Re: [Freesurfer] Brainstem segmentation

lesias.com On Sep 20, 2021, at 18:43, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Dear Experts, We hope to acquire some multishell dwi and structural data to investigate tracts passing through the Locus Coeru

[Freesurfer] Brainstem segmentation

External Email - Use Caution Dear Experts, We hope to acquire some multishell dwi and structural data to investigate tracts passing through the Locus Coeruleus (LC) and we want to apply the brainstem segmentation to our structural data to obtain subject specific LC masks. Is it

Re: [Freesurfer] Hippocampal subfields

5VfSe-gO2GqcRvGhQHCfYZw4IhoipbJUOi9v0tL5ajYH_Hv7r1WXRikWcSkenidoPo0bU8j8yPC21LqHlMB6c51XU6vq9XyKWHpExMjlIdUrOvuDxTOVyvXXGX6Z6Vom55EXxKNHs5XA4SgCapcbUOZufvnpzZ1tIw/http%3A%2F%2Fwww.jeiglesias.com On Aug 28, 2021, at 08:20, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Hi Eugenio So I ran the new Amygdala and hippocampus tool on my longitudinal data

Re: [Freesurfer] Hippocampal subfields

-dobHYl3W_y6GhIsiANkJk6bKdBmRwDZDkB7o8lLevPO3On0jPYRQRhL13Rhgg/http%3A%2F%2Fwww.jeiglesias.com On Aug 27, 2021, at 16:14, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External Email - Use Caution External Email - Use Caution Dear FS experts, I've run a lognitud

[Freesurfer] Hippocampal subfields

External Email - Use Caution Dear FS experts, I've run a lognitudinal hippocampal and amygdala analysis. I jave managed to extract the amygdala and the head body tail subfields bui I'm wondering how to extract the regular FS60 volume measures? I have the three versions (FS60,

[Freesurfer] longitudinal LME stats

External Email - Use Caution Dear FS experts, I have run the longitudinal pipeline on a dataset with three timepoints. I am particularly interested in the longitudinal hippocampal and amygdala data and want to run LME on these. I've made the qdec table with the id age, sex and t

[Freesurfer] Using The Buckner Cerebellum Parcellations

External Email - Use Caution Dear FS Experts, I'd like to use the Bruckner 7 Network parcellations and have downloaded the files as per the wiki link. My Freesurfer analysis on all my subjects is sub millimetre and I have conformed my data to that using the -cm in my recon_all.

[Freesurfer] Cerebellum Masks

External Email - Use Caution Dear Experts, Is it possible to use the SUITS labels (#601-628) in the LUT to make masks and extract volume measures. I ultimately want to use the masks for tractography purposes. Can I use the mri_extract to pull out the specific ROI's and if so do

[Freesurfer] SUIT cerebellum parcellations

External Email - Use Caution Dear FS Experts, Just wondering if it's possible to use the SUIT labels in the LUT to obtain cerebellar quantification measures and also to make masks for tractography specific to each area? Thanks in advance Erik __

[Freesurfer] Longitudinal processing and paralllel flag

hiatry Trinity College Institute of Neuroscience The Llyod Institute Trinity College Dublin D2 Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T:

Re: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview

d Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology http://www.jeiglesias.com From: on behalf of Erik O'Hanlon Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College

[Freesurfer] loading and rendering the Amygdala nuclei only in Freeview

can't seem to get it to work. Any pointers gladly accepted Thanks Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E:

Re: [Freesurfer] Using the new Thalamus tool

lf of Douglas N. Greve Sent: 11 September 2018 18:12:39 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Using the new Thalamus tool And just to be clear, you should run only the thalamus, hippo, amyg, brainstem segmentations in dev. Do not run recon-all using the dev version. Erik O&#

Re: [Freesurfer] Using the new Thalamus tool

list; Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool External Email - Use Caution 10-15 mins or so Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erik O'Han

Re: [Freesurfer] Using the new Thalamus tool

No need to rerun recon-all on the subjects. Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon Sent: Thursday, September 6, 2018 3:44:57 PM To: freesurfer@nmr.mgh.harv

[Freesurfer] Using the new Thalamus tool

s it best just to do another install with teh complete new Dev version? Is it possible to run the Thalamus analysis as an addtional component without having to rerun the recon_all again? Thanks and regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d

Re: [Freesurfer] Longitudinal errors, Voxel size differs

: you should use mri_convert --conform input output Best, Martin Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...

