[Freesurfer] Visualising surfaces at different fractional depths

e and this halfway surface overlayed on the volume. Any ideas? Thank you Kirstie -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3

Re: [Freesurfer] Visualising surfaces at different fractional depths

o sample is probably a better method than using profrac, although I expect > the differences will be small unless you have very highres data. > > cheers > Bruce > > > > On Mon, 20 Apr 2015, Kirstie > Whitaker wrote: > > > Hi experts, > > > > I've u

Re: [Freesurfer] Visualising surfaces at different fractional depths

this! Best wishes Kx On 24 April 2015 at 17:38, Bruce Fischl wrote: > Hi Kirstie > > I think you get to decide how you want the sampling done in mri_vol2surf. > > cheers > Bruce > > On Fri, 24 Apr 2015, Kirstie Whitaker wrote: > > Thank you Bruce - that's excel

Re: [Freesurfer] Visualising surfaces at different fractional depths

rstie > > you can pick the interpolation method with > > --interp > > where string is one of: > > nearest > trilinear > sinc > cubic > > > > cheers > Bruce > On Fri, 24 Apr 2015, Kirstie Whitaker wrote: > > I'm sorry, I did wo

[Freesurfer] Quality control with different pipelines

e conducted? Or does this "shortcut" not do what I think it does? Does anyone have any experience moving from one version of freesurfer to another without having to start from square one with the edits? Thank you again for the fantastic tools! Kx -- Kirstie Whitaker, PhD Research Associate

Re: [Freesurfer] Quality control with different pipelines

chool of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: on behalf of Kirstie > Whitaker > Reply-To: Freesurfer support list > Date: Wednesday, June 22, 2016 at 1:28 AM &

Re: [Freesurfer] Quality control with different pipelines

rsity School of Medicine > Department of Psychiatry, Box 8134 > 660 South Euclid Ave. Tel: 314-747-6173 > St. Louis, MO 63110 Email: mha...@wustl.edu > > From: on behalf of Kirstie > Whitaker > Reply-To: Freesurfer support list > Date: Wednesday, June 22, 2016 at 8:55

[Freesurfer] Destrieux atlas in FSL

? I'm afraid I've not been successful in my search of the mailing list archives. Thank you for your help. Kirstie -- Kirstie Whitaker, PhD Research Associate tel: +44 7583 535 307 Department of Psychiatry University of Cambridge Herchel Smith Building Robinson Way Ca

[Freesurfer] Postdoctoral Position within Cambridge Centre for Ageing and Neuroscience

ity. The University has a responsibility to ensure that all employees are eligible to live and work in the UK. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Douglas House 18b Trumpington Road Cambridge, CB2 8AH *Phone:

Re: [Freesurfer] group mean greater than X

ent 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 a

[Freesurfer] Postdoc job: Neuroimaging of mood disorders in adolescence at University of Cambridge

espondence about this vacancy. Thank you Kirstie Whitaker -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Elijah, Is there any chance you could attach a scatter plot? My suspicious mind thinks either a) there are outliers who are doing odd things, or b) the FA values are very different to those in other regions and therefore the correlation with MD wouldn't be expected to be the same. Kx Sent

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

I think eroding the region makes sense in general - you just have to be careful to exclude subjects who end up with no data (as you discovered!) You could also look into why these three subjects had such small wm regions under entorhinal cortex. My (still) suspicious mind wonders if there is a b

[Freesurfer] Visualising regional values on the surface

d to. It seems like I have to do something with the ?h.aparc.annot files and a colour lookup table but I'm not sure exactly what. Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Departme

Re: [Freesurfer] Visualising regional values on the surface

mns. >> Then simply load the color table in Freeview and use it to visualize >> the annotation. >> >> There are of course other ways, but this is probably the quickest. >> >> hth >> d >> >> >> On Tue, Mar 29, 2016 at 11:03 AM, Kirstie Whitaker &

Re: [Freesurfer] Visualising regional values on the surface

l.freesurfer.html#write-annot > > Best, > Michael > > On Tue, Mar 29, 2016 at 8:48 AM, Kirstie Whitaker wrote: > >> Thank you Michael! I <3 Pysurfer. >> >> (and freesurfer of course!) >> >> The *real* goal is to integrate the code that I've wr

