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30089 discussions

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

2 1

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

2 7

-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

2 1

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

1 0

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

2 1

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

2 1

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

2 1

general questions
by Deirdre O Shea 21 Sep '12

21 Sep '12

Hi all, I'm new to FreeSurfer and so have a few questions that you may be able to anwser. My first question is ; when I am making white matter edits do I need to edit every single slice where the inaccuracy is or would every second or third slice suffice to prompt FreeSurfer to autocorrect? Secondly, in many of our FreeSurfer images, the horn of the lateral ventricles in the coronal images are being excluded from the white matter - is there a way to stop this from happening? Finally, I find that Freeview is a good way to view the images and although I know it is possible to make some edits such as filling in voxels etc., I wanted to know if it was possible to add control points like that in tkmedit? Thanks, Deirdre

2 1

Correction: cerebellum volumes
by Rachel Steinhorn 20 Sep '12

20 Sep '12

We'd like to obtain total cerebellar volumes. There are errors within the cerebellar segmentation as revealed in the aseg.mgz file. Is there a method Is there a method to manually edit the cerebellar segmentation? Thank You, Rachel Steinhorn

1 0

Editing cerebellar aseg volumes
by Rachel Steinhorn 20 Sep '12

20 Sep '12

My lab would like to look at the cerebellar parcellation volumes, but looking through the aparc+aseg.mgz, we've noticed some areas where the cerebellar segmentation includes non-cerebellar tissue. Is there any way to edit the segmentation and recalculate the volumes to exclude the incorrect voxels? Thank You, Rachel Steinhorn Washington University in St. Louis School of Medicine

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