Re: [Freesurfer] Extract the entorhinal cortex as a mask

32 To: Freesurfer support list Subject: Re: [Freesurfer] Extract the entorhinal cortex as a mask I think you can use 1006 (left) and 2006 (right) cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Hi Bruce, > > > Thanks. So if

Re: [Freesurfer] Extract the entorhinal cortex as a mask

to extract EC as a volume mask cheers Bruce On Tue, 12 Jun 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Hi FS experts , > > > I'd like to make masks for the entorhinal cortex to use for tractography. Can > you advise what FS too

[Freesurfer] Extract the entorhinal cortex as a mask

? I'm sure it's straightforward Thanks for any advice Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740

Re: [Freesurfer] creating a mask for the thalamus parcellations

bject variability. Would this be vastly inferior to the subject specific way, realising that the subdivisions of theThalamus isn't available yet? Thanks and regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Erik O'Hanlon Sent: 01 Jun

Re: [Freesurfer] creating a mask for the thalamus parcellations

) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 31/05/2018, 17:46, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl" wrote: not yet, sorry. We are working on it Bruce On Thu, 31 May 2018, Erik O'H

[Freesurfer] creating a mask for the thalamus parcellations

L_Ant_thalamus.mgz Thanks Cheers Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.com

Re: [Freesurfer] hippo subfields and amygdala

http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9

Re: [Freesurfer] hippo subfields and amygdala

te binary masks. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Erik O'Hanlon Erik O'Hanlon Postdoctoral re

[Freesurfer] hippo subfields and amygdala

to use for each subject. Thanks for any information you can offer Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont D9 Ireland T: 80

Re: [Freesurfer] Longitudinal errors, Voxel size differs

so that people are aware of this potential bias - resample both time points to some 3rd space. Probably here simply conform them to 1mm isotropic. Best, Martin Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI Psychiatry Royal

[Freesurfer] Longitudinal errors, Voxel size differs

ime 1 before rerunning from scratch. I assume I can't avoid rerunning the initial reconall step once I resample my data. Any guidance is much appreciated Best regards Erik Erik O'Hanlon Postdoctoral researcher [cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png] RCSI P

[Freesurfer] Hippocampal and amygdala analysis with dev6 FS

0.03 Linux lonsdale-n148.cluster 2.6.32-696.18.7.el6.x86_64 #1 SMP Wed Jan 3 19:31:16 CST 2018 x86_64 x86_64 x86_64 GNU/Linux T2 hippocampal subfields exited with ERRORS at Fri Jan 26 20:00:45 GMT 2018 Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Irela

Re: [Freesurfer] making masks with subfields etc

Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/     From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 12 January 2018 at 15:13 To: Freesurfer support list Subject: Re: [Freesurfer] making masks with subfields etc   Hel

Re: [Freesurfer] making masks with subfields etc

.ucl.ac.uk/     From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 12 January 2018 at 13:07 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] making masks with subfields etc   Hi FS experts, I have run a hippocampal analysis with v6.0 in

[Freesurfer] making masks with subfields etc

Best regards Erik   Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MA

Re: [Freesurfer] new Amygdala and Hippocampus segmentation

ecent (dev) version. Cheers, /Eugenio   --  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 Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday,

Re: [Freesurfer] new Amygdala and Hippocampus segmentation

http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/     From: on behalf of Erik O'Hanlon Reply-To: Freesurfer support list Date: Friday, 8 December 2017 at 14:15 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] new Amygdala and Hippocampus segmentation   Hi

[Freesurfer] new Amygdala and Hippocampus segmentation

hippoSF and amygNuc) ?  segmentHA_T2.sh subject001 subject001_Flair.nni.gz T1andFlair USE_T1 /subject001    Will this overwrite any of my FS6.0 subfield measures present in the subject MRI dir? Thanks for any help you can provide . Erik Erik O'Hanlon Postdoctoral researcher

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 3 Feb 2017, at 11:32, Erik O'Hanlon <erikohan...@rcsi.ie> wrote: recon-all  -all -3T -s /sub008 -hippocampal-subfields-T1T2 /sub008/sub_00

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

ntensities in them. cheers Bruce On Fri, 3 Feb 2017, Erik O'Hanlon wrote: > Hi Experts, > > Just flowing on from Joe's question, I have run my analysis without the T2 or > FLAIR flag but have > specificed the T2 which is a FLAIR image for the hippocampal subfield > op

Re: [Freesurfer] Simple question regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed}

stion regarding -T2 and -FLAIR flags (freesurfer v6) {Disarmed} Thanks for the quick reply. I'll re-run my subjects with the -FLAIR flag. Joe Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 80937

Re: [Freesurfer] T2 voxel size needed for recon_all

Thanks Bruce, Much appreciated. Cheers Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFE

[Freesurfer] T2 voxel size needed for recon_all

Dear Freesurfer experts, I'm wondering if there is a minimum voxel size for the T2 iamge to be included in the recon_all. My T1 is .9mm isotropic but the T2 available is 0.5mmx0.5mmx3mm. Would this voxel size offer any benefit or would it be best just to run the recon_all with only the T1 imag

Re: [Freesurfer] Hippocampus visualisation

it is possible to display only certain subfields (say the CA1 and Subiculum rendered in 3D using freeview? Can I also render the entire hippocampus that is basically the addition of all the subfields given in the table output? Sorry for the basic question, just trying to put together some images.

