Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Something wrong with fsaverage folder
by Minjeong Wang 04 Sep '14

04 Sep '14

Deal all I have some problem with my fsaverage folder. can i re-download this folder?? or do I need to download the whole freesurfer package again? my freesurfer version is ' freesurfer-i386-apple-darwin11.4.2-stable5-20130514'. Thank you. Sincerely Wang

1 0

Re: [Freesurfer] tracula: bvec-error
by Robby De Pauw 04 Sep '14

04 Sep '14

Hi Barbara and FS-community, I tried everything you suggested, but unfortunately the same error still occurs. Have you found a solution yet? Thanks for your help Best regards, Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent Robby.DePauw(a)Ugent.be Hi Robby, Try this (with the backslashes), applied only to bveclist, if that does not work, also to subjlist and dcmlist at the same time, and let me know please. I have started to process my data with a separate configuration file for every subject :( - as no combination of alterations to the multiple subject configuration file helped me. Maybe you are luckier though. And I am still not sure if there is another way to solve the issue... Thanks, Barbara set bveclist = ( INP_080_LISA_V_1/bvec.txt \ INP_091_KIVA_V_1/bvec.txt \INP_092_LACH_V_1/bvec.txt \ INP_097_LADH_V_1/bvec.txt \WAD_090_MASU_V_1/bvec.txt \ WAD_IWT047_KIMO/bvec.txt \ WAD_IWT043_NAME/bvec.txt \ WAD_IWT021_ALAS/bvec.txt \ WAD_057_PACA/bvec.txt \ WAD_047_JESE/bvec.txt \ WAD_019_NADE/bvec.txt \ WAD_017_CACO/bvec.txt \ INP_IWT046_KATU/bvec.txt \INP_IWT045_INDE/bvec.txt \ INP_IWT007_CIHA/bvec.txt \ INP_IWT001_MOTA/bvec.txt \ INP_082_JAPA/bvec.txt \ INP_081_ELBA/bvec.txt \ INP_079_STEVA/bvec.txt \ INP_063_STCO/bvec.txt \ INP_059_CABR/bvec.txt \ INP_058_NEVA/bvec.txt \ INP_054_LUSO/bvec.txt \ INP_045_ELDA/bvec.txt \ INP_028_JEVE/bvec.txt \ INP_024_LUDE/bvec.txt \ INP_012_JAGU/bvec.txt \ GEZ_078_HEVA/bvec.txt \ GEZ_075_ISKL/bvec.txt \ GEZ_074_FIOR/bvec.txt \ GEZ_049_ELWE/bvec.txt \ GEZ_042_MADE/bvec.txt \ GEZ_038_LIDA/bvec.txt \ GEZ_033_LOVE/bvec.txt \ GEZ_014_GRBU/bvec.txt \ GEZ_006_ELDE/bvec.txt \ GEZ_004_HACO/bvec.txt )

1 0

how generate a head model?
by gamaliel huerta urrea 03 Sep '14

03 Sep '14

Hi Experts I have been studying how to generate a head model, and is said to FreeSurfer software allows better tissue segmentation. I've driven German Gomez Herrero tutorial: http://www.germangh.com/tutorials/dipoles/head_model.htm I have installed freesurfer and matlab. I have verified that the initial elements to generate the model head is MRIs, which have them. I have also verified that using FreeSurfer for segmentation and reconstruction MNE to generate the following areas: 0003-inner_skull-5120.tri 0003-inner_skull-dense.tri 0003-outer_skin-5120.tri 0003-outer_skin-dense.tri 0003-outer_skull-5120.tri 0003-outer_skull-dense.tri My idea is to get the same files to generate my own models and then simulate them power over dipole sources. >From what I have researched the role mri_make_bem_surfaces segmented surfaces, but I only found this material: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_make_bem_surfaces Any help on how to achieve the above-named areas would contribute. Thank you Regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

1 0

prefrontal gyrification
by melinda dora 03 Sep '14

03 Sep '14

Dear list, how would I get gyrification for the prefrotnal cortex? there is no annotation for this structure? Do I need to make my own? and if so, how? best, Melly

2 1

mkanalysis-sess blocked design
by Milde, Christopher 03 Sep '14

03 Sep '14

Dear Freesurfer Experts, I want to run mkanalysis-sess for a blocked design, but unfortunately only the flags -abblocked, -event-related, -retinotopy and -notask do exist. How can I specify the designtype for a blocked design with one condition and on fixation with different block lengths for condition and fixation? I'm using Freesurfer 5.3 Thanks in advance, Chris

