Re: [Freesurfer] FS6.0 on 2yo subjects

Hi Dimitrios, Agree with Burce. The youngest we have processed with the standard pipeline was about 4.5yrs. Lilla On Wed, 18 Sep 2019, Bruce Fischl wrote: Hi Dimitrios it's kind of an empirical question. Lilla does have some newer tools you might consider instead of things aren't as accura

Re: [Freesurfer] FS6.0 on 2yo subjects

Hi Dimitrios it's kind of an empirical question. Lilla does have some newer tools you might consider instead of things aren't as accurate as you want cheers Bruce On Wed, 18 Sep 2019, Alexopoulos, Dimitrios wrote: External Email - Use Caution We have acquired 0.8mm isotro

Re: [Freesurfer] issue with lesions

External Email - Use Caution Thanks Doug. The problem is that for some patients the lesion affects the segmentation dramatically. For example I have one patient with a large lesion in the right cerebellum which is partly in GM and partly in WM. If I load the aseg file I see that a

[Freesurfer] FS6.0 on 2yo subjects

External Email - Use Caution We have acquired 0.8mm isotropic T1-mprage sequences on 2 year old subjects. Although the output looks good (see below), is it recommended to use FS6.0 on a young cohort? [cid:image005.jpg@01D56E40.7241E0E0][cid:image006.jpg@01D56E40.7241E0E0] [cid:i

[Freesurfer] Research Assistant Position (infant/pediatric MR imaging) Boston Children's Hospital/Harvard Medical School

The Gaab Lab (www.gaablab.com) is looking for a Clinical Research Assistant II to assist with all study phases of functional and structural MRI for our longitudinal infant MRI study. This position is ideal for anyone considering future graduate study in cognitive (developmental) neuroscience, co

Re: [Freesurfer] mkcontrast-sess question

Thanks a lot Doug! It was exactly what I needed. Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 From: freesurfer-boun

[Freesurfer] GNU R package to read and write FreeSurfer data

External Email - Use Caution Dear list, I needed some GNU R functions which read and write MGH/MGZ files including all the header information, so I wrote them and also put them into a package to share them. Support for binary 'curv' format morphometry files (like 'surf/lh.area

Re: [Freesurfer] qdec contrast and data extraction

External Email - Use Caution Hi, I tried that and it seemed to work. My averages between the 2 groups look different now instead of almost identical. Thanks! I have another similar question. I have a cluster that shows a significant difference between the groups when looking at

Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

Hi Vasudev -openmp N is the best way at the moment. Do you actually have 3 cores to dedicate? Usually due to memory access speeds and such we don't see much gain after N=4, but I'm surprised there is no effect cheers Bruce On Wed, 18 Sep 2019, Dev vasu wrote: External Email - Use

Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

External Email - Use Caution I would recommend GNU parallel. I have 2 scripts here: https://github.com/dfsp-spirit/shell-tools/tree/master/gnu_parallel_reconall_minimal and an explanation of what they do and how to use them at https://www.xsmd.org/brain/2019/03/13/using-gnu-

Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

External Email - Use Caution Hi Vasudev, in case you use v6, you can use the -parallel flag to process the hemispheres (and a few other things if I remember correctly) in parallel. Note that doing so will parse the -openmp flag to all instances. E.g. recon-all -all -openmp 4 -p

[Freesurfer] How to fasten recon-all execution time without using CUDA

External Email - Use Caution Dear all, I am using - openmp 30 to run recon-all, i see now change in the execution time period. Could you please highlight me a method to reduce the execution time for recon-all, if possible some parallel script to do that same. Thanks Vasudev ___

Re: [Freesurfer] negative values of hippocampal subfields volumes

Dear Chris, Can you please send us the output txt file? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Krzysztof Gbyl Reply-To: Freesurfer support list Date: Wednesday, 18 September 2019 at 08:4

[Freesurfer] Names of the segmentation volumes in lh.hippoSfLabels-T1.v10.mgz

External Email - Use Caution Hi FS experts, I am using the module of segmentation of hippocampal subfields. About the output of lh.hippoSfLabels-T1.v10.mgz, could you pls provide the correspondence between the values of segmentation volumes in the image file and the anatomical