Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

Hi, Bruce The command line I used is:  mris_fill -r 1 -c rh.white rh.white.nii.gz I attached the rh.white in my previous mail. Could you see it in the attachment? Thank you! Longchuan From: Bruce Fischl To: Longchuan Li Cc: FreeSurfer Sent: Tuesday, Mar

Re: [Freesurfer] Brainsuite --> FreeSurfer

I could see the created surface in MAtlab ( 'read_surf,) but I could't open the file in Freesurfer with tksurfer VP From: pval...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400 Hi, I've done a segmentation with B

[Freesurfer] Brainsuite --> FreeSurfer

Hi, I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be usable with Freesurfer. Then, I tried to get measurements with the command .'mris_anatomical_stat

Re: [Freesurfer] Medial orbitofrontal QA question

actually, I think you need to look up his email at UCSD as his MGH one bounced Bruce On Wed, 20 Mar 2013, Alice Burnett wrote: > Thanks very much, Doug and Bruce! > > > > > This e-mail and any attachments to it (the "Communication") are, unless > otherwise stated, confidential, may contain copy

Re: [Freesurfer] Medial orbitofrontal QA question

Thanks very much, Doug and Bruce! This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender i

Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

can you send your mris_fill command line? And maybe the lh.white surface you are trying to fill? Bruce On Tue, 19 Mar 2013, Longchuan Li wrote: Hi, Bruce This is the lh.white that gives me the empty volume when I use mris_fill to sample it to the volume space. Could you help diagnose what is c

Re: [Freesurfer] multi-echo mprage

Hi Souheil I would run the two sets of scans separately; I would expect a T2 bias in the sample if they are run together with ones that have no T2. Perhaps see how T2 images influence the output (maybe have a .fsgd file with T2/noT2 as two levels) to see if there are significnt differences- no? H

Re: [Freesurfer] multi-echo mprage

Hi Souheil we usually compute the RMS across echoes and give that to recon-all as a normal mprage. It's a reasonable (although of course not optimal) weighting since the earlier echoes have more signal and more contrast. For the T2s, there's a new post-hoc procedure for deformaing the surfaces

[Freesurfer] multi-echo mprage

Hi All, I have some multi-echo mprage images from a sequence and protocol set up to emulate Andre's 2008 paper. What's are the "best-practices" for using data from this type of sequence in Freesurfer? Related side questions: I have used the suggested morphometry protocols on the FS wiki (1mm

Re: [Freesurfer] longitudinal stream - template

Hi Yolanda, if you want to simulate a study where one obtains 2 time points (6 months apart) or 2 time points (12 months apart) and then compare the results, you would need to run these two independently through free surfers longitudinal stream (one time including 0 and 6 month, the other time

Re: [Freesurfer] Correspondence of Talairach coordinates from one subject to other

Hi Doug, I tried to do what you recommended but I am encountering an inconsistency. (Note: I obtain the same results in R (with ginv() ) and Matlab (with pinv() ) ) Could you please have a look at the code and the values please? I don't know what else to do right now... (it is possible to copy p

Re: [Freesurfer] longitudinal analysis

Hi Joy-Loi, yes, you can do that using the free surfer tools (e.g. check if 'atrophy', i.e. change across the two methods, is different from zero, meaning if there is a bias). Any of the statistical methods described here: http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalStatistics can do

Re: [Freesurfer] longitudinal analysis

Hello Martin, Thank you for your swift reply. I failed to make myself clear, and will try describing my study again. First, an important point: the study is not longitudinal per se, but I am interested in applying the methods of longitudinal analysis. I only have one time point, all the scans

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

Posting one of the brains. https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn It seems to me that neither version is perfect; however, 5.2.0 is capturing more "black spaces" in the region I'm looking at. It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20). Given that t

Re: [Freesurfer] longitudinal stream - template

Hi Martin, Thank you for your answer, but my idea was to compare the atrophy rates when using scans at 6 months (0 - 6 months) and scans at 12 months (0 - 12 months). If my templates are built with more time points, the results will be biased, right? Regards, Yolanda 2013/3/18 Martin Reuter : >