Re: [Freesurfer] Mean thickness estimation

Are you talking about outliers across subject? Or across region? I would just take the FS-supplied value instead of averaging the regions. On 11/19/2020 2:14 AM, Stephanie K wrote: External Email - Use Caution Hi Bruce, Thanks for the prompt reply. It is my understanding that l_thickne

Re: [Freesurfer] Mean thickness estimation {Disarmed}

nmovie_qt) Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Friday, November 20, 2020 6:25 AM To: Freesurfer support list Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed} External Email - Use Caution Hi Bruce, No, I don’t think that

Re: [Freesurfer] Mean thickness estimation {Disarmed}

t; Cheers > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Stephanie K > *Sent:* Thursday, November 19, 2020 4:19 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] Mean thicknes

Re: [Freesurfer] Mean thickness estimation {Disarmed}

, 2020 4:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] Mean thickness estimation {Disarmed} External Email - Use Caution Hi Bruce, Is it also necessary to remove outliers (eg. 3 SD from the mean) for Freesurfer structural measures of MRI images that have been visually

Re: [Freesurfer] Mean thickness estimation {Disarmed}

mr.mgh.harvard.edu> *On Behalf Of *Stephanie K > *Sent:* Thursday, November 19, 2020 2:14 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Mean thickness estimation > > > > *External Email - Use Caution* > > Hi Bruce, > > &

Re: [Freesurfer] Mean thickness estimation

Hi Stephanie I think that is always a good idea, unless for some reason it isn’t possible Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Thursday, November 19, 2020 2:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mean thickness

Re: [Freesurfer] Mean thickness estimation

External Email - Use Caution Hi Bruce, Thanks for the prompt reply. It is my understanding that l_thickness, r_thickness and estimated intracranial volume are accurately measured. Would I still need to identify and remove outliers if visual inspection of the images has not been do

Re: [Freesurfer] Mean thickness estimation

Hi Stephanie By using the average/std within region, then averaging those, you are weighting small regions more. I would just use the average/std across cortex. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Wednesday, November 18, 2020 12:24 PM To: f

Re: [Freesurfer] Mean thickness values from sig.mgh

you will have to create a binary mask from the sig map by thresholding at a given level, eg, mri_binarize --i sig.mgh --min 2 --o sig.bin2.mgh Then run mri_segstats --i y.mgh --seg sig.bin2.mgh --id 1 --avgwf y.bin2.dat where y.mgh is the --y input to mri_glmfit --id 1 means to take the forground

Re: [Freesurfer] mean thickness

@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Namens Bruce Fischl > Verzonden: zondag 6 maart 2016 16:14 > Aan: Freesurfer support list > Onderwerp: Re: [Freesurfer] mean thickness > > Hi Caroline > > how did you generate the Gnumeric file? And what

Re: [Freesurfer] mean thickness

Hi Caroline how did you generate the Gnumeric file? And what operating system/hardware are you using? Also, please send us the recon-all.log for one of the subjects that you see this happening cheers Bruce On Fri, 4 Mar 2016, Caroline Beelen wrote: Dear Freesurfer team,   Forgive me

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Thanks Doug, I used the first link and works perfectly now! Best regards, Amirhossein Manzouri On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve wrote: > > I just ran it, and it works fine. It may be that I need to give you more > libraries. > > Start with this one > ftp://surfer.nmr.mgh.harv

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Dear Doug, Kindly find attached a sample of my lh.aparc.stats file! Best regards, Amirhossein Manzouri On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve wrote: > Can you send me your lh.aparc.stats file? > doug > > > On 05/14/2014 01:41 PM, amirhossein manzouri wrote: > >> >> Yes! >> >> >> On

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Can you send me your lh.aparc.stats file? doug On 05/14/2014 01:41 PM, amirhossein manzouri wrote: > > Yes! > > On May 14, 2014 7:16 PM, "Douglas N Greve" > wrote: > > > Is the mean thickness in the ?h.aparc.stats file? Something like > > # Measure Cortex

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Yes! On May 14, 2014 7:16 PM, "Douglas N Greve" wrote: > > Is the mean thickness in the ?h.aparc.stats file? Something like > > # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm > > > On 05/13/2014 05:18 PM, amirhossein manzouri wrote: > >> Hi, >> The same result! the last is insula !

