[Freesurfer] LME

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g

[Freesurfer] LME

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g

[Freesurfer] Hippocampal segmentation flips on the left side

Dear Freesurfers, When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to segment an MNI152 template, the resulting segmentation of left hippocampus got flipped in left-right dimension. Otherwise the right hippocampus and other subcortical segmentations in the aseg-file look fin

[Freesurfer] Question about combine longitudinal analysis and xhemi

​ xhemireg.lh.log ​Thanks for replying me. But I still have two questions. Firstly, when I try xhemi on pre-possessed longitudinal data, it showed error like this: Performing left-right swap of l

[Freesurfer] Linear mixed model and samplesize calculation

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ ... The slope of g

[Freesurfer] Linear mixed model and sample size calculation

Dear Freesurfer experts, I have three groups g0, g1, and g2. I am trying to use LME model with random effects y-int and time from the base line. Based on the LME tutorial and the questions and answers from Freesurfer support list: Y=B1+B2*t+B3*g1+B4*g1*t+B5*g2+B6*g2*t+ … The slope of g0

Re: [Freesurfer] Lesion Volume Analysis

Sorry, you have to do the full recon-all On 01/08/2018 02:08 PM, Ledesma, Jason wrote: > > Hi, > > > I am aware that the recon-all command ultimately calculates statistics > on a given MRI sequence, including what is referred to as > "aseg.stats".  "Aseg.stats" includes the "WM-hypointensities"

[Freesurfer] Using MRS voxel mask in freesurfer surface space

Hi, We are obtaining MRS data and functional MRI data on two separate days for each subject. We use structural scan obtained during both these sessions for the freesurfer segmentation. MRS scan gives us a binary mask (nii format) in the same space as the structural image obtained during that partic

[Freesurfer] Lesion Volume Analysis

Hi, I am aware that the recon-all command ultimately calculates statistics on a given MRI sequence, including what is referred to as "aseg.stats". "Aseg.stats" includes the "WM-hypointensities" calculation, which I was told would be an equivalent to white matter lesion volume. Is there a way

[Freesurfer] Acquiring Exact p Values

Hello, I am conducting surface group analyses and would like to acquire exact p values. The FreeSurfer manual notes that the number listed after the peak coordinates and the vertex # is a "significance value," and that the "significance in this display is a -log(10)p value, and not a straight p v

Re: [Freesurfer] asegstats2table error message

Hi, This is a bug introduced by python3, you must run this script with python2 by either modifying the first line to say: #!/usr/bin/env python2 or by running: python2 $FREESURFER_HOME/bin/asegstats2table --subjects baseline 12m 24m 36m --meas volume --tablefile aseg_stats.txt best, Andrew O

Re: [Freesurfer] IndexError: list index out of range

Hi Doug, I sent you the tar files, but just wanted to update you that I tried running this with just one subjects and am still getting an error but a different one. The two inputs and output errors in the terminal are pasted below: [arkadiysimac:Freesurfer/Freesurfer_Files_with_Freesurfer_Masks

Re: [Freesurfer] viewing the flatten sheet

Have you tried loading it in freeview? You can load it like this: freeview -f lh.white:patch=lh.flaten.patch.3d Ruopeng On 01/08/2018 10:14 AM, N Saf wrote: Dear experts, I cut the inflated surface in tksurfer and obtain the flatten sheet by mris_flatten but I can not load the $h.flaten.pat

Re: [Freesurfer] Segmentation of hippocampal subfields and nuclei of the amygdala

Hi Carme, segmentHA_T1.sh is available in the fs dev version: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev best, Andrew On Jan 4, 2018, at 9:17 AM, Carme Uribe Codesal mailto:carme.ur...@gmail.com>> wrote: Dear FreeSurfer users, I wanted to run the new script that segments the h

[Freesurfer] viewing the flatten sheet

Dear experts, I cut the inflated surface in tksurfer and obtain the flatten sheet by mris_flatten but I can not load the $h.flaten.patch.3d not in freeview nor in tksurfer it somehow collapse! my laptop is RAM:6G , core i5 , would you please help me how can I see the 2D flatten sheet ?? many than

[Freesurfer] Is it poosible to redistribute a part of buckner_data for group work?

Dear FreeSurfer experts, We are planning to have a one-day neuroimaging workshop in Japan. One topic of the workshop is "FreeSurfer troubleshooting", in which we go through the online tutorial you provide ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData) in Japanese langu