[Freesurfer] unit for hippocampus segmentation results

Hi freesurfer experts, We used the development version of freesurfer 6.0 to segment hippocampus. We are wondering what the unit is for the segmentation results. Thanks, -- Fengji Geng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

[Freesurfer] freesurfer 6.0 release date

not, we will just switch to fs 5.3. Thanks! -- Fengji Geng ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it

[Freesurfer] Error using mkdir for the segmentation of hippocampal subfields using FreeSurfer 6

Dear FreeSurfer Users, I was trying to segment hippocampal subfields using FreeSurfer 6 with data that have already undergone the FreeSurfer 5 pipeline recon-all -all. According to the usage described on the webpage of HippocampalSubfields (http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSub

[Freesurfer] 'mkdir' error during the segmentation of hippocampal subfields using FreeSurfer 6 [2nd request for help]

Dear FreeSurfer Users, I sent an email to this maillist a couple of weeks ago asking help for the error that I encountered after running 'recon-all -s ${Mysubject} -hippocampal-subfields-T1' with freesurfer 6. The content of this email is attached below. Since then, my colleague and I have been

[Freesurfer] problem with hard coded directory (/scratch)

Dear all, I am currently using freesurfer 6.0 (development version) to run hippocampal subfields segmentation and encountered a 'mkdir' error, which is attached below. Our troubleshooting found that some scripts in the ...freesurfer/dev/sys/bin directory with things like: if(-e /scratch) se

[Freesurfer] FW: problem with hard coded directory (/scratch)

, - Fengji From: Fengji Geng Sent: Thursday, December 03, 2015 8:30 AM To: freesurfer@nmr.mgh.harvard.edu Subject: problem with hard coded directory (/scratch) Dear all, I am currently using freesurfer 6.0 (development version) to run hippocampal subfields

[Freesurfer] segmentation fault (core dumped)

Hi Bruce, I have uploaded all the data to the server. The command that I run is 'recon-all -all -s $s -hippocampal-subfields-T1T2 $s/T2/*.mgz T1T2'. It would be great if you could keep us updated on how the fixing is going. Thanks! --

[Freesurfer] FW: problem with hard coded directory (/scratch)

n the bin directory that match the string "scratch". Could you also fix them? Thank you! - Fengji ____ From: Fengji Geng Sent: Sunday, December 06, 2015 9:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: FW: problem with hard coded directory (/scratch)

[Freesurfer] FW: problem with hard coded directory (/scratch)

n the bin directory that match the string "scratch". Could you also fix them? Thank you! - Fengji ____ From: Fengji Geng Sent: Sunday, December 06, 2015 9:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: FW: problem with hard coded directory (/scratch)

[Freesurfer] FW: problem with hard coded directory (/scratch)

scratch)". However, there are still a lot of binaries in the bin directory that match the string "scratch", which cause the same error that I encountered before. I am wondering if it is possible for you to fix '/scratch' in the bin directory. Thank you! ----- Fengji

Re: [Freesurfer] FW: problem with hard coded directory (/scratch)

roblem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks l

[Freesurfer] FW: FW: problem with hard coded directory (/scratch)

Hi FS's experts, I sent out a couple of emails to seek for help on an error from running recon-all using freesurfer 6.0 beta. Could anyone help with the question? Thank you! - Fengji From: Fengji Geng Sent: Thursday, January 07, 2016 8:15 AM To: frees

[Freesurfer] FW: problem with hard coded directory (/scratch)

Hi Fengji, you have sent several emails. I keep asking you to give us a specific binary that has the problem, but you seem to ignore my request, wait a couple of weeks, then post the question back to the list. I'm happy to take look, but plea

Re: [Freesurfer] recon-all: core dumped error (Bruce Fischl)

. The good news is that it's fast - just a couple of min/hemi cheers Bruce On Tue, 26 Jan 2016, Fengji Geng wrote: > Hello fs experts, > > We ran a command like ?recon-all -all -s HMN002 -hippocampal-subfields-T1T2 > HMN002/T2/*.mgz T1T2?. Then, there was an error as ?A

Re: [Freesurfer] recon-all: core dumped error

mean. If you tell us your hardware/software environment Zeke can get you a binary On Thu, 28 Jan 2016, Fengji Geng wrote: > > Hi Bruce, > > Did you mean an updated version of mri_parcellate? If so, it would be gr

[Freesurfer] running two versions of fs in the same dataset

Dear fs developers, we are attempting to use the stable version of fs 5.1 for processing while also using the most current version for hippocampal segmentation on the same set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when the develop version of fs 6 was installed, we be

Re: [Freesurfer] running two versions of fs in the same

exist yet. cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: > Dear fs developers,? > > we are attempting to use the stable version of fs 5.1 for processing while > also using the most current version for hippocampal segmentation on the same > set of subjects (freesu