Re: [Freesurfer] Measuring cortical thickness

Hi Vasudev no, there is no alternative. Computing resources are cheap these days. Most cluster would let you run all your subjects in a single night. cheers Bruce On Thu, 14 Jul 2016, Dev vasu wrote:   Dear Sir / madam, I have 50 subjects (25 healthy controls and 25 patients with BLVP)

[Freesurfer] Measuring cortical thickness

Dear Sir / madam, I have 50 subjects (25 healthy controls and 25 patients with BLVP) , I would like to know how could i generate cortical thickness maps for multi subject group analysis. The initial pre-processing with recon-all takes several hours for single subject, is there any alternate way

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, Thanks again for your help so far. I had a few follow up questions: 1) As far as mapping the average thickness to fsaverage coords, when I was constructing the average thickness map I used mris_preproc with --target fsaverage (and then mri_concat), so it's already in fsaverage

Re: [Freesurfer] Measuring cortical thickness at a specific location

I see. Then measure the thickness normally, then see how it changes in those directions. You could average the thickness along each A/P coordinate - that wouldn't be a problem. You just don't want to measure it that way cheers Bruce On Mon, 12 May 2014, pfot...@nmr.mgh.harvard.edu wrote:

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, Just to clarify, when you say average the thickness along each A/P coordinate do you mean by looking up at the average cortical thickness of each parcellation and then calculating their average from P-A, or is there another way to find the average thickness of each slice and then see

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate cheers Bruce On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu wrote: Hi Bruce, Just to

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, I see, that's really helpful, thank you! Best, Panos Hi Panos I would make an average thickness map in fsaverage space, then in matlab divvy up the a-p direction into bins (say 100 of them) and compute the average in each bin based on the a/p coordinate cheers Bruce On Tue,

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, Sorry, I had a last follow up question. I just realized that the resulting bins will be in the fsaverage space, and hence I wouldn't be able to use mris_anatomical_stats to calculate the average thickness of the bins, since the fsaverage subject does not have a wm.mgz file. Did you have

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos no, mris_anatomical_stats won't do it. I would map the average thickness to fsaverage coords, then load that into matlab and go from there using the [xyz] coords of fsaverage for the binning, which is pretty much MNI305 cheers Bruce On Tue, 13 May 2014, pfot...@nmr.mgh.harvard.edu

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, I was having issues with the part after that, that is how to calculate the average thickness of those bins, after I create them. Thanks again Best, Panos Hi Panos no, mris_anatomical_stats won't do it. I would map the average thickness to fsaverage coords, then load that into

[Freesurfer] Measuring cortical thickness at a specific location

Hi FS experts, I was wondering whether it would be possible to measure the average cortical thickness at a specific slice (either axial, coronal, or sagittal). I read in Bruce's paper: Measuring the thickness of the human cerebral cortex from magnetic resonance images that Measuring the thickness

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Panos it would certainly be possible to make that measurement, but it wouldn't tell you anything biologically interesting. Why would you want to do such a thing? It will reflect the (arbitrary) image slice orientation and not the brain. cheers Bruce On Mon, 12 May 2014,

Re: [Freesurfer] Measuring cortical thickness at a specific location

Hi Bruce, Thank you for your reply. I was interested in looking how the thickness changes from the posterior to the anterior side of the brain and vice versa (the thickness gradient). Thank you again for your time! Panos Hi Panos it would certainly be possible to make that measurement, but

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

I usually can run one instance of FreeSurfer with 1GB if I use the -no-gut flag I have a benchmark of 4 recon-all running in a 4 Core AMD with 4GB RAM that took only 10% more time than one recon-all alone. 2011/7/6 John Jan Drozd john.dr...@gmail.com Hi Bruce, Thanks for pointing this out to

[Freesurfer] measuring cortical thickness using FreeSurfer

Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a reference web page listing what steps I need to type to process a series of MRI dicom slices and use FreeSurfer to measure cortical thickness for

