Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

intracranial volume and dicom
by Knut J Bjuland 25 Sep '12

25 Sep '12

Hi, I have calculated relative volume by dividing each volume by the intracranial volume and multiply it with 100. When I add the relative volume of total gray matter, cortical white matter, lateral ventricle, 3rd centricle, 4th ventricle and ventral DC, I get 82-86 %. Can this be caused by the fact that the intracranial volume is much larger than the brain? In which way can motion correction affect volume if I have series where some subjects have to dicom and other just have one dicom serie? Knut J

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Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer
by Fabian Schrumpf 25 Sep '12

25 Sep '12

Hi bruce, At first I want to build a voxel-based FEM-Model based on the surfaces freesurfer creates. For finally creating the models I want to use the MATLAB toolbox iso2mesh. But I would also be interested in building BEM models as a second approach. best regards Fabian ----- Ursprüngliche Mail ----- Von: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> An: "Fabian Schrumpf" <schrumpf(a)cbs.mpg.de> CC: "Matti Hamalainen" <msh(a)nmr.mgh.harvard.edu> Gesendet: Dienstag, 25. September 2012 15:36:50 Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer Hi Fabian can you cc the list so others can answer? Do you want a voxel-based head model? We generate surface models for BEM analysis that Matti (ccd) can tell you about if you are interested. You could generate a volume by fillin the interior of the various surfaces with mris_fill if you prefer. cheers Bruce On Tue, 25 Sep 2012, Fabian Schrumpf wrote: > Hi Bruce, > > thank you for your reply. I'm new to freesurfer. What I'm trying to do is to build a head model für MEG source localization. Therefore I have to divide the human brain in white matter, gray matter and CSF. After doing WM segmentation and cut/fill freesurfer comes up with a good segmentation of the brain in aseg.mgz. Unfortunately, this segmentation also contains many sub-cortical structures that I don't want to take into account for my head model. I'm trying to find a way to do a segmentation that only considers WM, GM and CSF. Additionally, reducing diversity of segmented tissue should perhaps reduce computation time? > > Best regards > > > Fabian > > ----- Ursprüngliche Mail ----- > Von: "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> > An: "Fabian Schrumpf" <schrumpf(a)cbs.mpg.de> > CC: freesurfer(a)nmr.mgh.harvard.edu > Gesendet: Dienstag, 25. September 2012 15:08:11 > Betreff: Re: [Freesurfer] Brain segmentation (gray, white, csf) using freesurfer > > Hi Fabian > > What are you trying to achieve? The easiest thing to do is to run recon-all > with the -all flag so we generate an aseg, then that can be collapsed into > different measures. > > cheers > Bruce > > > On Tue, 25 Sep 2012, Fabian Schrumpf wrote: > >> Hi folks, >> >> I successfully managed to do a brain segmentation using freesurfer. But the result after mri_fill has too much detail. I'd like to do a segmentation only dividing the brain into white matter, gray matter and csf. I suppose that I have to alter some options when registering and aligning the volume to the gca atlas. But i don't know which option that would be. On the other hand, is there any way to edit the atlas itself so that it just contains the regions I am interested in? Thanks in advance for your help. >> >> Best regards >> >> >> Fabian >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and properly > dispose of the e-mail. > > > >

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Brain segmentation (gray, white, csf) using freesurfer
by Fabian Schrumpf 25 Sep '12

25 Sep '12

Hi folks, I successfully managed to do a brain segmentation using freesurfer. But the result after mri_fill has too much detail. I'd like to do a segmentation only dividing the brain into white matter, gray matter and csf. I suppose that I have to alter some options when registering and aligning the volume to the gca atlas. But i don't know which option that would be. On the other hand, is there any way to edit the atlas itself so that it just contains the regions I am interested in? Thanks in advance for your help. Best regards Fabian

2 1

Comparing cortical thickness for 2 groups
by Ryan 24 Sep '12

24 Sep '12

Hello everyone, I'm analyzing the data for a training study looking to see if there are changes in cortical thickness as a result of training. We have pre and post scans (training) and control subjects (no training). How do I setup this design in the Xg.dat and matrix files so I can run mri_glmfit? Thank you. Best, -W. Ryan McGarry

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preproc-sess
by Andrew Bock 24 Sep '12

24 Sep '12

Hello, I am attempting to run preproc-sess on my functional data, and am following the tutorial found here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastPreProc I downloaded the tutorial data, and find that when I view fmcpr.up.sm5.mni305.2mm.nii.gz it looks quite ugly (i.e. does not look like a brain). I would expect this file to look like the fsaverage brain, is that not correct? Andrew

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-hpf and -polyfit in mkanalysis-sess also applied to predictors?
by Caspar M. Schwiedrzik 24 Sep '12

24 Sep '12

Hi all, when specifying -hpf and -polyfit in mkanalysis-sess, I understand that fourier pairs and polynomials are implemented in the design matrix. I was wondering whether the filtering is also applied to the predictors? I am doing a seed-based resting state analysis and applying the filters to the data and the predictor should improve the fit. If not what would be the easiest way to apply them to the predictors, too? Thanks, Caspar ps.: using freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full

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Insula question
by Weisinger, Brian (NIH/NIMH) [F] 24 Sep '12

24 Sep '12

Greetings, I had a question concerning which lobe of the brain the Insula would be accounted for in when computing the different total Lobar volumes. Is there a FreeSurfer standard or is this something the individual would decide? Thanks for the help, Brian

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Qdec
by Darren Gitelman 23 Sep '12

23 Sep '12

Dear List I'm wondering about the proper way to set up an analysis that includes site as a regressor, and whether this is possible in qdec? My qdec.table.dat file looks like this. fsid group site 1 grp1 1 2 grp2 2 3 grp2 2 4 grp1 3 .... and so on I then have .level files for group which has 2 levels, and site which has 7 levels. The type of question I want to answer for example is: Is there a difference between grp1 and grp2 regressing out the effects of site? Is this possible with Qdec? When I select the group variable on the design tab the analysis results shows the question of the form: Is there a difference between grp1 and grp2, but there is no mention of regressing out the site effect. Looking at the design matrix X.mat it only includes 2 columns which isn't right. If I select both group and site on the design page I get an error. Do I need to put together an FSGD file instead? Thanks Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073

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surface clustering
by Josef Ling 21 Sep '12

21 Sep '12

Hello, I'm trying to test the effect of thresholds on some sample data. I'd like to look at how many clusters survive different thresholds. I also want to filter out really small clusters. My data have already been projected onto the fsaverage template. In the simplified case below, I expect a report of clusters >= 10mm^2 whose value is > 1.0. Does the following command look reasonable? mri_surfcluster \ --in xxx.stat.fsaverage.mgh \ --subject fsaverage \ --hemi lh \ --surf inflated \ --thmin 1.0 \ --sign pos \ --thmax 100.0 \ --no-adjust \ --minarea 10 \ --sum pos.summary.txt thanks

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label in mni305
by peka Savayan 21 Sep '12

21 Sep '12

Dear FreeSurfer experts, I would like to get labels, get them in MNI305 space and to visualize them on the brain.mgz, which to be in MNI305. I used following: a) To get labels in MNI $FREESURFER_HOME/bin/make_average_subject --out asub1 --subjects sub1 #creat labels mkdir $SUBJECTS_DIR/sub1/labels $FREESURFER_HOME/bin/mri_annotation2label --subject sub1 --hemi lh --outdir #transform label to MNI305 $FREESURFER_HOME/bin/mri_label2label --srcsubject sub1 --srclabel $SUBJECTS_DIR/sub1/labels/lh.precentral.label --trgsubject asub1 --trglabel $SUBJECTS_DIR/sub1/labels/lh.precentral_mni305.label --regmethod surface --hemi lh b) To visualize tkregister2 --mov $SUBJECTS_DIR/asub1/mri/brain.mgz --noedit --s asub1 --regheader --reg $SUBJECTS_DIR/asub1/mri/register.dat $FREESURFER_HOME/bin/mri_label2vol --label ./lh.postcentral_mni305.label --temp $SUBJECTS_DIR/asub1/mri/brain.mgz --subject asub1 --hemi lh --o asub1_lh_postcentral305.nii.gz --reg $SUBJECTS_DIR/asub1/mri/register.dat $FREESURFER_HOME/bin/mri_convert $SUBJECTS_DIR/asub1/mri/brain.mgz $SUBJECTS_DIR/asub1/mri/abrain305.nii.gz Is this correct? Thank you. Peka

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Freesurfer September 2012