Freesurfer November 2011

freesurfer@nmr.mgh.harvard.edu

110 participants
165 discussions

Re: [Freesurfer] tcl script question: labl_set_color
by Justin Baker 04 Dec '11

04 Dec '11

I am trying to use tksurfer to script overlay of a label + functional map onto an fsaverage5 surface. In particular, I want to set the label to "fill" and color it red. I have: set labelstyle 0 labl_set_color 0 255 0 0 As you can see below, the output of label_print_list shows that the color of the label should be "255 0 0 " but it looks white in the output image. Am I missing something? Thanks ------------ subject is fsaverage5 hemi is lh surface is inflated Label 0 Name: lh.17Networks_LH_ContB_PFClv.label, 109 vertices Structure: -1 Color: 255 0 0 Visible: 1 Bounds: x -20.879234 12.792567 y -4.000000 109.853737 z -4.033233 4.040778

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Brain Volume measures
by Jeff Sadino 02 Dec '11

02 Dec '11

Hello, Thank you Bruce and Doug for your answers to my previous question about a bad talairach.lta file. I am now grabbing volumes using fs5.0.0 and would like to ask for clarification. On the Morphometry Stats page at http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats, it says that the cortex is based on the pial surface. I am wondering what this includes. I loaded up the pial surface in tkmedit along with aseg.mgz. It looks like the following regions are completely outside the pial surface: cerebellum, 4th ventricle, Brain-Stem, optic chiasm. Is it correct that these regions are excluded? And then it looks like the hippocampus, amygdala, and inferior-lateral-ventricle are only halfway outside the pial surface. Is that correct? If it is, then is there a recommended way to exclude the hippocampus, amygdala, and inferior-lateral-ventricle regions in the cortical gray matter? Do these regions get properly accounted for in the subcortical gray calculation? And then for the white matter, the webpage says that it is based on the white surface. Looking at the white surface (lh.white), all of the subcortical gray matter and ventricles are enclosed in the surface. Can someone explain how the subcortical gray gets excluded? Finally, for the SubCortGray reported in aseg.stats file, does that exclude the following areas: Left-Lateral-Ventricle Left-Inf-Lat-Vent 3rd-Ventricle 4th-Ventricle CSF Left-vessel Right-Lateral-Ventricle Right-Inf-Lat-Vent Right-vessel 5th-Ventricle Left-Cerebellum-White-Matter Right-Cerebellum-White-Matter WM-hypointensities What about the brain stem? Why is the cerebellum Gray Matter included? I ask because the only way I can get close to the SubCortGray by using the aseg file is by excluding those regions. Once again, thank you for your invaluable help! Jeff Sadino

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Computing Volume of Segmentation Label Above or Below a User-Defined Plane
by Joshua Lee 01 Dec '11

01 Dec '11

Hi All, I would like to determine the volumes of a segmented region below or above an arbitrary line in one of the planes. For example, what would be the remaining volume of a label when z >= nth slice, where I would have previously determined the appropriate value of n. Thanks, Josh

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Tracula: Small Tracts
by Tyler Blazey 01 Dec '11

01 Dec '11

Hi List, I recently ran a group of around 70 subjects through trac-all. I have started to check the results, and have noticed that Tracula will often produce a tract with a really small volume and a posterior distribution that consists of just 0s and 1000s. When this occurs, the end point images usually contain only one voxel greater than 0. I am not sure what, if anything, is going wrong. The original recons are all of good quality, and the registrations to MNI space look good (the end point images look fine in MNI space as well). I also noticed this same issue in the right SLFP (bbregister version) of the Tracula tutorial subject. Is this a fixable error, or is it actually expected behavior? Thanks for any help. - Tyler

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Re: [Freesurfer] Yeo_JNeurophysiol11_FreeSurfer networks
by Yolanda Vives 30 Nov '11

30 Nov '11

Hi Thomas, Thank you for your answer, I will try to project your parcellation in fsaverage space to BASGU space first. Regards, Yolanda 2011/11/26 Thomas Yeo <yeoyeo02(a)gmail.com> > Hi Yolanda, > > Just to understand what you are doing, you have run BASGU through > recon-all and you are trying to project the surface parcellation into > the anatomical volume of BASGU? > > The annotation we are providing is actually in fsaverage space, so you > need to first project the parcellation from fsaverage space to BASGU > native surface space before running mris_annot_to_segmentation to > project the parcellation into his/her anatomical volume. > > To project the parcellation from freesurfer surface space to the > subject's native surface space, I think you can use mri_surf2surf, > although I am not sure if there's a more specific freesurfer function > that is specialized for transferring annotation files. > > --Thomas > > On Thu, Nov 24, 2011 at 4:11 PM, Yolanda Vives <yvives(a)pic.es> wrote: > > Dear Freesurfer experts, > > > > I would like to use the Yeo_JNeurophysiol11_FreeSurfer parcellations > with my > > dataset and I am not sure what I have to do. I have used the > > mris_annot_to_segmentation command but I have the following error: > > > > mris_annot_to_segmentation BASGU lh inflated > > ./fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot > > ../Yeo_JNeurophysiol11_MNI152/Yeo2011_17Networks_ColorLUT.txt test > > reading /freesurfer/BASGU/surf/lh.inflated... > > reading colortable from annotation file... > > colortable with 18 entries read (originally MyColorLUT) > > mri_read(): couldn't determine type of file /freesurfer/BASGU/mri/T1 > > (null): could not read T1 for template volume > > > > I have a T1.mgz file inside mri/. Where could be the problem? Is this > > command appropriate? > > > > Thank you in advance, > > Yolanda > > > > _______________________________________________ > > 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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mac os questions and hypo/hyper intensity question
by Lindsay Ercole 30 Nov '11

