Freesurfer April 2009

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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

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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/

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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

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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

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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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Re: [Freesurfer] Comparison of cortical thickness results
by Nick Schmansky 28 Apr '09

28 Apr '09

Falk, If you have the .annot file for a subject, you can break that apart into individual label files using mris_annot2label. Then knowing which labels compose the parietal lobe (for the Desikan-Killiany atlas, superior and inferior parietal, supramarginal, precuneus and postcentral compose the parietal lobe), then you can create a new label file by combining the label files into one with a text editor (the second line is the number of vertices composing the label, so be sure to get that right). then use mris_anatomical_stats to get the stats on this new label. Nick On Mon, 2009-04-27 at 16:31 +0200, Falk Lüsebrink wrote: > Hi everyone, > > > > I’d like to compare the individual cortical thickness results of > Freesurfer with the results of another software. The other software > measures the cortical thickness for example across the whole left > parietal lobe. So I have to get the according value of the whole left > parietal lobe of Freesurfer’s results. But I don’t know exactly how to > do that. > > > > Does someone have any suggestions how to get this value? At first > glance I would weight the average thickness of every structure > belonging to the parietal lobe given in the aparc.a2005s file by the > number of vertices (or maybe the gray matter volume in case the volume > had a resolution of 1mm^3?). Sum everything up and divide it by the > number of vertices to get the mean average across the parietal lobe. > Would that result in the value I’m searching for? > > > > Thanks in advance, > > Falk > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_preproc really averages?
by Jeff Sadino 27 Apr '09

27 Apr '09

Hello, I think my message got scrubbed from my last post with the pictures. I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you! Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh'; %Read the thickness file curv=MRIread(path); %Select the volume attribute curv2=curv.vol; %Create a duplicate thickness array for manipulation curv3=curv2; %Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp' %Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end %Select just the first frame curv4=curv3(1,:,:,1); %Compute the average thickness curv.vol=curv4/m; %Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh'); _________________________________________________________________ Windows Live™ SkyDrive™: Get 25 GB of free online storage. http://windowslive.com/online/skydrive?ocid=TXT_TAGLM_WL_skydrive_042009

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Freesurfer April 2009