Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

ASeg Stats is done twice?
by Peter Wendorff 11 Sep '13

11 Sep '13

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi. I try to get information about the progress of my subjects out of the log files, writing a script that reports about the progress and sends progress messages. For that I try to get the individual stages as progress indicator from the recon-all.log. Usually lines like this indicate the start of a stage: #@# ASeg Stats Tue Sep 10 11:12:13 CEST 2013 the date of course is variable and indicates the current date. My problem now is exactly that Stage ASeg Stats, as it occurs twice. the first occurrence is after inflate2 (smooth2, inflate2, aseg stats), the second one is, as documented after cortribbon (parc stats 2, cortical ribbon mask, aseg stats, aparc-to-aseg). But [1] lists only the second occurrence. Is that wanted? is it due to my strategy to run autorecon1, autorecon2 and autorecon3 individually instead of autorecon-all -all? regards and thanks for your help Peter [1] http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/ iEYEARECAAYFAlIwONQACgkQi8ffXNvWmYQ5yACgiD/sgP/PR+xsuZJWtGoeFKlL LcYAniH2Q+SSHzPLAc2aTphUyoTm0bv2 =JLDM -----END PGP SIGNATURE-----

1 0

Number of independent vertices and Bonferroni correction
by Damien MARIE 10 Sep '13

10 Sep '13

Hello everyone, I'm using freesurfer for regression analyses and group analysis of cortical thickness, surface area, curvature and sulcal depth. I started to made illustrations and tables using the p < 0.05 FDR correction. However I have some p-value reaching 10^-32 and I would apply a Bonferroni correction. How determinate the number of independent vertices? Thanks a lot, best regards, Damien Damien Marie - Doctorant / PhD student E-mail: damien.marie(a)u-bordeaux2.fr Phone: +33 (0)5 57 82 09 39 Homepage: www.gin.cnrs.fr/spip.php?article23&lang=en Researchgate: www.researchgate.net/profile/Damien_Marie/ _______________________________________________ GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 - Université Bordeaux II Ségalen - CNRS - CEA 146, rue Léo Saignat - Case 71 33076 Bordeaux cedex _______________________________________________

3 2

Editing WM
by Francesco Siciliano 10 Sep '13

10 Sep '13

Hi, I've noticed that occasionally when I manually edit recons, the white matter surface will be drawn to include a portion of the volume where no white matter pixels are present. Therefore, when I go to correct the incorrectly drawn surface, there are no pixels to delete under the white matter mask. It is almost as if I have deleted the pixels already yet I have not and the white matter surface is still drawn to include an area where there are no white matter pixels. Why could this be happening? Does it matter as long as there are no pixels in the incorrect area? Thank you, Francesco Francesco Siciliano, B.A. Research Assistant Department of Child and Adolescent Psychiatry The New York State Psychiatric Institute Columbia University 1051 Riverside Drive, Unit 74 New York, NY 10032 (212) 543-6155

2 1

z-scores age
by olof lindberg 10 Sep '13

10 Sep '13

Dear Douglas, no I did not run in GLM-fit - I run in qdec The conversion into z-scores was done in a statistical program (statistica) and was calculated on basis of all subjects (both groups) - the thing that confuses me is that - if I understand it correctly from previous discussions on the mailing list - it should not be needed to demean age in order to correct for it? So in qdec I get completely different results if i use z-scores - than if I use the original raw age data. If I look at the plot of the z-scores versus raw age in qdec the distribution on the plot is exactly the same. So I would expect that no matter using raw age or z-scores would affect results the same? But the results look completely different (basically the raw-age corrected data looks wrong) Am I doing something wrong? thanks Olof

2 1

convert .mgh to .label?
by Yang, Daniel 10 Sep '13

10 Sep '13

Dear all, Is there a way to convert .mgh to .label? My .mgh is a ROI file from qdec-based group analysis and I don't want to draw the ROIs manually. Thanks! Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454

