Re: [Freesurfer] Sulcal depth maps and pli de passage

External Email - Use Caution I don't know. I don't think anyone has done a study on it. You'd have to label the pil de passages in a bunch of subjects and see if the pattern holds. On 7/4/2023 7:05 AM, Federica Santacroce wrote: External Email - Use Caution Hello

[Freesurfer] Sulcal depth maps and pli de passage

External Email - Use Caution Hello FreeSurfer Developers, I used the sulcal depth maps superimposed on inflated images (setting colour depth =< 0) to define the morphological sulcal pattern (continuous vs. interrupted). Is this method useful for detecting pli de passage that may

[Freesurfer] Sulcal depth and Gyrus height

External Email - Use Caution Hi, I want to obtain the gyral height and the sulcal depth for every region of the aparc atlas. I know that in the file lh.sulc the positive values are the depth of the sulcus and the negative one are the height of the gyrus. How can I obtain

Re: [Freesurfer] Sulcal depth units (Simon Vandekar)

Hi, I studied the FreeSurfer code for MRISinflateBrain and came across a discrepancy in how the sulcal depth is computed. This explains why the values are much smaller than expected. My question @Bruce is if this is intentional or (as the function names below indicate) possibly a bug in the

Re: [Freesurfer] Sulcal depth units (Simon Vandekar)

Hi Andreas I just took a look at the code and it seems you are correct! Thanks for catching this. I'll change the code base now and the fix will be in v6. Bruce On Fri, 22 Jan 2016, Andreas Schuh wrote: > Hi, > > I studied the FreeSurfer code for MRISinflateBrain and came across a >

Re: [Freesurfer] Sulcal depth units (Simon Vandekar)

Hi Bruce, The units are not standardized because the standard deviation across the surface does not equal 1. >From line 227 in mris_inflate.c it says that the sulc file is demeaned before >it is written out: MRISzeroMeanCurvature(mris) ; /* make sulc zero mean */ However I am still

Re: [Freesurfer] Sulcal depth units

Hi Simon I just took a look at the code and I believe that we make it 0 median (not mean) and unit standard deviation. The curvatures can get quite large in regions where the vertex spacing is small and the median is robust to this. cheers Bruce On Sat, 24 Oct 2015, Simon Vandekar wrote: >

Re: [Freesurfer] Sulcal depth units

Hi Bruce, I think that unnormalized sulcal depth would be useful. However, I am also curious what the units are in the standard output, because they appear to not be z-score standardized in each hemisphere. Thanks again, Simon >H I Simon >Do you need the unnormalized sulc? It would be pretty

Re: [Freesurfer] Sulcal depth units

Hi Bruce, I chose a random subject from the ADNI dataset and computed the mean and variance for the left and right hemispheres separately. It looks like the mean is close to 0, however the variance is not 1. Do you think it is possible that the surfaces are demeaned, but the units are still

Re: [Freesurfer] Sulcal depth units

H I Simon Do you need the unnormalized sulc? It would be pretty easy to put something in to generate it Bruce > On Oct 22, 2015, at 3:23 PM, Simon Vandekar wrote: > > Hi Bruce, > > I chose a random subject from the ADNI dataset and computed the mean and > variance

Re: [Freesurfer] Sulcal depth units

Hi Simon they are originally mm, but I believe we z-score normalize them so that the sulc file is 0 mean and unit variance. cheers Bruce On Wed, 21 Oct 2015, Simon Vandekar wrote: > Dear Freesurfer experts, > > I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, >

[Freesurfer] Sulcal depth units

Dear Freesurfer experts, I am reading the manuscript "Cortical Surface-Based Analysis II: Inflation, Flattening, and a Surface-Based Coordinate System" by Fischl, Sereno, and Dale (1999) where the estimation of sulcal depth is described on page 199, however from the description I am still

[Freesurfer] sulcal depth

Hi Freesurfer experts, I did thickness group analysis in pts and healthy subject groups in qdec (age corrected( and got thicker cortex in left insula and thinner precentral gyrus bilaterally that survived FDR 0.01 Surface area and curvature analysis found no difference. However, sulcal depth

[Freesurfer] Sulcal depth variations

Hello everyone, I'm working on a group analysis of cortical thickness, surface area, curvature and sulcal depth with FreeSurfer 5.3. However I'm in trouble concerning the interpretation or the meaning of my results, especially concerning curvature and sulcal depth. I understood that curvature

