Freesurfer

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30132 discussions

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

2 1

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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Number of maximal permutations / pooled variance estimates
by Jürgen Hänggi 30 Nov '11

30 Nov '11

Dear FS experts I have a question regarding the number of maximal permutations. I compare a single patient versus a group of six control subjects. Intuitively, I guess that only six different permutations are possible. However, when running 100 permutations in FS with mri_glmfit-sim, I get different results for each permutations as confirmed in the CSD file. So, I am not sure any longer whether the permutations are built by permuting the subjects or anything else. The other question is how mri_glmfit estimates the variance. Because I have only one subject in the patient group, there is not variance in that group and therefore I guess mri_glmfit used pooled (across both groups) estimates of variance, isn't it? Any comment is highly appreciated Thanks in advance Best regards Jürgen ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

2 4

bugs fix
by Knut J Bjuland 30 Nov '11

30 Nov '11

Which of the files in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos4_x86… should be download and added to Freesurfer 5.1 to fix bug? Knut J

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bbregister - measure of consistency
by Joana Braga Pereira 30 Nov '11

30 Nov '11

Dear Doug and Freesurfers, I have a structural MRI and DTI set of images that i've corregistered (individually) using bbregister. My mincost files show a value that varies between 0.1 and 0.2 for all subjects. I read the paper by Grieve et al., 2009 Neuroimage and was wondering whether it is correct to explain in the current paper that i'm writting that the values of my mincost files are the result of calculating AAD, which is a measure of registration consistency. I was planning on presenting the above values as a proof that bbregister performed an accurate registration between my MRI and DTI images. Is this correct? Many thanks for your help! Joana

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Re: [Freesurfer] Brain Volume measures
by Douglas N Greve 30 Nov '11

30 Nov '11

That is basically correct. mri_segstats uses the same functions internally that mris_volume and mris_wm_volume use. doug Alexopoulos, Dimitrios wrote: > Just for clarification, the surface-based cortical GM volumes in the 'aseg.stats' file are calculated using: > mris_volume hem.pial AND mris_volume hem.white > For each hemisphere, determine the total volume inside the pial surface and subtract > the total volume inside the white surface. > > Cortical WM volumes in the 'aseg.stats' are determined using" > mris_wm_volume subject hem > > Is this correct? > > Jim > > > > ________________________________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Wednesday, November 30, 2011 11:46 AM > To: Jeff Sadino > Cc: andrei.sherstyuk; skogachi(a)gmail.com; freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Brain Volume measures > > Hi Jeff, the total cortical gray matter is based on the volume between > the white and pial surfaces. The other structures you mention below are > based on the automatic volume segmentation. > doug > > Jeff Sadino wrote: > >> 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 >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)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 > 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 > > _______________________________________________ > 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. > > > The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email. > > > -- 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

1 0

Surface Area from mri_surfcluster versus mri_segstats
by MCLAREN, Donald 30 Nov '11

30 Nov '11

I've noticed that if I run mri_surfcluster to produce a label file, then merge the labels into a single label using mri_mergelabels, then mri_segstats with the slabel option with the fsaverage subject; I get different surface areas from mri_surfcluster (summed all the cluster areas) and mri_segstats (1 area). Is there something wrong with my implementation of these three commands or is it expected that the two methods would produce different values? Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

2 1

Freesurfer projecting vector results for segmented cortical regions
by Weisinger, Brian (NIH/NIMH) [F] 30 Nov '11

30 Nov '11

hello we are trying to project a vector of results for segmented cortical regions (i.e., ... "lh_middletemporal_thickness" 0.000757119 "rh_middletemporal_thickness" 8.06E-05 "lh_parahippocampal_thickness" -0.000510407 "rh_parahippocampal_thickness" 0.000625997 "lh_pericalcarine_thickness" 0.000499749 "rh_pericalcarine_thickness" 0.000903678 "lh_superiortemporal_thickness" 0.001732855 "rh_superiortemporal_thickness" 0.000184256 "lh_temporalpole_thickness" 0.001075362 "rh_temporalpole_thickness" -0.000381165 "lh_transversetemporal_thickness" 0.000558122 "rh_transversetemporal_thickness" 6.65E-05 ...) however, we are unsure of how to do this. so, our question is— what is the sequence of steps we need to take to visualize our results on the segmented 3D template in tksurfer. Thanks for your help, Brian Weisinger

4 4

Surface X, Y, Z to Tailarach or Volume Index
by Frank Leone 30 Nov '11

30 Nov '11

Dear all, I wrote my own function to show the 3D surfaces in Matlab, works splendidly. I now however want to be able to point out Tailarach/MNI coordinates on the 3D surface. I however only have the x, y, z format that is saved in the asc files, which is just where a certex is located in space, with no relation to the original brain whatsoever. The only thing I can retrieve is the vertex index (because that's in the asc file). How can convert the 3D X, Y, Z values (the same values you get in the console if you click on a point on the surface in tksurfer) to either Vertex RAS/Talairach or Volume index? I read the information on conversions between surface Talairach and Volume Index, that works, but this case is different: I am actually referring to the 3D locations of the vertices. Hopefully someone can help me, thanks a lot in advance, best, Frank

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