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferBeginnersGuide On Tue, Jul 5, 2011 at 13:14, John Drozd john.dr...@gmail.com wrote: Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using version: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0. Can anyone point me to a

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

recon-all \ -i one slice in the anatomical dicom series \ -s subject id that you make up \ -sd directory to put the subject folder in \ -all cheers Bruce On Tue, 5 Jul 2011, John Drozd wrote: Hi, I am running freesurfer on 64 bit Fedora 10 linux. I am using

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce and Pedro, Thank you both for sending me your suggestions. Just to let you know, because my .dcm (dicom) files had a space and two dots in the filenames: (e.g. 2008_12_08.ek -0035-0001-1.dcm ) (and using quotes around the file name or \ within the filename without the quotes did not

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

sorry, but the majority of the time is required. We're working to speed things up, but it is complicated software with multiple nonlinear warps, segmentation procedures, etc Bruce On Tue, 5 Jul 2011, John Drozd wrote: Hi Bruce and Pedro, Thank you both for sending me your

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce, Okay, thank you. I understand and can see that to do an accurate job, the pipeline must be complicated. I have eight processors on my linux desktop computer. Maybe some parts of recon-all are multi-threaded which could speed things up for me :-) Thank you, John 2011/7/5 Bruce Fischl

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Sorry, that won't help a single subject much, although there are options to run the hemis in parallel. You can run multiple subjects at the same time, which is what we usually do. Or you can use cuss On Jul 5, 2011, at 5:11 PM, John Drozd john.dr...@gmail.com wrote: Hi Bruce, Okay, thank

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce, Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. Take care, John 2011/7/5 Bruce Fischl fis...@nmr.mgh.harvard.edu Sorry, that won't help a single subject much, although there are options to run the hemis in parallel. You can run multiple subjects at the same

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

how much ram do you have? You'll need at least 2G/subject if not 3 On Tue, 5 Jul 2011, John Drozd wrote: Hi Bruce, Thanks for the suggestion, Bruce. I'll run 8 different subjects at once. Take care, John 2011/7/5 Bruce Fischl fis...@nmr.mgh.harvard.edu Sorry, that won't help a single

Re: [Freesurfer] measuring cortical thickness using FreeSurfer

Hi Bruce, Thanks for pointing this out to me about the RAM. I have 8 Gb of RAM. So I guess I can safely run 3 or 4 subjects simultaneously if each subject requires 2 to 3 Gb of RAM. Thanks, John Sent from my iPhone On 2011-07-05, at 6:08 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

RE: [Freesurfer] Measuring cortical thickness with high resolution data

PM To: Falk Lüsebrink Cc: freesurfer@nmr.mgh.harvard.edu; 'Nick Schmansky' Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data Falk, it looks like that file was somehow converted to DOS. try: dos2unix recon-all chmod a+x recon-all then re-run doug

RE: [Freesurfer] Measuring cortical thickness with high resolution data

-Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, April 02, 2009 3:28 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Measuring cortical thickness with high

RE: [Freesurfer] Measuring cortical thickness with high resolution data

: Freesurfer Mailing List Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data Falk, There are no plans in the near future, but in the long term we'd like to remove the dependence on conforming the data. It just occurred to me that you could have the best of both worlds: first

RE: [Freesurfer] Measuring cortical thickness with high resolution data

-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky Sent: Thursday, April 02, 2009 3:28 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] Measuring cortical thickness with high resolution data Falk, There are no plans

RE: [Freesurfer] Measuring cortical thickness with high resolution data

? Regards, Falk -Original Message- From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] Sent: Wednesday, April 01, 2009 7:53 PM To: Falk Lüsebrink Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Measuring cortical thickness with high resolution data Falk, Attached is a modified

Re: [Freesurfer] Measuring cortical thickness with high resolution data

Falk, Is it possible to send me an example hires volume that you are working with? I'd like to send it through the stream myself so that I can fix the problems encountered (with using hires data) first-hand. You can upload the dicom or the 001.mgz file to me here: