Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30087 discussions

reconstruction question
by Evan Luther 03 Feb '11

03 Feb '11

Hello, My name is Evan Luther and I have been working with Dr. David Ress at the University of Texas at Austin to create a high resolution (.7 mm) volume using FreeSurfer. In the last step of our data pipeline I enter the command: recon-all -segmentation -fill -tessellate -smooth1 -inflate1 -qsphere -fix -smooth2 -inflate2 -finalsurfs -cortribbon -s fsHighRes After running for several hours this reconstruction gets stuck in the mris_fix_topology command. This command does not have much documentation on the FreeSurferWiki although from what I understand it is ensuring that the cortical surface is topologically correct. It picks out about 216 topological errors and gets stuck on the 93rd. I left it running on this error for quite some time (>24 hours) and nothing occurred. Can anyone offer me any insight or help? Thank you very much, Evan Luther

2 1

fsl tutorial data
by Rita Loiotile 03 Feb '11

03 Feb '11

anyone have it saved anywhere?

1 0

Re: [Freesurfer] Regression: Activation as a function of condition
by Adam Nitenson 03 Feb '11

03 Feb '11

Hi Doug and Freesurfers, Now that I have re-processed some of my data in Stable 5, I would like to re-open a previous problem I was trying to tackle: " We are using the Sternberg Item Recognition Paradigm in our study, which involves the memorization and recognition of groups of 1, 3, 5, and 7 letters. Each run has two sets of each condition (load). We want to determine if any regions of the brain activate in a linear pattern with increased task load (# of letters). I have already done regression analyses using genotype, but that was between subjects, while this analysis would be within subjects. Does anyone know how I could structure an analysis that would allow me to look at this? Is this something I have to do at the mkanalysis-sess level?" I had tried doing this in Stable 4 using the method described here https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-December/016557… However, I was unable to generate the desired results, so I decided to switch over to Stable 5 as suggested. Thanks, Adam > > > ---------------------------- Original Message ---------------------------- > Subject: Re: [Freesurfer] Regression: Activation as a function of > condition > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > Date: Tue, January 11, 2011 11:52 am > To: "Adam Nitenson" <nitenson(a)nmr.mgh.harvard.edu> > -------------------------------------------------------------------------- > > You don't need to re-unpack. you don't run recon-all on the functional, > only the anatomicals. > > Adam Nitenson wrote: >> So this means I will have to start at the unpacksdcmdir command and then >> recon-all to rerun the functionals? >> >> >>> You don't need to re-run the anatomicals, but you will need to rerun >>> the >>> functionals. >>> >>> doug >>> >>> Adam Nitenson wrote: >>> >>>> Hmm...it appears that we might need to make the transition over to >>>> Stable >>>> 5 then. >>>> >>>> Would I have to reprocess all Stable 4 subjects again in Stable 5 >>>> (including the whole recon-all from bourget) process, or is there some >>>> sort of jumping off point from which I can start using the new stable? >>>> >>>> Thanks, >>>> >>>> Adam >>>> >>>> >>>> >>>> >>>>> you can't do it in stable4, but you can in stable 5. >>>>> >>>>> doug >>>>> >>>>> >>>>> Adam Nitenson wrote: >>>>> >>>>> >>>>>> Hello Freesurfers, >>>>>> >>>>>> We are using the Sternberg Item Recognition Paradigm in our >>>>>> study, >>>>>> which involves the memorization and recognition of groups of 1, 3, >>>>>> 5, >>>>>> and 7 letters. Each run has two sets of each condition (load). We >>>>>> want to determine if any regions of the brain activate in a linear >>>>>> pattern with increased task load. I have already done regression >>>>>> analyses using genotype, but that was between subjects, while this >>>>>> analysis would be within subjects. Does anyone know how I could >>>>>> structure an analysis (STABLE 4) that would allow me to look at >>>>>> this? >>>>>> Is this something I have to do at the mkanalysis-sess level? >>>>>> >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Adam Nitenson, B.S. >>>>>> Brain Genomics Lab >>>>>> Massachusetts General Hospital >>>>>> _______________________________________________ >>>>>> Freesurfer mailing list >>>>>> Freesurfer(a)nmr.mgh.harvard.edu >>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> -- >>>>> Douglas N. Greve, Ph.D. >>>>> MGH-NMR Center >>>>> greve(a)nmr.mgh.harvard.edu >>>>> Phone Number: 617-724-2358 >>>>> Fax: 617-726-7422 >>>>> >>>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>>>> >>>>> >>>>> >>>>> >>>>> >>>> Adam Nitenson, B.S. >>>> Brain Genomics Lab >>>> Massachusetts General Hospital >>>> >>>> >>>> >>>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> >>> >>> >> >> >> Adam Nitenson, B.S. >> Brain Genomics Lab >> Massachusetts General Hospital >> >> >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > > Adam Nitenson, B.S. > Brain Genomics Lab > Massachusetts General Hospital > > > Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

