Freesurfer

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 03 Aug '16

03 Aug '16

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mri_normalize, 110 is too dark
by tvg[fs] 03 Aug '16

03 Aug '16

Dear community and developers, I am experiencing issues during the normalization step, converting NU.mgz to T1.mgz. Gray matter is falsely recognized as white matter and high intensity WM is ignored. The resulting T1.mgz collapses the wrong voxels into the 110 bin. It seems that what mri_normalize assumes a peak in the WM intensity distribution that is too low. In NU.mgz WM seems centered around 140 not 110. Note that this is not due to RF-field inhomogeneities. It is likely of physiological origin - Is there a way to explicitly tell mri_normalize to use a different intensity peak? I realize that correction can be done with control points, however I understand that does not compute a new intensity distribution, but merely adds voxels around CPs. This is undesirable since I have >20 scans to process. Also this will not correct the falsely tagged GM voxels. I've tried to trick mri_normalize by adjusting NU.mgz intensity by -30 (140-30 = 110). This did not give me the wished-for effect. - Is it possible to bypass preprocessing steps of mri_normalize before collapsing? - In general it would help if there is some elaboration on the options: -no1d, -nosnr, -gentle, -f vs -fonly, -prune, -g, -monkey - is [-monkey] just shorthand for [-no1d -n 1]? Thanks, Tom System: Mac OS X 10.10.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 > mri_normalize --version stable5

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Anonymizing FreeSurfer files
by Keefe, Sarah 03 Aug '16

03 Aug '16

Hi, I'm involved in a project that requires anonymizing FreeSurfer data to remove all patient information. I've found that the subject folder number is sometimes included in text files and logs in a FreeSurfer folder. Is there any patient information stored in any of the non-text files? Is there a way I could check other files for any stored patient information? Thanks, Sarah ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying 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 mail.

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 03 Aug '16

03 Aug '16

2 1

mapping error
by Caroline Beelen 03 Aug '16

03 Aug '16

Dear FS, An aparc.annot ctab file was created but I got the following error: Colortable:aparc.annot.ctab Annotname: myaparc Nhitsfile nhits.mgh Nlabels 6 Labeltresh 0 0.00000 Loading freesurfer/fsaverage/surf/lh.orig 1 -1 not found 2 -1 not found 3 -1 not found Etc... Mapping unhit to unknown Found 132101 unhit vertices Writing annot to freesurfer/fsaverage/lh.myaparc.annot I guess my ctab file is incorrect? I included an example of a label with it. Thanks again for your help. Caroline

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Re: [Freesurfer] DTI of frontostriatal tracts
by Anthony Dick 02 Aug '16

02 Aug '16

Hello, See the paper at this link: http://www.ncbi.nlm.nih.gov/pubmed/25086832 Anthony > On 8/2/16 12:26 PM, Ritobrato Datta wrote: >> Hello All, >> >> We are studying adolescents with HIV and are interested in >> frontostriatal tracts (anything from frontal cortex to >> caudate/putamen/nucleus accumbens) and tracts connected to the amygdala. >> >> Is anyone aware of DTI based atlases where these tracts are defined >> in MNI or some other standard space ? >> >> Any suggestions will be very helpful. >> >> Best >> >> Ri >> _______________________________________________ >> 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. >> > -- Anthony Steven Dick, Ph.D. Associate Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://myweb.fiu.edu/adick Join the Society for the Study of Human Development: http://www.sshdonline.org

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Re: [Freesurfer] MNI coordinates of all the vertices of fsaverage
by Douglas N Greve 02 Aug '16

02 Aug '16

By default they are in talairach. But you can get mni305 by adding --nofixmni to the surfcluster command line On 08/02/2016 03:36 PM, Sabin Khadka wrote: > Hi Doug, Thanks. Are these coordinates in talairach or MNI space? From > previous post you mentioned these are in mni305 space but if I look at > the log file it say TalX, TalY, TalZ. I am a little confused. > > And how can I convert these coordinates to MNI152 space? > > thanks for your help. > > Cheers, > Sabin Khadka > > On Mon, Aug 1, 2016 at 9:24 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > ps. you can always just load the xyz in the label into matlab and > compute the centroid > > > On 8/1/16 10:23 AM, Sabin Khadka wrote: >> Anyone? >> >> Cheers, >> Sabin Khadka >> >> On Fri, Jul 29, 2016 at 2:47 PM, Sabin Khadka >> <mr.sabinkhadka(a)gmail.com <mailto:mr.sabinkhadka@gmail.com>> wrote: >> >> Hi Doug, I tried to pick up from the thread below to get MNI >> coordinates of each destrieux parcellation region. >> >> >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-July/032037.html >> >> I created label files from >> mri_annotation2label --subject fsaverage --hemi lh(/rh) >> --annotation aparc.a2009s --outdir label_destrieux # which >> works fine >> >> And I tried to get the coordinates of each labels using >> >> mri_surfcluster --in ~/subjects/fsaverage/surf/lh.thickness >> --clabel <label file> --sum <output file> --centroid --thmin >> 0 --hemi lh --subject fsaverage >> >> But, all left labels would produce the same coordinates and >> so does right labels. (I've attached few example files here >> with). Also, it says TalX, TalY, TalZ are these coordinates >> in MNI or Talairach? >> >> Thanks for help. >> >> > > 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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Save Overlay via Command Line
by Jordan Chad 02 Aug '16

02 Aug '16

Hello, I am trying to perform between-subject statistics on cortical DTI data in certain ROIs. I can do this by overlaying the DTI data on the surfaces on tksurfer, load and mask the label with the ROI, and then go to File -> Save Overlay. After doing this for all subjects I can perform statistics on the output files. However, it is not practical to do this for all >200 subjects for each ROI. Is there a way to go about this process on the command line? Thank You, Jordan Chad

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 02 Aug '16

02 Aug '16

2 1

DTI of frontostriatal tracts
by Ritobrato Datta 02 Aug '16

02 Aug '16

Hello All, We are studying adolescents with HIV and are interested in frontostriatal tracts (anything from frontal cortex to caudate/putamen/nucleus accumbens) and tracts connected to the amygdala. Is anyone aware of DTI based atlases where these tracts are defined in MNI or some other standard space ? Any suggestions will be very helpful. Best Ri

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