Re: [Freesurfer] Amygdala segmentation runtime error

Hi Emily, When did you download the dev version? Was it very recently? Cheers, /E -- 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 Emily K Clarke Reply-To: Freesu

[Freesurfer] why freesurfer is not able to segment frontal cortex

Respected Sir Does freesurfer segments frontal cortex? If yes the how we can do that I have tried to do it by using the command :mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_superior.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_inferior.nii --match 1154 mri_binarize --i aseg

[Freesurfer] why freesurfer is not able to segment frontal cortex

Does freesurfer segments frontal cortex? If yes the how we can do that I have tried to do it by using the command :mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_superior.nii --match 1156 mri_binarize --i aseg.mgz --o ctx-lh-s_frontal_inferior.nii --match 1154 mri_binarize --i aseg.mgz --o ctx-lh

[Freesurfer] no skullstrip

Dear free surfer developers, Because I work with neonatal scans the skullstrip phase cannot be applied correctly (it removes too much skull). To avoid this problem I added the -noskullstrip option. However, I do still need the brain mask output of this phase. How can I work around this? Kind r

[Freesurfer] making masks with subfields etc

Hi FS experts, I have run a hippocampal analysis with v6.0 including the subfields and am now in the process of running an  addtional analysis using the dev6.0 version for the amygdala and posterior/anterior hippocampal measures. I also want to use the 3D rendered volumes of the hippocampus an

[Freesurfer] PET partial volume correction

Dear Dr Greeve, I interestingly read the manuscript "Different partial volume correction methods lead to different conclusions: An (18)F-FDG-PET study of aging" Thank you for publishing this data. I understood from this paper that he recommended stream for PVC is to correct the PET images using

Re: [Freesurfer] Amygdala segmentation runtime error

Hi Juan, Yes, it was right at the end of December — the version file in the install is freesurfer-x86_64-unknown-linux-gnu-dev-20171228, and it looks like it was updated again January 2. Best, Emily From: "", Eugenio mailto:e.igles...@ucl.ac.uk>> Reply-To: Freesurfer support list mailto:free

Re: [Freesurfer] making masks with subfields etc

Dear Erik, I might be missing something here, but: the subfield segmentation, rawavg.mgz, etc, are all already in native subject space… Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.

Re: [Freesurfer] making masks with subfields etc

Hello Eugenio, Thanks for your reply. When I'm in freeview, the hippocampus and even the amgydala from the aseg align nicely with my input T1 image. I suspect that it could be an issue when export ing them from freeview. I just saved the hippocampus etc as nii volumes and then tried to open th

Re: [Freesurfer] Dear freesurfer users

yes, that is correct cheers Bruce On Fri, 12 Jan 2018, 주요한 wrote: Dear all,   I’m a beginner in FreeSurfer.   Actually I tried to get an information for cerebellum volume.     Thus I installed the FreeSurfer and typed recon-all ~ ...   After the processing, I got an information from as

Re: [Freesurfer] PET partial volume correction

Hi John Doug is out of touch for a week. Maybe you can post this again at the end of next week or early the following if he hasn't responded? cheers Bruce On Fri, 12 Jan 2018, John Anderson wrote: Dear Dr Greeve, I interestingly read the manuscript "Different partial volume correction m

Re: [Freesurfer] making masks with subfields etc

OK, got it. The problem is that your images are aligned in physical coordinates, but not in voxel coordinates. FreeView handles that nicely, but I don’t know about FSLview. The subfield code also generates files named *.FSvoxelSpace.mgz, which are in the same voxel coordinates as the recon-all f

[Freesurfer] ROI statistics and median values

I can use mri_segstats to get mean and std dev for values within a segmented image. Is there any way I can get median values? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The i

Re: [Freesurfer] LME

Hi Getaneh, thanks for the additional information. I suspect that one source of confusion was that we have to distinguish the univariate and the mass-univariate processing stream in the LME toolbox.  The univariate stream is about a single measure like left or right or bilateral hippocampal volu

Re: [Freesurfer] making masks with subfields etc

Brillant. Thanks Eugenio. I'll use the voxel files. Cheers and enjoy the weekend Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 12 January 2018 15:41 To: Freesurfer support lis

Re: [Freesurfer] LME

Kersten Thank you so much. With regards Getaneh -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Diers, Kersten /DZNE Sent: Friday, January 12, 2018 9:50 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Fre

Re: [Freesurfer] no skullstrip

Hi Aicha. We have a different processing stream for infants. It is not only the skullstripping that will not work for your cases but much of the remaining pipeline. We are getting ready to release that pipeline. Lilla On Fri, 12 Jan 2018, Dijkshoorn, A.B.C. (Aicha) wrote: Dear free surfer

[Freesurfer] external WM and GM masks as input to recon-all?

Dear FreeSurfer experts, Could you please advise on whether it would be possible to run recon-all in FreeSurfer 6.0 using externally-derived probabilistic white matter and grey matter masks, both of which include the cerebellum but not the ventricles, and if so, how? Would the flag -autorecon2

[Freesurfer] Jittering Fixation Time

Dear FreeSurfer Experts, I have a question about jittering the fixation point and how Freesurfer handles it. Is it ok to have different rest times in the paradigm file for FS-FAST pipeline? In the paradigm file, I am giving it an actual onset time and for the length of the rest block I am giving

Re: [Freesurfer] external WM and GM masks as input to recon-all?

Hi Shadia no, not easily. sorry, Bruce On Fri, 12 Jan 2018, MIKHAEL Shadia wrote: > Dear FreeSurfer experts, > > Could you please advise on whether it would be possible to run recon-all in > FreeSurfer 6.0 using externally-derived probabilistic white matter and grey > matter masks, both of whi

Re: [Freesurfer] TRACULA path segmentation fault error because of bedpostx?

Hi Carissa - One possibility is that you may be running out of memory. What are the dimensions of your diffusion images? a.y From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Carissa Nicole Weis Sent: Thursday, January 11, 2018 4:55:47 PM To: Freesur

Re: [Freesurfer] Using subject specific template, atlas, & TPM

Hi Ramesh if you have segmentations in our aseg format (or edited asegs for that matter if you find them not accurate enough), you should be able to use mri_ca_train to genenerate a new .gca file and apply it to your subjects. Read the help and wiki and see if you can make it work, and let us

Re: [Freesurfer] Inquiry about process time by use "recon-all"

Hi Ritthikrai the amount of time depends on both how abnormal the anatomy is and how high the CNR of your scan is. If you send us some details about your acquisition we might be able to help optimize it, but otherwise you might be stuck with long running time. You can also use more than 1 thre

Re: [Freesurfer] White/pial surface failure

Hi, Just wanted to follow up on this and see if anyone had a chance to look at it. Thanks, Trevor Get Outlook for Android From: Trevor K Day Sent: Thursday, December 14, 2017 4:09:44 PM To: Freesurfer support list Subject: RE: [Freesurfer]

[Freesurfer] Freesurfer compilation for supporting cuda9.1

Hi Freesurfers, I tried different ways to compile freesurfer for support cuda 9.1. Unfortunately, I still cannot get it work. While I tried to compile a specific module freesurfer/utils where the errors generated, I got the error message. Any suggestions would be appreciated! gcc -DHAVE_CONFIG_H