Freesurfer April 2008

freesurfer@nmr.mgh.harvard.edu

67 participants
102 discussions

problematic pial
by Jamie Hanson 07 Apr '08

07 Apr '08

Hi Freesurfers- I was trying to run freesurfer on a study template and was having major problems with pial surface generation. Orig and Main surfaces seem to be ok, but there are major missing chinks in pial surface. Just to give some background, the template was being using for Diffeomorphic Image Registration, so it is a very unique volume.I know it is likely it is an intensity value issue.I wondered what folks have done previously to correct similar issues? It appears to be across a massive proportion of the brain, so correcting by hand (by altering intensity values seems a bit labor intensive and perhaps questionable in terms of reliability). I also thought of trying to rerun some of the initial preprocessing (autorecon1 + 2) with some more 'expert settings'. Initially, I was running with no skull strip and no n3 flag (b/c the template has already been skull-stripped and massive preprocessed), but was looking for some additional advice and guidance. Any thoughts or suggestions would be greatly appreciated. Best, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

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Data Discrepancies
by Jared Morton 07 Apr '08

07 Apr '08

I am using Freesurfer to analyze a set of brains of subjects with temporal lobe epilepsy. The brains are being run at two different locations. In addition, the brains at one location have been run on two different computers, with two different freesurfer builds. The problem that I am having is that that each time the data are run, they are markedly different. The differences are substantial, more than should be accounted for by using different versions. In some cases, the differences are from 10-30% off. Has anyone else had this problem? -- Jared Morton M.S. Rosalind Franklin University of Medicine and Science

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Estimating the difference in cortical thickness between two groups
by jorge luis 07 Apr '08

07 Apr '08

Hello all We are comparing the cortical thickness of two groups with the following fsgd file: GroupDescriptorFile 1 Title Thickness-subj Class contr Class modif Input subj1 contr Input subj2 contr Input subj3 contr Input subj4 contr ... Input subj36 modif Input subj37 modif Input subj38 modif Input subj39 modif ... (the same number of subjects) We are using the contrast vector: 1 -1 and DOSS codification for the design matrix. The generated beta.mgh file contains two frames, I think one is for the coefficients of the first regressor and the other is for the coefficients of the second one. Now we want to infer the groups difference in cortical thickness at each 'activated' vertice (the change in mm). Can we do that by simply taking de difference between thouse first and second regression coefficients? I think this value can be seen as the slope of the difference between the first and the second group. Is it true? Any tip is welcome In advance thank you ______________________________________________ ¿Con Mascota por primera vez? Sé un mejor Amigo. Entra en Yahoo! Respuestas http://es.answers.yahoo.com/info/welcome

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Cortical parcellation
by hakon.grydeland＠psykologi.uio.no 07 Apr '08

07 Apr '08

Dear FreeSurfers, I am analyzing data from a few patients with quite severe unilateral temporal lobe damage (no or little brain tissue left both medially and laterally). The cortical parcellation in the damaged hemispheres seem - compared to the presumably unaffected contralateral hemisphere and other "normal" brains - all right in some parts, while other labels are misplaced due to the placing of temporal lobe labels which no longer exist. I was looking for some advice as to how to proceed: Is it advicable to use the labels from the original (recon-all) cortical parcellation that seem well parcellated, and create ROIs manually by drawing in tksurfer/tkmedit the parts of the brain where the labels have been misplaced? Or should I create ROIs manually and don't use the automated cortical parcellation? Or is yet another approach more appropriate, for example changing the input used in the parcellation so that Freesurfer don't expect to find and label temporal lobe structures in the damaged hemisphere? Thanks! Håkon Grydeland

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What is function of selxavg-jk-sess?
by Zhen Zonglei 06 Apr '08

06 Apr '08

Dear, Dr. Greve: Sorry for bothering you again. Can you explain us what is function of selxavg-jk-sess? We have searched its information in FS wiki and mailing list many times, but nothing is found. Now we want to do leave-one(run)-out feature selection, we hope this command can help us, but not sure. Please give us some details on this command, especially, its computational process and output. Please help us. Thanks in advance. Zonglei Zhen