2 5

Surface area interpretation confusion
by Jürgen Hänggi 03 Feb '11

03 Feb '11

Dear FS experts Sorry, for reposting this question, but I'am not sure whether something went wrong. We divided the superior temporal sulcus derived from the aparc.a2009s.annot into parcellations of 300mm2 in size (using mris_divide_parcellation) and computed the mean cortical thickness within each parcellation. But after running mris_anatomical-stats, we noticed that each parcellation has a unique surface area that deviates largely from 300mm2 (ranging between 96mm2 to 480mm2). Does anybody have any ideas? Is this a bug or is this what one should expect? We defined the parcells on the fsaverage template and transformed them back into the native space of each individual. Therefore, we expected some variation in the surface area, but not such large differences. Thanks in advance Regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 1

Am I losing T2* info in MEMPRAGE data by differential scaling?
by Carl Anderson 02 Feb '11

02 Feb '11

Dear Freesurfer, I am concerned that I may not be processing the MEMPRAGE images to full take advantage of the T2* info in the multi-echos. I have been separating each echo as 001.mgz, 002.mgz, 003.mgz & 004.mgz when using recon-all. This works well if motion exists in any of the individual echos. However of late, I have noticed a that a reference was made to the problem of losing T2* info by differential scaling in the archive if a particular file format "memprage_echo0.mgz" was not used. Here is the link to the archive note: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15303.html It has been hard to identify a difference between our standard MPRAGE images and the MEMPRAGE images (we currently collect both on our Siemens 3T 32 channel system). Am I processing the MEMPRAGE correctly? Thanks! -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

3 3

using mri_glmfit-sim
by Chris Hyatt 02 Feb '11

02 Feb '11

I've read both Hagler et al 2006 Neuroimage (Smoothing and cluster thresholding for cortical surface-based group analysis of fMRI data) and B. Douglas Ward's description of AlphaSim that both describe clusterwise correction for multiple comparisons. I recently found, however, an MGH Freesurfer presentation that mentioned that after synthesizing Gaussian noise and smoothing (Monte Carlo), the rows of the design matrix were permuted. Does the mri_glmfit-sim clusterwise correction method permute rows of the design matrix? I'm still a bit confused about the exact method the clusterwise correction for multiple comparisons work in Freesurfer. Thanks for your help. Christopher Hyatt, PhD IOL/Olin Neuropsychiatry Research Center Hartford, CT

2 1

Jacobian values
by Larissa Stanberry 02 Feb '11

02 Feb '11

Afternoon greetings, upon inspection of ?h.jacobian_white files, I realized the values are all positive. I was expecting to see some negative determinants, perhaps I'm missing something. Any input is appreciated. Cheers Larissa

1 0

transform to original mri
by Seok Lew 02 Feb '11

02 Feb '11

Dear all, I am trying to transform the reconstructed surface like rh.pial into the original mri's (like 001.mgz) coordinate. I found some matrices in the ./transform directory, but not sure of which one (or a set of matrices) would do the transform? Seok slew(a)nmr.mgh.harvard.edu

2 1

error during autorecon2-wm routine
by Larissa Stanberry 02 Feb '11

02 Feb '11

Dear experts, after correcting WM, I got the following error running recon-all - autorecon-wm -subjid XXX ERROR: _FindFacePath: could not find path! It happens in the middle of the correcting topology routine. I'd appreciate any input on as to why it happens and how to fix it. Cheers Larissa

2 1

One Way Anova and multiple comparisons
by marco battaglini 02 Feb '11

02 Feb '11

Hi to everybody, I am a very inexperienced users of FreeSurfer. I have 3 groups of subjects and I have run recon-all and checked the results for all the subjects (very good results). Now what I need to do, is to calculate the differences in the regional cortical thickness between these 3 groups (using age and gender as covariates) and to perform multiple comparisons, in order to detect possible local differences in cortical thickness. Is it possible to perform this kind of analysis also for comparing surfaces between different groups? Could you give me a short "pipeline" about the steps I need to do, or redirect me to some focused documentation? Thank's. Marco

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