[Freesurfer] Hippocampus visualisation

ields given in the table output? Sorry for the basic question, just trying to put together some images. Thanks in advance  erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...

Re: [Freesurfer] hippocampal subfields

txts etc. Just wanted to be sure before I kick it off on the complete data set. Thanks again for all the help. Cheers Ertik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...

Re: [Freesurfer] hippocampal subfields

disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message ----- From: "Erik O'Hanlon" To: "Freesurfer support list" Sent: Monday, May 25, 2015 6:53:54 PM Subject: Re: [Freesurfer] hippocampal subfields Hi FS Experts, I'm tryi

Re: [Freesurfer] hippocampal subfields

/ dir. Any pointers how to resolve ? Any help greatly appreciated Cheers Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEAL

Re: [Freesurfer] hippocampal subfields

That is super Nick, I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6? Thanks again for all the help Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal

Re: [Freesurfer] hippocampal subfields

Hi Eugenio, Sorry, forgot to ask if I can run it with the longitudinal pipeline too? Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 08 May 2015 14:36 To: Freesurfer su

Re: [Freesurfer] hippocampal subfields

ww.bcbl.eu/legal-disclaimer - Original Message ----- From: "Erik O'Hanlon" To: freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 8, 2015 2:07:18 PM Subject: [Freesurfer] hippocampal subfields Hi FS experts, I completed an analysis including the hippocampal subfield options

[Freesurfer] hippocampal subfields

Kind regards  and thanks in advance Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE

Re: [Freesurfer] Hippocampal subfields

Hi FS experts, Yes, I'm in the same position and have been trying to do it longitudinally. Does this mean that the outputs are completely unreliable and unstable? Should it be parked until the release of version 6? Thanks Erik Erik O'Hanlon Postdoctoral researcher RCSI Psychi

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

Hi Eugenio, Should I send the files via dropbox, as it appears that the last one I sent is waiting approval due to size etc. Thanks and sorry for the hassle Erik From: Erik O'Hanlon Sent: 20 November 2014 15:51 To: Freesurfer support list Subjec

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

_ABD/sub040_tp1.long.sub040_T1_baseimage$ To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any ideas very much appreciated. Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

ted. Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@rcsi.ie] Sent: 18 November 2014 20:42 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields That's

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

bject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, no need to re-run . no need even to do -all, just do the subfields. Best, Martin On 11/18/2014 12:57 PM, Erik O'Hanlon wrote: Thanks Martin, Could I also ask that if the -long command was run without the subfi

Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Erik, yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base. Best, Martin On 11/18/2014 11:41 AM, Erik O'Hanlon wrote: Dear FS Experts, I'm running a longitudina

[Freesurfer] Longitudinal analysis and hippocampal subfields

Dear FS Experts, I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too? Thanks in advance for any input. Kind regards Erik Erik O'Hanlon Po

Re: [Freesurfer] FW: registration difficulty

subfieldaligned_orig file to the No_diff image using mdi_vol2vol with the regsiterNodiff2orig.dat file and the --inv flag. I know it's probably not the best way to do it but it all aligns nicely. Thanks for the pointers Cheers Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researc

Re: [Freesurfer] FW: registration difficulty

the interface. but I might not understand what is going on ... doug On 04/02/2014 03:03 PM, Erik O'Hanlon wrote: > Apologies. > > forwarded it on now > > Thanks a million > > Erik > > Dr. Erik O'Hanlon PhD MSc BScEng > Post Doctoral Researcher > > > RCS

Re: [Freesurfer] FW: registration difficulty

Apologies. forwarded it on now Thanks a million Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.ie W: www.rcsi.ie RCSI DEVELOPING HEALTHCARE LEADER

[Freesurfer] FW: registration difficulty

this due to the different FOV for the subfields? Can anyone advise how to get these volumes to transform correctly? Any help would be greatly appreciated. Thanks Erik Dr. Erik O'Hanlon PhD MSc BScEng Post Doctoral Researcher RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Bea