Re: [Freesurfer] Sulcal depth variations

Hi Damien, yes, that's correct. The sulc is the integrated dot product between the movement vector and the surface normal, so things that move consistently outwards (like sulci) will be positive, and gyri will be negative. cheers Bruce On Sat, 21 Sep 2013, Damien MARIE wrote: Hello

Re: [Freesurfer] sulcal depth/cortical folding

sorry, it fell through the cracks. Please feel free to resend if I don't get back in a reasonable amount of time... Try this command instead mri_segstats --annot subjectname lh aparc --sum lh.sulc.sum --i surf/lh.sulc the output will be lh.sulc.sum doug On 08/16/2012 07:02 PM, Hugh Pemberton

Re: [Freesurfer] sulcal depth/cortical folding

Hi Hugh, you can run mris_anatomical_stats passing it the sulc file as input. This will give you averages within aparc. I'm not sure what you mean by measuring cortical folding. What measure would you accept? There's the sulcal depth and then there's curvature (?h.curv). There are two types of

Re: [Freesurfer] sulcal depth/cortical folding

HI Doug, I tried the mris_anatomical_stats and may well be doing it wrong but got this as the result: hughp@naoshi-WS:~/freesurfer/subjects$ mris_anatomical_stats -a ABM/surf/lh.sulc -b ABM lh computing statistics for each annotation in ABM/surf/lh.sulc. reading volume

[Freesurfer] sulcal depth

Is there a way to extract sulcal depth statistics for a group of subjects using a function like aparcstats2table for mean curve, thickness, volume, etc.? Thanks, Heather ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] Sulcal depth and width

Hello,   How can I calculate the sulcal depth and the sulcal width for each hemisphere and for specific ROIs?    Thanks and regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados

Re: [Freesurfer] Sulcal depth and width

This paper may help you:http://www.jneurosci.org/cgi/reprint/25/34/7840.pdf http://www.jneurosci.org/cgi/reprint/25/34/7840.pdfAnd also this threads: http://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2005-December/002092.html

[Freesurfer] Sulcal depth measures

Is there any way of measuring sulcal depth with FreeSurfer? Or is sulcal depth simply measured by the positive values in ?h.sulc - i.e. negative values are 'gyral heights' and positive values are 'sulcal depths'? If so is it possible to calculate these values for certain parcellated regions such

Re: [Freesurfer] Sulcal depth measures

Hi Christine, yes that is essentially what is measure in ?h.sulc - the integrated signed dot product of the movement vectors during inflation with the surface normal (so outward movement in sulci is positive). Certainly you can specify sulc in mris_anatomical_stats, although I can't remember

RE: [Freesurfer] Sulcal depth

: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:33 AM To: Fornito, Alexander Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you might be able to use mri_segstats. Give it the thickness file as --in, and use the sulc as the mask and use

[Freesurfer] Sulcal depth

Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the depth of a sulcus within an ROI, and if so, how you would extract the relevant measures, i.e.., would it be obtainable through mris_anatomical_stats? Thanks, Alex

Re: [Freesurfer] Sulcal depth

not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering if it is possible to use this to get the

RE: [Freesurfer] Sulcal depth

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm

RE: [Freesurfer] Sulcal depth

, 2005 5:37 PM To: Bagnato, Francesca (NIH/NINDS) [F] Cc: Fornito, Alexander; freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth you mean in a parcellation unit? It's whatever the parcellation unit is defined to be. On Thu, 22 Dec 2005, Bagnato, Francesca (NIH/NINDS) [F] wrote

RE: [Freesurfer] Sulcal depth

Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 9:30 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm

RE: [Freesurfer] Sulcal depth

Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth. I'm wandering

RE: [Freesurfer] Sulcal depth

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Sulcal depth not all that easily, although I guess we could write out something from mris_inflate that has the units of mm. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Hi all, From my understanding, ?h.sulc can be used to measure sulcal depth

RE: [Freesurfer] Sulcal depth

of Melbourne [EMAIL PROTECTED] -Original Message- From: Bruce Fischl [mailto:[EMAIL PROTECTED] Sent: Fri 23/12/2005 10:36 AM To: Fornito, Alexander Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] Sulcal depth sure, just sum them separately. Would be easy to do in matlab (we did

RE: [Freesurfer] Sulcal depth

Subject: RE: [Freesurfer] Sulcal depth I think they are volume RAS coords, with 0,0,0 at the center of the volume. I think we distribute a read_label.m or load_label.m that can read it into matlab. On Fri, 23 Dec 2005, Fornito, Alexander wrote: Famous last words, but seems simple enough