3 5

statistically truncate negative values
by Maya Rosen 10 Sep '13

10 Sep '13

Hi All, I have two conditions of interest in my GLM analysis, Condition A and Condition B. I would like to make a contrast of Condition A and Condition B that includes only those vertices that are significantly positively activated when compared to the Passive Viewing baseline. In other words, I would like to mask anything that is Passive > Condition A or Passive > Condition B and only include Condition A > Passive and Condition B > Passive when contrasting Condition A and Condition B, so as to limit my contrast to changes in *activation *in the two conditions, not *deactivation *. I see that in an older version, when isxavg-re-sess was used, there was a flag --trunc that would allow you to set the negative values to 0. If there is a way to do this in the v 5.1.0, I could then perform a second level contrast of positively activated Condition A and Positively activated condition B. Is there a way to exclude the negatively activated voxels from the Condition A vs Passive and Condition B vs Passive contrasts when looking at Condition A vs Condition B? I would like to do this statistically, not just at the map level. Thank you for your help! Maya

2 1

controlling for age in qdec
by olof lindberg 10 Sep '13

10 Sep '13

Dear Freesufer experts. I am trying to run attached fsgd file in qdec or in GLM-fit. I just want to do a group comparison in which I compare cortical thickness between groups controlling for age. when I run the analysis with age as a raw score - the results seems very strange - if i on the other hand convert age to z-scores (with a mean of 0) then results seems to be as I would expect As I understand it - I do not need to centre Age in order to control for it? So what is then going wrong when I run the analysis? thanks Olof

2 1

how does norm.mgz affect the behavior of mri_pretess?
by David Romano 10 Sep '13

10 Sep '13

Hi everyone, I was hoping that someone could clarify for me the role played by norm.mgz in the command mri_pretess filled.mgz 255 norm.mgz filled-pretess255.mgz from the -tessellate step of the -autrecon2 section on the page http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable. My understanding is that this command will (roughly) perform the following tasks for a given voxel v in filled.mgz with intensity 255: 1) Determine whether there are any other voxels of intensity 255 in the 3x3x3 cube centered at v. 2) If so, then further determine whether none of these share a face with v. 3) If so, then let S be the set of all such voxels, together with v itself, and identify an "optimal" collection of the remaining voxels in the 3x3x3 cube to add to S so that every voxel in S shares a a face with at least one other voxel in S, where "optimal" means that the added voxels should have intensities as close as possible to 255 in norm.mgz. Does this capture the role played by norm.mgz? Or am I way off? Thanks in advance for your help, David Romano

2 2

recon-all for multiple subjects
by Anupa AV 10 Sep '13

10 Sep '13

Dear Sir, I'd like to know the command lines for running recon-all for multiple datasets. Can you please help me on that? I've tried using the following command lines cd /home/john/Anu (where I kept all the .nii files) for x in * do recon-all -i SZ*.nii -s $x -all done But this is not working

4 5

Issue running Longitudnal Analysis
by Ray, Siddharth 09 Sep '13

09 Sep '13

Hi all, I was trying to run freesurfer longitudinal analysis for my subjects at 2 time points and when I ran the pre_proc step it gave me an error that file 'lh/rh.thickness is missing'. Here is what I have done. 1) Run the Freesurfer till CA Normalize stage (till norm.mgz stage). 2) Created unbiased template - log file showed 'exited without error' (and it looks fine) 3) Run longitudinal processing - log file showed 'exited without error' , but when I closely looked at the file there was following error: #@# Talairach Failure Detection Wed Sep 4 14:22:01 CDT 2013 /work/02510/sray2/Free_Sub/FS_output/54062.long.54062_59467/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0124, pval=0.0000 < threshold=0.0050) Do you where is I am doing wrong. Why is the log file showing 'exited without error' if there was an error at Talairach Detection. Please let me know. Thanks, -Siddharth

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