Re: [Freesurfer] trouble in manual editing of pial surface

2018-11-30 Thread 박경일
External Email - Use Caution Thanks for you quick reply. I am uploading a compressed file to filedrop (example1.zip). Which email should be filled up in recipients's email to reach you? Kyung 2018년 11월 30일 (금) 오전 12:34, Bruce Fischl 님이 작성: > Hi Kyung > > it's impossible to tell

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

2018-11-30 Thread Diamond, Bram Ryder
It's strange, but I'm not having the same issue. Can you try downloading 5.3 again and see if that fixes your issue? Bram From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Batuhan Erkat Sent: Friday, November 30, 2018 12:49:42 PM To: freesurfer@nmr.m

Re: [Freesurfer] Segmentation of hippocampal subfields on FS v6 stable data?

2018-11-30 Thread Iglesias Gonzalez, Eugenio
External Email - Use Caution Nope, please don't rerun the recon-all with dev. Just run the hippo+amyg module on the 6.0-reconned data. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and

[Freesurfer] Using the SUIT atlas

2018-11-30 Thread Nillo, Ryan Michael R
External Email - Use Caution Hi FreeSurfer users, I am using the SUIT atlas (http://www.diedrichsenlab.org/imaging/suit.htm) to parcellate the cerebellum.To ensure there are no problems with registration, the SUIT pipeline requires that the origin of the input images are centere

[Freesurfer] mkcontrast-sess and mkcontrast2 matlab errors

2018-11-30 Thread Emily Levin
External Email - Use Caution Hi FreeSurfer experts, I'm trying to run mkcontrast-sess using the newest development version of freesufer from Nov 30th, 2018, and I am getting a matlab permission denied error (see mkcontrast-sess_error text file). It seems to be happening around li

Re: [Freesurfer] Two problematic participants -- unable to run recon-all

2018-11-30 Thread Bruce Fischl
no worries On Fri, 30 Nov 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution Oh, sorry Bruce for not understanding it. I sent the files directly to you. Sorry for that as well as this is something it should never be done. Please, accept my apologies. Yours sincer

Re: [Freesurfer] Two problematic participants -- unable to run recon-all

2018-11-30 Thread Rosalia Dacosta Aguayo
External Email - Use Caution Oh, sorry Bruce for not understanding it. I sent the files directly to you. Sorry for that as well as this is something it should never be done. Please, accept my apologies. Yours sincerely, Rosalia On Fri, Nov 30, 2018 at 7:14 PM Bruce Fischl wrote:

Re: [Freesurfer] Two problematic participants -- unable to run recon-all

2018-11-30 Thread Bruce Fischl
you don't need a password. Just use anonymous as your user name and your email as the password I think On Fri, 30 Nov 2018, Rosalia Dacosta Aguayo wrote: External Email - Use Caution HI Bruce, I would like to use Email File Drop but I am having problems, not sure if with my

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

2018-11-30 Thread Batuhan Erkat
External Email - Use Caution Done On Fri, Nov 30, 2018 at 8:46 PM Diamond, Bram Ryder < brdiam...@mgh.harvard.edu> wrote: > Can you please upload the BE2_T1.nii? > > > Bram > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@

Re: [Freesurfer] Recon-all - mghRead could not read rawavg.mgz

2018-11-30 Thread Diamond, Bram Ryder
Can you please upload the BE2_T1.nii? Bram From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Batuhan Erkat Sent: Thursday, November 29, 2018 12:35:06 PM To: freesurfer@nmr.mgh.harvard.edu Cc: batuhan.er...@umram.bilkent.edu.tr; astev...@nmr.mgh.harvar

Re: [Freesurfer] Two problematic participants -- unable to run recon-all

2018-11-30 Thread Rosalia Dacosta Aguayo
External Email - Use Caution HI Bruce, I would like to use Email File Drop but I am having problems, not sure if with my email or with my password. Could you help me with this? Thanks On Tue, Nov 27, 2018 at 4:27 PM Bruce Fischl wrote: > instructions are here: > > https://surfe

Re: [Freesurfer] Correspondence between regions of Harvard-Oxford & DKT atlases

2018-11-30 Thread Tudor Popescu
External Email - Use Caution Hi Bruce, I don't think it is.. It would of course be impossible to establish a 1:1 correspondence between regions, given that the H.-Oxf. is based on volumetric labeling of folding patterns. Assuming there is no quantitative correspondence/transforma

[Freesurfer] Segmentation of hippocampal subfields on FS v6 stable data?

2018-11-30 Thread ts+ml
External Email - Use Caution Dear FreeSurfer experts, we would like to use the 'Segmentation of hippocampal subfields and nuclei of the amygdala' feature [1] that is available in the development version of FreeSurfer. However, we already pre-processed all subjects from the stu