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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

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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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FreeSurfer Course Registration now open!
by Allison Stevens 02 Aug '16

02 Aug '16

The Freesurfer group is offering a four-day Freesurfer Tutorial and Workshop September 26th to 29th, 2016 at the Martinos Center in Charlestown, MA. You can register for the course on our course website: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an email confirmation that you successfully secured a seat in the course. Allison Stevens > Lab Manager > FreeSurfer Development Team > Laboratory for Computational Neuroimaging > Massachusetts General Hospital > Athinoula A. Martinos Center for Biomedical Imaging > Bldg. 149, 13th Street, CNY 2301 > Charlestown, MA 02129

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Re: [Freesurfer] brain mask and T1 are not the same size
by Isabelle Deschamps 01 Aug '16

01 Aug '16

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Where are time series from adjusted (post selxavg3) ROIs
by ERIK JAHNER 01 Aug '16

01 Aug '16

Dear Freesurfer experts I have been going through the documentation trying to figure out how to extract the time series for an ROI (Posteriorcingulate) after removing the regressors that I put in my mkanalysis-sess. I have run the selxavg3. 1. Is this time course what is in the meanfunc.nii.gz? 2. If it is, how do I pull this out in matrix format (.mat) out of the where I basically get one mean adjusted value for the ROI at each timepoint? (e.g. For the Posteriorcingulate, I want 210 values representing the mean activation after removing the effect of my covariates wm and css for each of the 210 timepoints). 3. Is this information in the X.mat file? If so, what is its location? Thanks Erik Jahner

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Running Retinotopy in FSFAST, Design Matrix has Empty Regressors
by Taylor, Johnmark 01 Aug '16

01 Aug '16

Hello, I am trying to run a retinotopy analysis in fsfast, using only polar angle. However, when I try to run it, I am getting the error "Input to SVD must not contain NaN or Inf." I have traced this error and it looks like the design matrix X has 12 regressors (the first 12) that consist solely of zeros. I am using the following commands: mkanalysis-sess -analysis retinotopy -fsd bold -runlistfile runlist.txt -native -funcstem fmc -nuisreg mcextreg 3 -retinotopy 36.4 -per-session -paradigm retino.par -inorm -spmhrf 0 -TR .650 -polyfit 2 -nskip 19 selxavg3-sess -analysis retinotopy -sf sublist.txt -df sessdir Any idea what the first 12 regressors in the design matrix might correspond to in retinotopy analyses and why they'd be empty? I have looked at the documentation and there doesn't seem to be a clear labeling of the retinotopy design matrix anywhere, although perhaps I'm missing something. Thank you very much, JohnMark

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Fwd: question about volume of mask
by Dorsa Haji Ghaffari 01 Aug '16

01 Aug '16

Hi Bruce, I was able to reslice the thalamus mask correctly, but when I measure the volume of the resliced thalamus, is not the same as the original thalamus. I was wondering why that is happening and which volume is more accurate. I appreciate any suggestions. I have attached both masks. Also can you tell me how to measure the volume of the resliced thalamus in Freesurfer? Thank you Dorsa

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