1 1

Group cortical thickness QDEC help
by Taylor North 02 Sep '14

02 Sep '14

Hello, I am having some troubles using QDEC to analyze the thickness changes in my group study and I was hoping someone may be able to give me a hand. The steps I have done are as follows: I am working on a study looking at 40 subjects scanned at two time points (base and 6 months after). I have followed all the steps for longitudinal processing for each subject (cross,base, and longitudinals) and made edits where they were necessary to the base. I then entered all 40 subjects into a QDEC table as follows fsid fsid-base time gender age crosstpN1 base1 0 female 20 crosstpN2 base1 6 female 20 .......... continues for rest of the subjects then I ran the QCHACHE on the data, made a Qdecrc. file in the subject DIR, and then transformed the longitudinal QDEC table into a QDEC table which looks like: fsid time gender age Base1 3 female 20 .......... continues for the rest of the subjects. I then followed the QDEC steps outlined In the group tutorial. (import cross sectional table, generate stats data table, import aseg volume, set longitudinal dependent variables and pick continuous variable. 1) the first problem I am having is that when I go to process the longitudinal group results through QDEC it makes me pick a continuous variable when I just want to analyze the dependent variable The symmetrized percent change. So I have tried picking different continuous variables ( such as age or importing rhcortex volume etc...) with choosing symmetrized percent change as the dependent variable. No matter what continuous variable I pick the question: ``does the average symmetrized percent change differ from zero"? always comes up, the problem is depending on what continuous variable I pick the results change. Is there a way to just look at the longitudinal thickness changes across a group alone, because I first want to look at the atrophy across the whole group over 6 months and then compare the differences in atrophy against the diagnosed and non diagnosed group. 2) another thing I don't quite understand is it seems like the longitudinal qdec tables are made with the cross of the subjects under fsid, but why wouldn't you use the longitudinals under the fsid for the longitudinal table instead? Also it seems like in the cross sectional qdec table the base is the subject being analyzed under fsid, which also doesn't make sense to me because in the tutorial it says base should not be used directly for analysis. thanks for the help! Taylor

1 0

Job offer: 1 PhD and 1 PostDoc in Neuroimaging of Epilepsy - Tübingen, Germany
by Niels Focke 02 Sep '14

02 Sep '14

We currently have two open job opportunities at the University of Tübingen, Germany. Both in the field of neuroimaging in epilepsy. 1) PostDoc to work on post-processing of functional and structural MRI / network analysis (graph-theory, classification algorithms, EEG-fMRI) 2) PhD-Student to work on structural post-processing using multispectral MRI and automated lesion detection Details can be found on: http://www.hih-tuebingen.de/stellenangebote/stellenangebote-fuer-wissenschaf tler/translational-neuroimaging-ag-focke Short-URL: http://goo.gl/bA5h1D __________________________________________________________________________ Dr. Niels Focke Oberarzt Abt. Neurologie mit Schwerpunkt Epileptologie Universitätsklinikum Tübingen AG Translationale Bildgebung Hertie Institut für Klinische Hirnforschung Werner Reichhardt Centre for Integrative Neuroscience

1 0

longitudinal base problem - bad surfaces
by Koolschijn, Cédric 02 Sep '14

02 Sep '14

Dear experts, I'm performing a longitudinal analysis, and have done so before, but I encounter an error after running -base for one subject which I haven't seen before. The cross surfaces of both timepoints look OK, but the base surface is seems to be shrunken for unknown reasons. I reran all steps, but with the same results. The log file also doesn't provide any useful information, no errors were reported. Below, please find screenshots of the surfaces for each tp. tp1: https://www.dropbox.com/s/5cwksrzqyw9jxxo/n4t1.tif?dl=0 tp2: https://www.dropbox.com/s/858062gh1uwigo2/n4t2.tif?dl=0 base: https://www.dropbox.com/s/hutaarl7jvthwcy/n4base.tif?dl=0 Do you have any idea what caused the mess-up in -base, and how to fix this? It will be a lot of editing should this be done manually, so I'm hoping for a better option. Many thanks! Best, Cédric

2 1

Questions about mri_make_bem_surfaces function
by gamaliel huerta urrea 01 Sep '14

01 Sep '14

Hi experts I need use the mri_make_bem_surfaces function to generate the three surfaces from brain MRIs patient exam. I have installed Freesurfer and I have my series of MRIs in 001.mgz file. would be helpful if you could provide some material to use this function. regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso*

1 0

questions about qdec, group and age interaction
by yaya ya 01 Sep '14

01 Sep '14

Dear all, I encountered several questions when using freesurfer. Although I searched carefully in this mailing list, I am still not very clear about some issues. My issues are described below: Based on a bunch of information, I know that before describing my results, I need to check whether there is an interaction effects between group and age. In order to do it, I demean my age variable and add it as a continuous covariate in Qdec. My discrete variable is group. Then I run the analysis on cortical thickness, producing several results. But I am not very sure about which of them described the group*age interaction effects in my data so that I could check the interaction results. That is why I need your help with confirming it. The name of several results are listed here: 1. does the average thickness differ from zero? (I don't think this is interacton effect) 2. does the correlation between thickness and demean-age, accounting for group, differ from zero? (this is not the interaction either. this should be the relation between thickness and age across 2 groups.) 3. does the average thickness differe between the two groups? (this should be the group main effect) 4, does the thickness-age correlation differ between 2 groups (*I think this should be what I need*). If so, I further checked whether the fourth one could survive the corrected threshold using monte carlo stimulation (threshold 1.3, p<0.05). two clusters survived. But one interesting thing is that the results from above 3 and 4 produced the same results except one thing. 3 gave the hightened thickness of several regions in patients groups compared with controls. In contrast, 4 found the same region but the opposite pattern (decresed thickness in patients compared with controls). When I add my age as a nuisance covariate, I get the same results 3. I don't know which one should report. Do my results make sense? My last question is that I could not find the data file which includes the thickness values from each subject resulting from above analysis because I want to do some correlation analysis with other clinical variables. I hope that it is clear to you all. Thank you for your help in advance. Best, Lickey

1 0

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