[Freesurfer] Accuracy of D-K atlas for different age ranges

imply asking you to recommend good references rather than searching for them in PubMed! Thank you! Kirstie x -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing S

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

rson 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 >

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

Hi Foucault, In the snippet you added you don’t define the labels variable (which you subsequently loop over in for label in ${labels}). There are two possible mistakes that are easy to fix. One may be that you forgot to read in the labels! And the other is that to get all the values in an arr

Re: [Freesurfer] Extracting the centroids from Desikan-Killiany atlas

cts/fsaverage/surf/rh.white >> Done reading source surface >> Computing metric properties >> Loading source values >> number of voxels in search space = 5963 >> Done loading source values (nvtxs = 163842) >> overall max = 3.19752 at vertex 122846 >> overall

[Freesurfer] tracula update link not working

Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of

Re: [Freesurfer] tracula update link not working

Yep! Working now - thank you very much :) Kx > On 20 August 2014 12:23, Anastasia Yendiki > wrote: > > Hi Kirstie - This was a glitch related to yesterday's storage cluster > maintence. It's been fixed now, so please try again. > > a.y > > On Wed

[Freesurfer] Some notes on getting Tracula to work for newbies

in for the really excellent software. And please correct anything that I've written here if it's wrong! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir Wil

Re: [Freesurfer] Some notes on getting Tracula to work for newbies

7;t been able to ascertain is whether I have an old version of mri_convert that should be able to concatenate the six listed volumes! (The next section of code seems to look like its trying to concatenate volumes so it might be expecting a 4D file? Or multiple lowb.nii.gz volumes?) I hope this all

Re: [Freesurfer] Some notes on getting Tracula to work for newbies

lowb.nii.gz volumes?) I haven't seen this problem crop up in any later processing but it may do?? I hope this all makes sense! Thank you again for all your hard work! Kx > On 20 August 2014 14:27, Anastasia Yendiki > wrote: > > Thanks a lot, Kirstie. Nice job on finding solutio

[Freesurfer] anatorig vs anat in dlabel

't line up nicely. They did line up with anatorig though. Is this what you'd expect? Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Stre

[Freesurfer] Appropriate levels of surface smoothing

but would a range of, say, 3 to 5mm sound good? Or more like 10 to 15mm? Currently I'm considering cortical thickness analyses, but I may extend into functional analyses in the future. If there are any references that you can recommend I'd appreciate that very much. Best wishes Kirs

[Freesurfer] mri_vol2surf --prodist measuring from pial surface

;s jumping out at me, is there an obvious option I'm missing?! Thank you! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3

Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

> doug > > > On 11/27/14 1:24 PM, Kirstie Whitaker wrote: > > Hi, > > I was wondering if it's possible to sample x mm from the pial surface > using mri_vol2surf (or another tool!). The point is that I'd like to be > agnostic about exactly where the grey/wh

Re: [Freesurfer] mri_vol2surf --prodist measuring from pial surface

pial \ --hemi lh \ --regheader Kx On 4 December 2014 at 20:41, Kirstie Whitaker wrote: > Thank you, Doug. > > Can I just check that projdist is the same as projabs but with a different > name? > > Just in case I'm using an o

[Freesurfer] Version 6.0.0 or 6.0.1?

any other differences? I'm having a lot of difficulty getting recon-all to run reliably with 6.0.0 (some subjects are fine, others not!) and I'm wondering if that's because I'm supposed to be using 6.0.1? Thank you for your help! Kirstie -- Kirstie Whitaker, PhD Research

Re: [Freesurfer] Version 6.0.0 or 6.0.1?

having with 6.0.0? > > > > Best, > > Andrew > > > > > > *From: * on behalf of Kirstie > Whitaker > *Reply-To: *FS Help > *Date: *Tuesday, December 11, 2018 at 4:28 AM > *To: *FS Help > *Subject: *[Freesurfer] Version 6.0.0 or 6.0.1? > >

[Freesurfer] Makefile for Tracula

x27;m not 100% sure on which other files have dependences on the reconstructions :) (The surfaces got pretty messed up in this update so I'd like to go back to basicswithout having to rerun things we KNOW aren't related to the surface reconstructions.) Thank you! Kirstie -- Kirstie Whi