Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

longitudinal processing
by Dana W. Moore 29 Apr '09

29 Apr '09

FreeSurfers, I am using the longitudinal processing stream to look at change in the lateral ventricles at several timepoints. As a control measure, we are running two consecutive baseline images in the scanner. These images were done back-to-back, exactly the same, and the subject did not get out of the scanner nor reposition. Motion was not a problem. I have processed this first subject, and the longitudinal stream gives me a 2% change in lateral ventricular volume, comparing the two baseline scans. This is bigger than I'd like to see, as we are interested in changes over time as small as 2%. Is this kind of variability expected, or am I doing something wrong? I just used the first baseline as tp1, processed it cross-sectionally, and then longitudinally, and then I used the second baseline as tp2. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology & Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2003(a)med.cornell.edu

2 1

(no subject)
by Elina Pitri 29 Apr '09

29 Apr '09

Hello Freesurfer Creators, I am wondering how much time should Volume and Surface processing (using recon-all commands) take. thanks, Elina

3 2

(no subject)
by Elina Pitri 29 Apr '09

29 Apr '09

Hello, Do you know how can I convert my images which are in ctf format to a freesurfer compatible format? thanks, Elina

1 0

longitudinal stream
by Bruce Fischl 28 Apr '09

28 Apr '09

Hi All, We have recently tracked down a bias in the longitudinal processing stream. We believe we have a fix for the problem, but it will take us a bit of time to get it working and well-tested. We'll keep you posted as to when we will have a new version. Feel free to email me if you have any questions. sorry :<. Bruce

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skull strip problem
by Wilson, Benjamin 28 Apr '09

28 Apr '09

Hi, I am trying to run freesurfer on some SPGR sequences that I have on a few subjects. I managed to import and convert the DICOM files to .mgz with success, but when I ran the skull strip I have a significant amount of skull left in some places and a large chunk of brain missing in other planes on the same brain. I am wondering if there is a problem with intensity normalization (most of my brain appears to be close to an intensity of 110), but I do not know how to fix the problem. Can anybody offer some suggestions on how to fix the problem? Thanks. Sincerely, Ben Wilson

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Custom Aseg Atlas Question.
by Jamie Hanson 28 Apr '09

28 Apr '09

Hi Freesurfer folks- I am in the midst of creating a custom aseg atlas and had a quick question regarding when to use v. discard subjects. I just ran the second iterations of mri_ca_train (when you use all the subjects in subjects.csh and are training from segmented subjects using M3D_ONE) and I have 6 (of 18) subjects "with bad labels". Is it best to discard those subjects and just use the successfully labeled subjects? I wasn't sure if only included those good subjects would perhaps boost my aseg atlas accuracy. Thanks much. Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53705 Email: jamielarshanson(a)gmail.com Homepage: http://tezpur.keck.waisman.wisc.edu/~hanson/

3 4

Freesurfer Brain Region Ontology
by Stephan Gerhard 28 Apr '09

28 Apr '09

Hi! I am rather new to the Freesurfer Software, so I'll start with an easy question. Currently I am involved in a SemanticWiki project called ConnetomeWiki, which deals with Brain Regions and their connectivity. This needs to setup a good ontology to start with and I am in the process of merging some of the Neuroscience Information Framework, Wikipedia, Foundational Model of Anatomy and some other vocabularies. Since there is a big community behind Freesurfer, I also looked into what is available here and I found the files: FreeSurferColorLUT.txt and surface_labels.txt. Am I missing some important files related to this? Now I thought that it would be nice to "align" my work with the FreeSurfers vocabulary for the benefit of everybody. So could anybody point me to the people that are involved in building the ontologies and inform about the current state of research in this field? Thanks to anybody helping me with this issues! Stephan

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Label to annot
by Wayne Su 28 Apr '09

28 Apr '09

I have the trouble to convert the BA label to annotation file. The Freesurfer 4.3.0 is on Mac OS 10.5.6. First, I got the BA label: mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/lh.BA1.label --trgsubject 001 --trglabel 001/label/lh.BA1.label --hemi lh --regmethod surface This works. I can load the label onto the surface by using tksurfer. Select File->Label->Export Annotation. The Terminal window shows ³writing color table into annotation file...² and stop here. I checked the lh.BA1.annot, it¹s about 1MB. But when I try to load this annotation, the surfer warning me no lables imported and annotation was empty. I went to the command line and type in: mris_label2annot --s 001 --h lh --ctab 001/label/ba1.annot.ctab --l 001/label/lh.BA1.label --a BA1 Here is the message. subject 001 hemi lh SUBJECTS_DIR /Applications/freesurfer4.3/subjects ColorTable 001/label/ba1.annot.ctab AnnotName BA1 nlables 1 Loading /Applications/freesurfer4.3/subjects/001/surf/lh.orig 001/label/lh.BA1.label 001/label/lh.BA1.label 1 14465659 BA1 Mapping unhit to unknown Found 129453 unhit vertices Writing annot to /Applications/freesurfer4.3/subjects/001/label/lh.BA1.annot writing colortable into annotation file... This seems work because I can load the annotation onto the surface. But what are the ³unhit vertices²? Is this normal? The last question: how can I get the voxel number (volume) of this label? Thanks. Wayne

2 2

recon-all settings
by Ed Gronenschild 28 Apr '09

28 Apr '09

Hi, I want to use parameters different from default for mri_nu_correct.mni. This command uses nu_correct for which I would like to set the following options: -distance 25 -stop 0.0001 -fwhm 0.1 These settings are more approriate when using 3T T1 data. How can I invoke these in recon-all? Can I use an options file? Ed

2 1

is there a command to give resolution information?
by jake＠nmr.mgh.harvard.edu 28 Apr '09

28 Apr '09

Hi, This may be a frivolous question but I was just wondering if anyone knows a quick way to find out resolution of an image file, i.e., if I wanted to look at an older scan and wanted to check its resolution. I couldn't find any information in the wiki, but I may have just missed the correct area in my text search. Also, what if I wanted to confirm slice thickness? Thanks in advance! Jake

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