Freesurfer

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30086 discussions

release v5.0.0
by Jose Luis Cantero Lorente 24 May '10

24 May '10

Hi there, does anybody know when the Freesurfer release v5.0.0 will be downloadable? Best, Jose --- Jose L. Cantero, Ph.D. Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla - Spain - Phone: +34 954 977433 Fax: +34 954 349151 Email: jlcanlor(a)upo.es http://www.upo.es/neuroaging/en/

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up-sampling by mri_convert
by EDSB EDSB 24 May '10

24 May '10

Hi all, I have a question on the mri_convert command. I should up-sample my dataset (a list of COR files contained in the folder T1) that has a matrix of 256 x 256 x 256 and a voxel size of 1 mm. I'm using the command mri_convert --in_orientation LIA -ois 0.1 -ojs 0.1 -oks 0.1 T1 T1_resampled.nii In effect I obtained the resampled image but the final dimension is still 256 x 256 x 256, so my image result cropped. how can I obtain the entire field of view? Thanks in advance for your help Paolo Landini _________________________________________________________________ Spazio gratis di 25 Gigabyte per archiviare ciò che vuoi http://www.windowslive.it/skyDrive.aspx

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FW: labels don't match with tkmedit and tksurfer
by Prapti Gautam 23 May '10

23 May '10

Dear all, Reposting the following question again, Thanks, To: freesurfer(a)nmr.mgh.harvard.edu Subject: labels don't match with tkmedit and tksurfer Dear FreeSurfers, I am having some problems creating a label in tksurfer and subsequently converting it into a volume file. I have created a custom label in a test subject using tksurfer which loads correctly onto the surface when viewed with tksurfer. However, when I load the label into tkmedit in the same subject - it seems to be labelling regions that are not on the surface of the brain, but lie somewhat haphazardly in the cortex near the surface. Do you know why this is happening? I further need to convert the label into a volume file and have used mri_label2vol to do this. Mri_label2vol -- label subject/label/pfc.label -temp subject/mri/brainmask.mgz --o subject/label/pfc.mgz However, perhaps since I can see that the label does not sit correctly on the surface in tkmedit, the volume file is also not on the cortical surface, but runs below it. Can anyone point me in the right direction as to where I might be going wrong? Thanks, Prapti

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Re: [Freesurfer] Roi label mapping
by Lena Palaniyappan 23 May '10

23 May '10

Dear Martin I believe QDEC design currently allows only DODS for my model nevertheless, will this produce gross differences as I am observing? Thanks for your help Lena On 23/05/2010 18:42, "Martin Kavec" <martin.kavec(a)gmail.com> wrote: > Hi Lena, > > One can do a DODS (different offset different slope) and DOSS (different > offset same slope) GLM analysis in qdec. Did you take this into account in > your ROI analysis? > > Cheers, > > Martin > > On Sun, May 23, 2010 at 7:09 PM, Lena Palaniyappan > <Lena.Palaniyappan(a)nottingham.ac.uk> wrote: >> While doing an age corrected qdec comparison between two groups, the analysis >> resulting from ¹Does the average thickness differ between two gps¹ showed >> some potential areas of interest. I then created labels from these areas and >> mapped them back to all subjects. But when I extracted thickness values and >> looked at the means, I could not see the same direction of effect why could >> this be? Is this a problem with smoothing (I used FWHM 20 for looking at >> whole brain comparisons) >> >> Cheers >> Lena >> >> _______________________________________________________ >> Lena Palaniyappan >> PhD student & Honorary StR | Division of Psychiatry ( University of >> Nottingham) >> South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH >> >> >> >> This message has been checked for viruses but the contents of an attachment >> may still contain software viruses which could damage your computer system: >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> >> _______________________________________________ >> 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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Roi label mapping
by Lena Palaniyappan 23 May '10

23 May '10

While doing an age corrected qdec comparison between two groups, the analysis resulting from ¹Does the average thickness differ between two gps¹ showed some potential areas of interest. I then created labels from these areas and mapped them back to all subjects. But when I extracted thickness values and looked at the means, I could not see the same direction of effect why could this be? Is this a problem with smoothing (I used FWHM 20 for looking at whole brain comparisons) Cheers Lena _______________________________________________________ Lena Palaniyappan PhD student & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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White matter volume corresponding to a surface ROI
by Lena Palaniyappan 22 May '10

22 May '10

Dear all, I have 4 ROIs created from a whole brain group comparison. I want to examine the differences in white matter volume immediately beneath these rois. Wmparc contains whitematter segmented in accordance with the inbuilt annotations is it possible to extract wmparc info for GM rois? Cheers Lena _______________________________________________________ Lena Palaniyappan PhD Student & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Reporting coordinates from Group analysis
by Rajagopalan, Venkateswaran 21 May '10

21 May '10

Dear All, I checked the archives but couldn't get a complete answer. I performed group analysis of cortical thickness using mri_glmfit. I am wondering how to report the coordinates of regions where cortical thickness is significantly different, i used FDR for multiple comparisons in tksurfer. So how to get these coordinates after FDR where is this file stored. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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Re: [Freesurfer] tksurfer tcl scripting: Environment variables for hemisphere and subject
by Andreas Schindler 21 May '10

21 May '10

Thanks! :-) btw: Is there a tcl interface for View -> Configure -> Phase Encoded Data Display: Angle Cycles ? bw Andreas Bruce Fischl wrote: > Hi Andreas, > > the tcl variables $subject and $hemi should be set properly by tksurfer, so > you can use them generically. > > cheers > Bruce > > On Fri, 21 May 2010, Andreas Schindler wrote: > > >> Hello >> >> I am currently writing a tcl script for tksurfer which I am using for >> several subjects. >> That's why I am wondering if it is possible to avoid adapting this tcl >> script for every subject by >> reading out tksurfer's variables for hemisphere and subject as they are >> committed by the shell, anyway. >> >> Many thanks >> >> bw >> >> Andreas >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > _______________________________________________ > 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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tksurfer tcl scripting: Environment variables for hemisphere and subject
by Andreas Schindler 21 May '10

21 May '10

Hello I am currently writing a tcl script for tksurfer which I am using for several subjects. That's why I am wondering if it is possible to avoid adapting this tcl script for every subject by reading out tksurfer's variables for hemisphere and subject as they are committed by the shell, anyway. Many thanks bw Andreas

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transform ribbon to FSL-diffusion space
by Theodor R?ber 20 May '10

20 May '10

Dear Freesurfers, I am trying to transform a Freesurfer-generated white matter mask (ribbon) to FSL diffusion space in order to use it as a stop-mask in fibertracking. I have tried to coregister and reslice it to the normalized dti_FA with SPM and I also tried to transform it with FSL-FLIRT and FSL-FNIRT as described on http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html. Unfortunately, neither approach yielded satisfying results. What steps would you recommend to turn the Freesurfer output into a FSL-FDT compatible white matter mask? Thank you very much in advance. Your help will be greatly appreciated. Best, Theodor

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