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Is the mean thickness in the ?h.aparc.stats file? Something like # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm On 05/13/2014 05:18 PM, amirhossein manzouri wrote: > Hi, > The same result! the last is insula ! > > > Best regards, > Amirhossein Manzouri > > > > > On Mon, May 12, 20

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Hi, The same result! the last is insula ! Best regards, Amirhossein Manzouri On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve wrote: > Try this version > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ > greve/aparcstats2table > > > On 05/12/2014 03:41 AM, amirhossein manzouri wrot

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table On 05/12/2014 03:41 AM, amirhossein manzouri wrote: > Hi again, > I think I missed my question, How can I get the Mean Thickness of each > hemisphere for several subjects using the aparcstats2table com

Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats

Hi again, I think I missed my question, How can I get the Mean Thickness of each hemisphere for several subjects using the aparcstats2table command? On Fri, May 9, 2014 at 4:28 PM, amirhossein manzouri wrote: > Dear Doug, > I have read this post( > https://www.mail-archive.com/freesurfer@nmr.mgh

Re: [Freesurfer] mean thickness over hemisphere in stats file

vard.edu Subject: Re: [Freesurfer] mean thickness over hemisphere in stats file Hi Ines I think mris_anatomical_thickness is your best bet. You probably want to specify the ?h.cortex.label file with the -l flag so that it ignores non-cortical regions cheers Bruce On Fri, 9 Aug 2013, Mürner-

Re: [Freesurfer] mean thickness over hemisphere in stats file

you can also use mri_segstats with the --slabel option (spec ?h.cortex.label) and the thickness as the input On 08/09/2013 09:36 AM, Bruce Fischl wrote: > Hi Ines > > I think mris_anatomical_thickness is your best bet. You probably want > to specify the ?h.cortex.label file with the -l flag so

Re: [Freesurfer] mean thickness over hemisphere in stats file

Hi Ines I think mris_anatomical_thickness is your best bet. You probably want to specify the ?h.cortex.label file with the -l flag so that it ignores non-cortical regions cheers Bruce On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote: Dear experts, please excuse my question, I'm a beginner

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

is, MO 63110 Email: mha...@wustl.edu > > From: "Laura M. Tully" > Date: Saturday, March 9, 2013 5:58 PM > To: "Anderson M. Winkler" > Cc: free > Subject: Re: [Freesurfer] mean thickness covariate, mean area covariate, > & mri_anatomical_stats for multip

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

ental Disorders Washington University 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: "Laura M. Tully" Date: Saturday, March 9, 2013 5:58 PM To: "Anderson M. Winkler" Cc: free

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

Hi Laura, I think yes, sounds right. Maybe run both ways and see if the results agree or differ. All the best, Anderson 2013/3/9 Laura M. Tully > Hi Anderson, > > Thanks, that reference is particularly helpful. > > Re: the usage of the white versus pial area question - I believe that the > defa

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

Hi Anderson, Thanks, that reference is particularly helpful. Re: the usage of the white versus pial area question - I believe that the default area calculation in freesurfer is the white surface area, so unless one specifies the pial in calculations, the standard surface area output for surface a

Re: [Freesurfer] mean thickness covariate, mean area covariate, & mri_anatomical_stats for multiple subjects

Hi Laura, >1. Is there a paper that I could cite that recommends using mean >cortical thickness rather than ICV? > > If it helps, we used cortical thickness and area as covariate for the respective analysis of regional thickness and area. Brain volume, which is more closely related to ICV

Re: [Freesurfer] mean thickness of whole cortex

you mean of both hemispheres together? We don't explicitly compute it, but the mean of the two hemisphere means should be pretty close, since they are similar in size On Mon, 9 Jul 2007, Wang, Xin wrote: Hello, Group Could anybody please tell me how to get the mean thickness of whole cortex