Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

o option improves things even further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is that option at all possible with the available FS version or in the works? Best, Jorge On 05/09/2016 16:13, Iglesias, Eugenio wrote: The same one; just change the input file and the analysis ID

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

e subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is that option at all possible with the available FS version or in the works? Best, Jorge On 05/09/2016 16:13, Iglesias, Eugenio wrote: The same one; just change the input file and the analysis ID - T2: recon-all -s mySubject -hippocampal-su

Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

The same one; just change the input file and the analysis ID - T2: recon-all -s mySubject -hippocampal-subfields-T1T2 myT2scan.nii.gz T2 - FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 myFLAIRscan.nii.gz FLAIR Cheers, /Eugenio Juan Eugenio Iglesias Senior Research Fellow

Re: [Freesurfer] hippo sf segmentation 6.0 dev

Hi Renata, In general, mixing’n’matching is not a good idea, since different sequences bias the volumes in different directions. Now, if the differences in sequences were independent of whether subjects are patients or controls, it wouldn’t be *that* bad. But, if patients have different

Re: [Freesurfer] Brainstem nucleus

Hi Mohamad, For now, our brainstem module separates this structure into midbrain, pons, medulla and SCP - please see this link: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures If you want to segment more specific nuclei, we don’t have a tool capable of doing that yet. Cheers,

Re: [Freesurfer] version 6 NOT released yet

You can! It just makes your results harder to reproduce (running recon-all with one version, and the subfields with the other). Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 24 Aug 2016, at 17:01, Douglas

Re: [Freesurfer] dividing Freesufer subfields into one anterior, middle and posterior region

Hi Erik, there’s no FreeSurfer program to do this in a straightforward manner. But you can: 1. read in the hippocampal subfield segmentation into matlab with the MRIread function in the $FREESURFER_HOME/matlab directory. 2. extract the major axis with the hippocampus using PCA. 3. Subdivide

Re: [Freesurfer] output with input matrix size and referential

You can always run mri_convert with the -rl (“reslice like”) flag to achieve this. Something like: mri_convert input.mgz output.mgz -rl reference.mgz -odt float If it’s a segmentation volume, you should add -rt nearest, in order to use nearest neighbor interpolation. Cheers, Eugenio Juan

[Freesurfer] recent problems with hippocampal subfield and brainstem modules

Dear users, Many of you have recently experienced problems with the hippocampal subfield and brainstem substructure segmentation modules. These modules have been broken in the dev version for a couple of weeks. All the problems have now been fixed internally. The updates will be incorporated

Re: [Freesurfer] Freesurfer dev version

Hi Daniel, The issue is fixed, but I don’t know if the updated version is already in dev. Zeke, can you shed some light on this? Cheers, /Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 1 Aug 2016, at

Re: [Freesurfer] V6.0 Hippocampal subfield segmentation

Dear Xiaowei, That beta version was taken down because it had several problems. I would recommend that you wait until the next beta comes out (hopefully in 2 weeks or so), or that you download the development version (in that case, I’d do it next week because we currently fixing an error I

Re: [Freesurfer] Recent error in the dev version

Hi Daniel, the problems was that I accidentally compiled the module against dynamic rather than static libraries. The code will be fixed in the development version very soon. Also, I introduced some changes in the code so that it can handle high resolution T1s, but the behaviour on standard

Re: [Freesurfer] New hippocampal subfields

It need to run some additional tests, but I'm almost sure it is solved. The fixed code will be in the development version very soon, with some other updates. Stay tuned! Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

in kvlClear (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 133) MATLAB:invalidMEXFile". Does anyone have any idea about a solution ? Cheers, Pierre On Wed, Jul 13, 2016 at 12:22 PM, Iglesias, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>>

Re: [Freesurfer] Hippocampal subfields total volume differences

study, same modality) to make more precise measurements? For example by using T1 from the same subject / different time instead of T2 in subfields? Thanks! Mojmir On Wed, Jul 13, 2016 at 5:15 PM Iglesias, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: Hi Mojmir, ASEG

Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?

://cmictig.cs.ucl.ac.uk/ On 14 Jul 2016, at 10:05, Fernando Pérez-García <fepe...@gmail.com<mailto:fepe...@gmail.com>> wrote: I am using Ubuntu 14.04.4. Please let me know if you need some more info. Cheers, Fernando 2016-07-14 10:59 GMT+02:00 Iglesias, Eugenio <e.igl

Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?

Dear Fernando, Are you using the MAC version? I haven’t finished fixing the bugs in that one yet. If you’re using the Linux version: Zeke, can you please shed some light on what the problem might be? Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London

Re: [Freesurfer] Hippocampal subfields total volume differences

Hi Mojmir, ASEG typically gives a larger estimate of the volume, though highly correlated with that from the subfield package. We have found the measurements from the subfield package to be a bit more reliable, though. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

And thanks to Zeke, of course ;-) Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13 Jul 2016, at 11:19, Iglesias, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: Dear all

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

). You can downloaded the latest development version from our website. Thanks everyone for your feedback. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 8 Jul 2016, at 12:14, Iglesias, Eugenio

Re: [Freesurfer] {Filename?} Hippocampal subfields --> Can't find a *ctf file?

I think I identified the problem; hopefully this will be sorted out very soon. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 7 Jul 2016, at 19:23, Perea Camargo, Rodrigo Dennis

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Iglesias, Eugenio [e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>] Sent: Friday, June 10, 2016 3:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields segmenta

Re: [Freesurfer] hippocampal subfields command

Hi Jim, the latter command uses a new, higher resolution atlas based on ex vivo scans. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios

Re: [Freesurfer] Hippocampal Subfields Segmentation

Dear all, We are working on this; I'll write again when the problem is solved (hopefully soon!) Cheers Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From:

Re: [Freesurfer] Hippocampal Subfields Segmentation

Jun 2016, at 15:43, Iglesias, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: Hi Pierre, Due to some technical problems, it might take me a couple of days to figure out what’s going on. But it definitely sounds funny that it is asking for the CTF, since this

Re: [Freesurfer] Hippocampal Subfields Segmentation

Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> wrote: Hi everyone, you need to install the Matlab 2012b runtime as explained in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Tra

Re: [Freesurfer] Hippocampal Subfields Segmentation

Hi everyone, you need to install the Matlab 2012b runtime as explained in the wiki: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 27

Re: [Freesurfer] unit for hippocampus segmentation results

If you mean the new subfield module, then the answer is: cubic mm. Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] using both T1/T2 and resolutions

I think he is just after cortical surfaces. Matt. From: <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Iglesias, Eugenio" <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> Reply-To: Freesurfer

Re: [Freesurfer] using both T1/T2 and resolutions

Hi! I actually sent out an email yesterday regarding this. The way that the subfield module is set up, you cannot take advantage of your full res T1 and your T1. We are working on a solution. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London

Re: [Freesurfer] Brainstem Substructures does not work.

FreeSurfer 6.0 is not available yet, but you can download the development version to take advantage of this functionality. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 10 Jun 2016, at

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

d.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Iglesias, Eugenio [e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>] Sent: Thursday, June 09, 2016 2:36 PM To: Freesurfer support list Subject: Re: [Freesurfer] H

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Matt, you can use strategy 3 of my previous email ;-) Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 9 Jun 2016, at 19:31, Matt Glasser > wrote: I

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

Hi Fernando, Unfortunately, FreeSurfer does downsample the T1s to 1mm, and the subfield code assumes that the T1 comes from FreeSurfer… For the paper, I hacked the code to take advantage of multiple images with higher resolution, but it hasn’t been thoroughly tested and it’s not publicly