30 Nov '11

Has anyone else had problems installing FS 5.1 on a Mac running OS 10.7.2? (i.e. Lion) Also - are the hypo and hyper-intensities only calculated for given regions, or are they segmented no matter where they occur in the tissue? Thanks, Lindsay

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Four Groups (Two Factors/Two Levels), One Covariate with very strange results
by Knut J Bjuland 30 Nov '11

30 Nov '11

I have ran an analysis similar to the analysis listed http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V. I get a results that was quite different from group analysis controlled for age compared to group difference controlled for both gender and sex. I have similar picture analyzed with a previous version of Freesurfer 4.30 that has different part of the brain highlighted. I get quite similar results for the group analysis when comparing Freesurfer 4.30 and Freesurfer 5.1. Knut J

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Re: [Freesurfer] Sub-cortical structure
by Douglas N Greve 30 Nov '11

30 Nov '11

Hi Jie, what do you mean they don't work? I don't know what the difference between mri_mc and mri_tesselate is (another good reason to post to the list so that others who might know can answer the question). doug Jie Shi wrote: > Sorry I have forgot to describe our surface format. > > Vertex 1 x1 y1 z1 > Vertex 2 x2 y2 z2 > . > . > . > Vertex n xn yn zn > Face 1 v1 v2 v3 > . > . > . > > > On Tue, Nov 29, 2011 at 5:10 PM, Jie Shi <Jie.Shi(a)asu.edu > <mailto:Jie.Shi@asu.edu>> wrote: > > Hi, thanks for your previous help, but I have more questions to > bother you. I have tried mri_tesselete and converted the resulting > surfaces into ascii format. These surfaces work in Matlab but in > our mesh format like the following they don't. If I tesselate the > surface by command mri_mc, the surfaces work in our format. So > what is the difference between mri_tesselate and mri_mc? Since the > resulting surfaces are not good enough (some of them have holes), > I would line to know if FreeSurfer can generate surfaces for > subcortical structures like it does for cortex? Thanks a lot. > > Jie > > > > On Wed, Nov 9, 2011 at 5:24 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > yes, that has the subcortical segmentation based on the > automatic algorithm and any changes that you might have made > manually. The "auto" is only the result from the automatic method. > doug > > Jie Shi wrote: > > Thanks a lot. Will try. Basically, is aseg.mgz the > resulting file which contains the results of FreeSurfer > subcortical segmentation? What role is the aseg.auto.mgz? > > Jie > > > On Wed, Nov 9, 2011 at 5:15 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > cd $SUBJECTS_DIR/subject/surf > mri_tesselate ../mri/aseg.mgz 17 lh.hippocampus; # this > generates > a surface with jagged edges > mris_smooth -nw -n 10 lh.hippocampus lh.hippocampus.sm10; # > smooths surface 10 smoothing steps is just a guess > > # Visusalize the surface > tksurfer subject lh hippocampus.sm10 > # See the surface overlaid on the volume > tkmedit subject orig.mgz lh.hippocampus.sm10 -aseg > > Not that when you run the tkmedit/tksurfer commands, > they will > complain that the surface does not match. This is not a > problem > for this application. > > doug > > > Jie Shi wrote: > > Hi, thank you very much. Actually we do want to > know how to > get the surfaces in order to compare with ours. > > Jie > > > On Wed, Nov 9, 2011 at 4:59 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > You can extract a binary mask for any structure with > mri_binarize --i aseg.mgz --match XX --o > yourmask.mgh > where XX is a number from > $FREESURFER_HOME/FreeSurferColorLUT.txt > (eg, 17 = left hippo) > It is possible to generate hippo surfaces, but > we cannot > guarantee > accuracy. Let me know if you want to know how. > doug > > Jie Shi wrote: > > Hi, experts. We need to use FreeSurfer to > process some > analyze > image data. More specifically, we want to > extract the > hippocampus surfaces. We know that > FreeSurfer has done > subcortical segmentation during -autorecon2 > stage in > recon-all. We have checked the resulting > aseg.mgz file and > found that it contains all substructures. So > we wonder if > there is a way to get the separated .mgz > files for each > substructure or could FreeSurfer generate > the subcortical > surfaces? Thanks a lot. > > Best, > Jie > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > <tel:617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>>> > > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > > 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. > > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 > <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: > 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Convert non-surface labels to volume masks
by konglq＠nmr.mgh.harvard.edu 30 Nov '11

30 Nov '11

Dear Freesurfers, I am trying to convert a non-surface label into a binary volume mask (does that make sense?). To create the label I used tkmedit (brush tool) to select the voxels I need on the appropriate slices and saved as a label file. Then I tried to use mri_label2vol to convert this label to a binary volume mask by doing: mri_label2vol --label lh-test.label --temp 100101AA/bold/006/f.nii --reg 100101AA/bold/register.dat --proj frac 0 1 .01 --subject AA --hemi lh --o 100101AA/bold/masks/lh-volmask.nii I got an error: Loading ./lh-test.label ERROR: label ./lh-test.label is not a surface label. So looks like mri_label2vol only works on surface labels. Is there a way to convert a label defined by tkmedit on the volume into a binary volume mask? Or is there a better way to do this? Thank you. Lingqiang Kong

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color scale interpretation retinotopy eccen maps
by Erhan Genc 30 Nov '11

30 Nov '11

Dear freessurfer experts, I created my polar und eccen maps using the retinotopy pipeline. I also visualize them using the the rtview command on the inflated surface. But how can I interpret the colors (red to blue in the RYGB Wheel) in my eccen map? Which color refers to which timepoint (volume) of my functional run? Best, Erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: genc(a)mpih-frankfurt.mpg.de http://www.mpih-frankfurt.mpg.de/global/Np/Staff/genc.htm

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Freesurfer November 2011