Re: [Freesurfer] recon-all -hires option

If you want to try to do it systematically, you can add -wsless (should reduce the agressiveness of the skull strip) On 1/4/2021 3:52 AM, falk.luesebr...@med.ovgu.de wrote: External Email - Use Caution Hi Simon, in case your surfaces (and other out

Re: [Freesurfer] recon-all -hires

on it. Thanks Mona From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Friday, February 22, 2019 1:07:42 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all -hires sometimes the -hires flag does not work

Re: [Freesurfer] recon-all -hires

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <mailto:fis...@nmr.mgh.harvard.edu> Sent: Thursday, February 21, 2019 2:23:14 PM To: Freesurfer support list Subject: Re: [Freesurfer] recon-all -hires Hi MO

Re: [Freesurfer] recon-all -hires

Hi MOna what was your full command line? And can you send us the recon-all.log file? cheers Bruce On Thu, 21 Feb 2019, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts I was running recon-all command with hires flag for our high resolution fMRI  data, but it has been in a constant sta

Re: [Freesurfer] Recon-all Hires Segmentation Failure

Hi Gio, did you check the output of the skull stripping? It is the most likely culprit. It's hard to tell from those images, but if the lateral cortex gets significantly darker than more medial stuff (which happens at high field) you might need to add some control points in the white matter o

Re: [Freesurfer] Recon-all -hires

I'm glad to hear it worked out Bruce On Tue, 28 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Thanks for your tip. Actually, it didn't work for me. I went to ask one of my colleagues, Martin Reuter, for help, and it turns out that the permission of my files in the $FREESURFER_HOME/bin folder have

Re: [Freesurfer] Recon-all -hires

Dear Bruce, Thanks for your tip. Actually, it didn't work for me. I went to ask one of my colleagues, Martin Reuter, for help, and it turns out that the permission of my files in the $FREESURFER_HOME/bin folder have been changed to 'read only'. Martin helped me to change the files in the $FREESURF

Re: [Freesurfer] Recon-all -hires

you need to change your path so that which recon-all gives you the v6 one. something like: set path = ($FREESURFER_HOME/bin $path) rehash where FREESURFER_HOME points to the v6 version cheers Bruce On Wed, 22 Nov 2017, Hwee Ling Lee wrote: Dear Bruce, Sorry about the screenshot of text.

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] 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

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

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

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

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

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, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-

Re: [Freesurfer] Recon-all -hires

Dear Bruce, Thanks for your reply. I checked the folder and did not find the file that was requested. What I have in the average folder that has 'RB*.gca' are 'RB_all_2016-05-10.vc700.gca' and 'RB_all_withskull_2016-05-10.vc700.gca'. The other file in that folder is 'RB_all_2008-03-26.mni152.2mm.

Re: [Freesurfer] Recon-all -hires

Hi Hweeling what is FREESURFER_HOME set to in the environment? Does that file exist? It is a standard part of our distribution cheers Bruce On Tue, 21 Nov 2017, Hwee Ling Lee wrote: > Dear all, > > I have T1 images collected from the 7T MRI scanner. > > I downloaded the most recent frees