Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Yes, absolutely! -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of "Alexopoulos, Dimitrios" Reply-To: Freesurfer supp

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Thanks for the quick evaluation. So your conclusion based on this evaluation is to the use the –hires flag? Jim “The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised t

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Thanks Jim, The segmentations look nice, though the head is slightly undersegmented in the right hippo. You can barely discern the molecular layer so, even though the subfields surely carry useful information, they won’t be as precise as with a dedica

[Freesurfer] QDEC vs. Command Line Stream

External Email - Use Caution Dear experts, I'm about to start my cortical thickness analysis for my groups, and I was just wondering what seems to be the consensus when it comes to using QDEC as opposed to using the command line stream? I've seen QDEC used plentifully in the l

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Eugenio, I have uploaded a dataset for you to review. The file is ‘chd_auck_Bs44_6yr_fs.zip’. It was processed with the following command using FS 6.0. The native resolution is 0.82x0.82x0.85mm recon-all -s chd_auck_BS44_6yr_fs -i T1..dcm -hippocampa

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Of course! https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Thanks for the input Eugenio. Could you review one of our submillimeter T1 datasets processed using FS6.0? If yes, where can I upload to? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of I

[Freesurfer] SLURM - speed processing

--- > ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 > > Possible problem with experimental design: > Check for duplicate entries and/or lack of range of > continuous variables within a class. > > I'm assuming this is b

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution You can but recon-all will resize to 1mm isotropic and you’ll lose your submil resolution. Of course, you could technically also use recon-all at 1mm, and then use the submil T1 as additional volume, but that’d be a bit inefficient… -- Juan Eugenio I

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Ok. Can you run -hippocampal-subfields-T1 without the -hires flag using a submillimeter T1? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Friday, April 20, 2018 2:24

Re: [Freesurfer] Calculation of surface area

External Email - Use Caution Dear Douglas, Thank you for your quick answer! The thing is, we don't have access to the original surface area files which were created by FreeSurfer anymore. Thus, we were wondering if we can calculate a region's surface area if we have its volume & c

Re: [Freesurfer] fmriprep to fsfast interface

Thank you for the response! I'm interested primarily in tal space, but potentially native as well. For tal space, is there no easy way to just directly transform the data into tal space or provide an identity matrix for the registration? From: freesurfer-boun..

[Freesurfer] 8th Annual Brain-Art Competition @ OHBM open for submissions!

External Email - Use Caution In order to recognize the beauty and creativity of artistic renderings emerging from the neuroimaging community, we are launching the eighth annual Brain-Art Competition. Countless hours are devoted to the creation of informative visualizations for com

Re: [Freesurfer] FSGD design for multi-centre study

External Email - Use Caution Thanks a lot for the explanation. The issue is that I don't think Freesurfer will run a design for which there are no subjects for a given class. So if I keep the classes (24 classes since 6 centres x 2 gender x 2 groups (patient vs. control), and ha

Re: [Freesurfer] SLURM - speed processing (Alexandre Obert)

External Email - Use Caution Hi Alex, I am also running FreeSurfer 6.0.0 on SLURM and recently did some tests on how to parallelize it, how much ressources to ask for… This is what I learned: 1) FreeSurfer 6.0.0 is able to use OpenMP parallelization (I guess for the comma

Re: [Freesurfer] using T2 for hippo subfields

External Email - Use Caution Sorry, I’m not sure I follow. But, if you run recon-all with the hires flag, then you can just run –hippo-subfields-T1 and it’ll take advantage of the high resolution. -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group Un