 643 589 rostral ACC 1583 578 692 623 PCC 1942 721 616 749 OFC 2632 1345 1844 1652 parahip 1198 346 271 394 insula 1410 1033 1096 1017 The outliers are different subject in every region, and I checked the parcellation output of them, that looks fine. We are wondering what could be the cause of this, do you have any ideas? Thank you in advance, Kind regards, Laura ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

3 2

Adjust lighting in Freeview
by Martijn Steenwijk 12 Jul '13

12 Jul '13

Hi all, Is there a way to ajust the camera lighting / add lights in Freeview? Currently the lighthing is such that the surface with normal pointing upwards are illuminated well, but the surface with normal pointing downwards not that good. Thanks for replies in advance, Martijn

1 0

Pearsons r / adj. r squared
by Martijn Steenwijk 12 Jul '13

12 Jul '13

Dear all, Is there a way in freesurfer to compute surface wise pearsons r (for simple correlations) or adjusted r square / the vertex-wise explained variance for a GLM? Best, Martijn

2 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer