Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

mri_glmfit-sim cluster correction threshold inquiry
by Arsenije Subotic 08 Mar '19

08 Mar '19

External Email - Use Caution Hello, I am planning on running a correction for multiple comparisons, and I was hoping to use a vertex wise cluster forming threshold of 1.3, however after reading more when I ran the mri_glmfit-sim —help command it recommends using the permutation test if you are planning on using 1.3 as a threshold. Is there any reason why it is not recommended to use the 1.3 cluster threshold? My study is fairly exploratory so I was hoping to be a bit more lenient when it comes to adjusting the threshold. Thanks! Arsenije

2 1

projfrac question
by Nasiriavanaki, Zahra 08 Mar '19

08 Mar '19

Dear Freesurfers Hi I was trying to look at the activation in different cortical layers in a single subject. I ran my preproc-sess command three times, once without using -projfrac flag, once -projfrac 0.5 and lastly -projfrac 0.2 The activation patterns are exactly the same. My voxel sizes are 1.1*1.1*1.1 . My question is: 1-Is it normal that the activations do not change at all the more I get closer to white matter? 2-when I use -projfrac 0.2 , does it mean that I am averaging the activation between white matter layer to 0.2 of gray matter layer? Or is it averaging the activation between pial surface to 0.2 gray matter? I hope my questions are clear. Thanks Mona

2 11

Re: [Freesurfer] Accounting for family relation in FS
by Greve, Douglas N.,Ph.D. 08 Mar '19

08 Mar '19

Yea, the real hard part is figuring out how to model the twins that are split between groups. You might be able to create a bunch of groups. If you've already created a design in FSL that you like, you can extract the design matrix and use it in mri_glmfit with the --X option. Not sure about correcting for multiple comparisons though On 3/8/19 3:13 AM, Julian Macoveanu wrote: External Email - Use Caution Thank you for the reply. The original idea was to have an ANOVA with a group factor “diagnosis” with three levels. We could use an F-test to check for an effect of diagnosis and then perform 3 pairwise group tests (LR vs HR, LR vs ILL, HR vs ILL). Would it help to only implement the two-sample group tests? However, the critical issue to account for correlated data remains since about 80% of the subjects have their co-twin in the same group. The idea behind the model that has a variable with 1s for each twin pair is to model out each pair’s mean. I implemented the model I described in the FSL GLM and estimated with FEAT for the functional data of the group. The second option I had was to perform a permutation based estimation as implemented in PALM and restrict the permutations to between pairs and single subjects. Would any of these options work in FS? Maybe clustering the subjects somehow? Julian

1 0

Re: [Freesurfer] Extraction of anatomical locations using Matlab
by Sparsh Jain 07 Mar '19

07 Mar '19

External Email - Use Caution Good evening. Thanks a lot for the help. It worked ! While most of the labels were correct, the matlab script returned the wrong location for one point . The script returned the label 'right cerebral white matter' for a point that seems to lie in the middle of the right amygdala. I have attached the screenshots. I do not think that there is a white matter area close enough to confuse the script. Could you tell me why this may have occurred? When I write the line "crs = round(inv(aparcaseg.tkrvox2ras)*[tkr tka tks 1]')+1" , is there an error due to rounding in the conversion? I was planning to inflate a sphere around each electrode point and get the neighboring anatomical regions as well. Sparsh

2 1

Re: [Freesurfer] matrix is ill-conditioned or badly scaled, condno = 1e+08
by Arsenije Subotic 07 Mar '19

07 Mar '19

External Email - Use Caution Hi Doug, I realized this error a couple of days ago and now it works. Thank you, Arsenije

1 0

Accounting for family relation in FS
by Julian Macoveanu 07 Mar '19

07 Mar '19

External Email - Use Caution Dear FS List, (apologies for reposting under different title) I wanted to check if my GLM design for a surface based analysis is sound. I am new to FS so please don’t skip over details. I have 3 groups of monozygotic twins: low-risk, high-risk, ill. Twin pairs may be present in the same group (e.g both are in the low-risk) or between groups (one of them in high-risk one in affected). Not all twins have their co-twin in the analysis though. In order to account for with-pair variance correlation I was wondering if this FSGD example with 9 subjects might do it or if there might be better options. GroupDescriptorFile 1 Title … Class LR Class HR Class ILL Variables age sex TIV Pair_no1 Pair_no2 Pair_no3 Input subject1 LR 30 M 123456 1 0 0 Input subject2 LR 30 M 123456 1 0 0 Input subject3 LR 23 F 123456 0 0 0 Input subject4 HR 20 F 123456 0 1 0 Input subject5 HR 21 F 123456 0 0 1 Input subject6 HR 22 M 123456 0 0 0 Input subject7 ILL 20 F 123456 0 1 0 Input subject8 ILL 21 F 123456 0 0 1 Input subject9 ILL 35 F 123456 0 0 0 I do have 60+ pairs so it will be a lot of variables. I know that PALM has an options to provide an exchangeability file, but FsPalm seems to perform corrections for multiple comparisons only. Julian

2 1

Gray matter segmentation
by Maxime Perron 07 Mar '19

07 Mar '19

3 5

PETSurfer: Equivalence between surfaces un gtmseg space and native surface?
by Matthieu Vanhoutte 07 Mar '19

07 Mar '19

External Email - Use Caution Dear Douglas, RBV PVC use the advantage of upsampled gtmseg space at 0.5 mm3 to compute PVCorrected images. Would it be beneficial to project this PVCorrected images onto gtmseg space surfaces to keep this upsampled resolution ? Or would it be equivalent to project these PVCorrected images on gtmseg space onto native surfaces using --reg rbv2anat.lta ? Best, Matthieu

3 3

Creating Labels
by Jahan, Bushra 07 Mar '19

07 Mar '19

Hello, I am wondering how to generate a label in FreeSurfer from peak activation in a cluster - is there a specific command? Thank you.

2 1

Re: [Freesurfer] Resampling a gifti image to nifti using mri_surf2vol fails
by CAGNA Bastien 07 Mar '19

07 Mar '19

External Email - Use Caution Hi, First I tried to use my original mask which is a gifti with a single darray as NIFTI_INTENT_ESTIMATE that contains 0 or 1 for each vertex. But I got it: " ** DA[0] has coordsys with intent NIFTI_INTENT_ESTIMATE (should be NIFTI_INTENT_POINTSET) MRISreadGiftiAsMRI: no overlay data found in file [filename] " So I changed darray to a new one that contains only the list of the point coordinates where my mask is equal to 1 (and use NIFTI_INTENT_POINTSET) and now I have only this error: " MRISreadGiftiAsMRI: no overlay data found in file [filename] " Bastien

2 1

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