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Re: [Freesurfer] autorecon3 issue / cortical parcels error.
by Jamie Hanson 05 Apr '08

05 Apr '08

Just checked me results and still no luck / similar technicolor labels. Any further thoughts? Best, jamie. > > that usually means that the parcellation is out of date with the surface. > > Can you just rerun the mris_ca_label step and see if it works > > > > cheers, > > Bruce > > > > > Just checked me results and still no luck / similar technicolor labels. > Any further thoughts? > > Best, > jamie. > > > > > > > > > On Sat, 5 Apr 2008, Jamie Hanson wrote: > > > > > > > Hi Freesurfer folks- > > > > > > Something went awry with the autorecon3 portion of recon-all. After > > > one iteration of autorecon2, I ended up editing my wm.mgz and adding > > > control point. I got some (what looked like) fabulous cortical > > > surfaces, then ran autorecon3. When I went to load the labels > > > resulting from autorecon3, I got quite a technicolor result (see > > > attached). > > > > > > Any thoughts? Thanks much, > > > jamie. > > > > > > > > > > > > > > > > > > > > > > > -- > Jamie L. Hanson > Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab > University of Wisconsin - Madison > 1500 Highland Avenue > Madison, WI 53706 > ***Please note my new email: jamielarshanson(a)gmail.com*** > -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

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autorecon3 issue / cortical parcels error.
by Jamie Hanson 05 Apr '08

05 Apr '08

Hi Freesurfer folks- Something went awry with the autorecon3 portion of recon-all. After one iteration of autorecon2, I ended up editing my wm.mgz and adding control point. I got some (what looked like) fabulous cortical surfaces, then ran autorecon3. When I went to load the labels resulting from autorecon3, I got quite a technicolor result (see attached). Any thoughts? Thanks much, jamie. -- Jamie L. Hanson Waisman Laboratory for Brain Imaging & Behavior | Child Emotion Research Lab University of Wisconsin - Madison 1500 Highland Avenue Madison, WI 53706 ***Please note my new email: jamielarshanson(a)gmail.com***

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Longitudinal capabilities
by Sky Raptentsetsang 03 Apr '08

03 Apr '08

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how does qdec make a contrast.mat file...?
by Cameron Ellis 03 Apr '08

03 Apr '08

Hi, I have been running analyses in qdec and glmfit and comparing the results. I am puzzled by the results of one analysis that compares two groups. When I loaded a table.dat file in qdec and selected the variables of interest, an fsgd file containing only those variables was generated in the analysis, no problem so far. The problem is that the contrast.mat file contains more "identifiers" than variables I selected. The generated fsgd file looks something like this: Class a Class b Variables x Input subj1 a 1 Input subj2 b 4 Input subj3 a 2 Input subj4 b 1 and the generated contrast.mat file looks like this: 0 0 +1 -1 I thought that to generate a contrast for these two groups of the correlations between thickness and variable x I shouldn't the contrast.mat file that looks like this: +1 -1 1 Thanks for any insight, Cameron

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Local Gyrification Index in Freesurfer
by Marie Schaer 03 Apr '08

03 Apr '08

Dear Freesurfer's users, Just a small e-mail to announce the availability of a new feature for quantifying cortical morphology in the latest Freesurfer release. It is called local Gyrification Index (lGI) and is derived from the surface-based Gyrification Index which was traditionally measured on 2D coronal slices (Zilles et al., 1988). Simply run it with recon-all -lgi (~3h per hemisphere, requires Matlab to be installed). Details on the processes and the validation paper can be found at http://surfer.nmr.mgh.harvard.edu/fswiki/LGI Many thanks to Nick, Bruce, Rudolph and Doug for their help in making this tool widely available, Marie Schaer marie.schaer(a)medecine.unige.ch Geneva Child Psychiatry Department & Swiss Federal Institute of Technology Switzerland

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Freesurfer April 2008