Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Image normalization outcome and adjustment
by David Warren 12 Sep '11

12 Sep '11

Hi all, I'm attempting to use FreeSurfer 5.1 (version block below) to process some older T1 scans collected on a 1.5T magnet with a native voxel size of 0.9375x0.9375x1.5mm. Overall, FreeSurfer seems to deal with these scans just fine (resampling to 1 mm isotropic, etc.), but I'm a little concerned about the results of the built-in image normalization. The potential issue is illustrated in an image that I've posted to http://imgur.com/NiEVQ. The isolated plot to the right shows the intensity histogram that we've observed for more recent 3T T1 scans, with an obvious WM peak at 110 and a GM peak around 65. Meanwhile, each of the six plots to the left is the intensity histogram for one of our 1.5T scans. Although they are internally consistent (with the upper-leftmost example being something of an outlier), the GM peak is much closer to the WM peak, with a mode around 85. I'm wondering whether this reduced GM/WM separation is likely to influence the tissue segmentation process, and if so how I might best remedy the situation. At a guess, mri_normalize or mri_ca_normalize seem like useful functions, but I haven't found the documentation for either to be of much help. Any assistance or advice would be greatly appreciated! Thanks, Dave Warren -- Post-doctoral Fellow Neurology Department University of Iowa Hospitals and Clinics davideugenewarren(a)gmail.com -------- freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) $Id: FreeSurferEnv.csh,v 1.79.2.1 2011/03/29 22:06:48 greve Exp $ FREESURFER_HOME /usr/freesurfer FSFAST_HOME /usr/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/freesurfer/subjects MNI_DIR /usr/freesurfer/mni FSL_DIR /usr/fsl

3 2

recon-all excluding parts of hippocampus
by Sheeva Azma 12 Sep '11

12 Sep '11

Dear Freesurfer List, I am using recon-all to measure cortical thickness in a population of Alzheimer's patients and I have noticed that in many patients the pial surface does not include the whole brain. This seems to be because there are hippocampal lesions that are dark spots in the image which throw off the segmentation. I have tried adding control points, but that is only for the white matter boundary, and so I was wondering if you could provide any insight as to how to correct the pial surface so that the entire hippocampus is included. I have attached an example image from tkmedit showing the pial and white boundaries. Thank you, Sheeva Azma

2 1

Project full annotation files from one subject to another
by mbrickho＠nmr.mgh.harvard.edu 12 Sep '11

12 Sep '11

Hi FS team, Is it possible to project an entire annotation file from one subject's surface to another? I haven't been able to find a command for this, but I might just not be looking hard enough. My intent is to project an annotation I've made on fsaverage to every member of a cohort of 500+ subjects, and then extract thickness data from each newly created annotation file. Currently, I do mri_annotation2label to split the original annotation into its individual labels. Then I project each label, one at a time, with mri_label2label. Then, I combine them back into an annotation with mri_label2annot for every subject. While this method works fine, it seems like it's more cumbersome than it has to be. Any help/advice would be appreciated. Thanks! Mike

2 1

mri_vol2vol
by Constantin Anastasopoulos 12 Sep '11

12 Sep '11

Hellom I coregistered manually a aparc+aseq.nii file to my DWI-space with tkregister2. I saved the .dat file and applied it later to the T1 image in order to apply the same spatial coregistration as to the aparc+aseg. For woth the aparc+aseg and the T1 I used the command mri_vol2vol --mov was the b0image --targ was the aparc+aseg and T1 respectively --o was the output (a .nii in both cases) --reg was the .dat file and at the and --inv. While the aparc+aseg registration to the b0 worked, the T1-registration gave a false result (altough it had the same dimensions and was in the same space with the aparc+aseg). What am I doing wrong? Is the mri_vol2vol command the wrong one? I want to apply the same changes as to the aparc+aseg, as they are saved in the .dat file. Thanks a lot, Constantin

2 3

some very basic Recon-all questions
by Martijn Cloos 10 Sep '11

10 Sep '11

Hi, When running something like: "recon-all -autorcon1 -i file1.nii.gz -s subject" it first converts the nifti file to the mgz format (orig.mgz, i think). In the proses the data appears to get converted to 8bit integers. Starting with float data how does this impact the analysis? It seems to me that the range selected in "orig.mgz" is not optimal and this appears to be resampled in T1.mgz. Are there ways to use a higher dynamic range, by forcing it to use floats or 16bit/32bit integers? Or should I just manually optimize/verify "orig.mgz" before running recon-all? Also, are there ways to use the original resolution instead of resampling to 1mm iso? Thanks! Martijn

2 1

bedpostx changes in past 2 years?
by swoodman＠nmr.mgh.harvard.edu 09 Sep '11

09 Sep '11

Hi all, We always run bedpostx in the developement (nmr-dev-env) environment, and after some digging around, we've noticed some differences in outputs between 2008 and now. Has anything changed with bedpostx in dev environment since 2008, that would effect data and/or analysis? There seem to be more log files in the bedpostx log directory in the sessions that were run more recently. So this is mainly why we are wondering if something has changed in the bedpostx program between October 2008 and October 2009 that affects the tractography data. Thank you! Sandra

2 1

autorecon1 output is just a white block
by Christopher Luna 09 Sep '11

09 Sep '11

Hello, After running an *.img file through autorecon1. Freesurfer says it finishes with errors, but I cannot find any error messages in the command line output. Checking the tkregister2 of the output shows that the "Target" is just a white box, while the "Moveable" stills eems like a typical image that I would find in any other output. Are there some settings I need to alter for mri_convert? The IMG file looks fine before running autorecon1. Thanks, Christopher Luna MIT Brain and Cognitive Sciences, Class of 2012 Desimone Lab, McGovern Institute for Brain Research MIT Archery Club Alpha Kappa Psi Colony at MIT

3 2

Ventricular structures - exact definitions
by mschwei1＠gwdg.de 09 Sep '11

09 Sep '11

Hello, as I am interested in the volume of ventricular structures in the brain, I would like to more precisely understand the labels given by /stats/aseg.stats in Freesurfer. Most importantly, what is the precisely defined difference between Left-Lateral-Ventricle and Left-Inf-Lat-Vent? Would you always combine these two in a volumetric study? Why are they separately segmented? And what exactly is the 5th-Ventricle? Less importantly, how exactly do you define CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior, and CC_Anterior? Is there a paper or homepage defining these exactly? Any help appreciated! Thanks a lot, Meike

2 1

structure volume
by Adil Javed 09 Sep '11

09 Sep '11

Hi, After running dti_recon and recon_all, I noticed that they produce different volumes of structures for the same brain. Just trying to understand why that is? best, AJ

1 0

refeventdur in mkanalysis-sess
by Maryam Vaziri Pashkam 08 Sep '11

08 Sep '11

Hi, I am making an analysis in freesurfer 5.1 using mkanalysis-sess and I am a bit confused about the flag refeventdur. In the help it is said that it should be set to the event duration if the events have similar durations. I have four conditions that last for 16 second each in a block design paradigm, but my fixation condition lasts for 8 second. What should I set the refeventdur to? Also I have an event related design with variable fixation durations. what should it be in that condition? How about if I have an event related design with variable stimulus durations? How does this value influence the design matrix? Thanks, Maryam

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