Re: [Freesurfer] Recon-all -hires

Hi Bruce, I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)". Cheers, Hweeling On 21 November 2017 at 23:57, Bruce Fischl wrote: > oh, this may be a version mismatch then. Which version of FS are you using? > > On Tue, 21 Nov 2017, Hwee Ling Lee wrote: > > Dear Bruce, >> T

Re: [Freesurfer] Recon-all -hires

Dear FS developers, I have problem as follow when I tried file input/output (original images can not be identified) Xues-MacBook-Air:0001 DannyDeng$ recon-all -i im_0001.dcm ERROR: must specify a subject id Xues-MacBook-Air:0001 DannyDeng$ recon-all -i IM_0001.dcm -s anon mkdir: /Applica

[Freesurfer] make_average_subject label files

Dear Freesurfer experts, I have a question related to make_average_subject command and Freesurfer versions. When I used to create my average subject with Freesurfer 5.3, I got lh.cortex.label and rh.cortex.label files inside label folder with 149955 vertexs. Moreover, lh.Medial_Wall.label and

Re: [Freesurfer] Tessellation: factors that could affect number and size of faces

Hi Avi 1. the size of the triangles is currently specified more-or-less by the resolution of the input data. We cover the surface of voxels. 2. The triangles start life as uniform, but then smoothing and topology correction will make them different sizes. It's hard to predict where. cheers

Re: [Freesurfer] Back to native space after registration

Hi Avi we do all our analysis in native space, so there is no "putting back". cheers Bruce On Wed, 22 Nov 2017, Avideh Gharehgazlou wrote: Hi experts, Will you please briefly explain to me the rationale behind why subjects put back into their original space after alignment to the template

Re: [Freesurfer] Problems with FtpFileExchange

Hi Rosalia at that point you should just be able to type: put S_001.zip which should copy it to our ftp site. cheers Bruce On Wed, 22 Nov 2017, Rosalia Dacosta Aguayo wrote: Dear FreeSurfer Developers, I am having problems with FtpFileExchange. I am trying to upload a compressed file

Re: [Freesurfer] Recon-all -hires

can you send us the recon-all.log? On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Hi Bruce, I downloaded the latest version of freesurfer, "CentOS 6 x86_64 (64b)". Cheers, Hweeling On 21 November 2017 at 23:57, Bruce Fischl wrote: oh, this may be a version mismatch then. Which version of F

Re: [Freesurfer] Recon-all -hires

Hi Danny you need to specify a subject name/id with -s cheers Bruce On Wed, 22 Nov 2017, Danny Deng wrote: Dear FS developers, I have problem as follow when I tried file input/output (original images can not be identified) Xues-MacBook-Air:0001 DannyDeng$ recon-all -i im_0001.dcm ERRO

Re: [Freesurfer] Recon-all -hires

Hi Hweeling please don't send us screenshots of text - either attach the file or include text in the email. I'm pretty sure you are using an older recon-all script with a newer FREESURFER_HOME. Try typing: which recon-all I bet it points to somewhere other than your V6 FREESURFER_HOME/bin

[Freesurfer] Eklund's 2016 and FreeSurfer

Hi, I was wondering if there is any paper published by FreeSurfer team or FreeSurfer experts (after Eklund's 2016 paper) stating that the cluster failure issue is not an issue in FreeSurfer toolbox and/or whether CFT of less than 0.05 or 0.01 to estimate cortical thickness/volume/area maps is fine

[Freesurfer] Job opening: postdoc in AFNI group of NIH

Hello- The Scientific and Statistical Computing Core (a.k.a. the AFNI group) at the NIMH, NIH (Bethesda, MD, USA) is lookin' to hire a postdoc, particularly someone with C and/or C++ experience, with Python and OpenGL skills also being quite useful. If you like problem solving and working with a

Re: [Freesurfer] Recon-all -hires

Dear Bruce, Sorry about the screenshot of text. You are right that it still uses the older version of recon-all. How do I fix this then? I can't delete the older version because I don't have access to it at all. Thanks for your patience. Cheers, Hweeling On 22 November 2017 at 15:52, Bruce F

Re: [Freesurfer] Skullstrip commands not working {Disarmed}

ing with a fun group of people, then check out the attached advertisement for details. (And please feel free to forward on.) --pt -- next part -- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20171122/e12d

Re: [Freesurfer] QC on CVS registration

Hi Chintan, Can you send your snapshot again? I do not have access to the attachment. Best, Lilla On Mon, 13 Nov 2017, Mehta, Chintan wrote: Dear FreeSurfer users, I'm using FS 6.0. I registered MRI scans to the CVS-Avg35 template (mri_cvs_register) and viewed output. While the nonlinear

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Could tell me which is the whole brain volume,please? I'm not sure which is right. I need your help. Thanks very much. Zheng At 2017-11-22 11:07:36, "Bruce Fischl" wrote: >no, eTIV is the estimated volume of the intracranial vault, so it >included sulcal CSF. I think

Re: [Freesurfer]  hippocampus subfields

Sorry, I don’t remember. You can search on the wiki or maybe someone else will chime in Bruce > On Nov 22, 2017, at 8:30 PM, 郑凤莲 <13181786...@163.com> wrote: > > Hi Bruce, > > Could tell me which is the whole brain volume,please? I'm not sure which > is right. I need your help. > > Th

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, It's OK. Thank you very much for your reply ! I will find it in other way. Sincerely, Zheng At 2017-11-23 11:37:37, "Bruce Fischl" wrote: Sorry, I don’t remember. You can search on the wiki or maybe someone else will chime in Bruce On Nov 22, 2017, at 8:30 PM, 郑凤莲 <13181786...

[Freesurfer] LGI

Hi experts, I am using Freesurfer 6.0 for LGI. I ran recon-all and got the map of LGI. My question is that can I get the specific value of every gyrus as the value of thickness in the file of lh.aparc.stats? I can't find it from stats direction. Thanks a lot ! Zheng__

[Freesurfer] Qdec

Hi professors, I am using Qdec in Freesurfer. I want to study the relationships between age and cortical thickness, age and cortical volume, age and surface area. Is it necessary to corrected by eTIV for volume and surface area in Qdec? I am looking forward to your reply. Thanks, Z