Re: [Freesurfer] bvals and bvecs for dt_recon

s. On Thu, 13 Mar 2014, Chris Watson wrote: > dcm2nii should give you bvecs and bvals > If you just want to transpose the file, I wrote a script to do it (attached). > > On 03/13/2014 04:50 PM, Gennan Chen wrote: > > Anastasia, > > The thing not clear from me is the format

Re: [Freesurfer] bvals and bvecs for dt_recon

Message- From: Anastasia Yendiki [mailto:ayend...@nmr.mgh.harvard.edu] Sent: Thursday, March 13, 2014 1:37 PM To: Gennan Chen Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bvals and bvecs for dt_recon How is the format different? Is it in 3 rows instead of 3 columns? If so, it

[Freesurfer] bvals and bvecs for dt_recon

Hi! All, Is there an utility to extract bvals and bvecs from GE’s DTI dicom files into the format dt_recon can use? I try to run dt_recon as it is but it did not pick up those values. Those files are from ADNI. Gen This email message is for the sole use of the

Re: [Freesurfer] dt_recon error for Siemens mosaics image

Subject: Re: [Freesurfer] dt_recon error for Siemens mosaics image has it been anonymized? On 02/11/2014 02:23 PM, Gennan Chen wrote: > HI! All, > > I got an error when I ran dt_recon > > WARNING: file /Users/gnchen/tmp/3011_DTI/orig/MR01.dcm does not > contain a Siemens AS

[Freesurfer] dt_recon error for Siemens mosaics image

this?? -- Gennan Chen This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient

[Freesurfer] algorithm developer position open

. Good problem solving, technical troubleshooting, organizational, interpersonal and team skills. Gennan Chen Engineering Manager, Synarc This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information

[Freesurfer] possible pial surface editing

Hi! All, We ran into a few cases which the wm matter surface is pretty decent but pial surface did not go far enough to include all gray matter. Is there a way to fix this? Gen This email message is for the sole use of the intended recipient(s) and may contain

Re: [Freesurfer] error while running autorecon1 and autorecon2 in fs-v5.3

Does 5.3 assume recon-all -all will always run first? Since ribbon.mgz will not get created till autorecon3. In V4, that is part of autorecon2 though. Gen On Thu, May 30, 2013 at 12:24 AM, Mehul Sampat wrote: > ps: i believe my error is the same as the one in this thread: > > http://www.mail-a

Re: [Freesurfer] FS 5.2-beta run-times on Amazon Web services (AWS)

I agree with Pedro. For running a large dataset on ec2, it is better to launch a lot of instances m1.medium. Gen From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Pedro Paulo de Magalhães Oliveira Junior Sent: Saturday, February 02, 2013

[Freesurfer] position open

development. Please send resume to me directly. Thanks Gennan Chen (gennan.c...@synarc.com) Engineering Manager, Engineering Department, CCBR-Synarc (www.synarc.com) Algorithm Development Engineer Analyzes, prototype, designs, programs, debugs, and modifies medical imaging processing algorithms

Re: [Freesurfer] Errors with recon-all -autorecon2

Linda, You might want to check if the disk is full or not by using df command. Gen On Nov 19, 2011, at 12:13 AM, Linda Zhang wrote: Hi, I'd been having trouble with "recon-all -all -subjid [mysubject]", so I broke it down with -autorecon1 and -autorecon2. -autorecon1 worked fine, it seems th

Re: [Freesurfer] iPhone and IPad FreeSurfer based atlas

Hi! Pedro, Do you plan to release the source code? I did write an iphone app last year for a lung cad product. We abandon the project at the end. The biggest problem we have is finger is not really great for point and click compared to stylus. It always stand in the way between your eyesight and t

Re: [Freesurfer] scp issue??

11 AM, Gennan Chen wrote: > Hi! All, > > I download and install > freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 on my macbook pro > yesterday. After that, scp command from terminal is not working > anymore. Below is an example: > > gnc...@mbp:tmp]$ scp -i ~/.ssh/id

[Freesurfer] scp issue??

Hi! All, I download and install freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 on my macbook pro yesterday. After that, scp command from terminal is not working anymore. Below is an example: gnc...@mbp:tmp]$ scp -i ~/.ssh/id_dsa.pub sdg.zip macpro:~/tmp freesurfer-Darwin-leopard-i686-s

Re: [Freesurfer] ftp server down??

Working now. Gen On Tue, Aug 24, 2010 at 8:49 PM, Gennan Chen wrote: > Will do. > > Gen > > > On Tue, Aug 24, 2010 at 8:10 PM, Paul Raines > wrote: >> Try back in 24 hours.  Our storage servers are down right now >> >> On Tue, 24 Aug 2010, Gennan Chen wr

Re: [Freesurfer] ftp server down??

Will do. Gen On Tue, Aug 24, 2010 at 8:10 PM, Paul Raines wrote: > Try back in 24 hours.  Our storage servers are down right now > > On Tue, 24 Aug 2010, Gennan Chen wrote: > >> No. Still down. >> >> Gen >> >> >> >> On Tue, Aug 24, 2

Re: [Freesurfer] ftp server down??

No. Still down. Gen On Tue, Aug 24, 2010 at 6:30 PM, Bruce Fischl wrote: > Hi Gen, > > yes, we've had some local hardware issues. Is it up now? > > cheers > Bruce > On Tue, 24 Aug 2010, Gennan Chen wrote: > >> Hi! >> >> I cannot download any

[Freesurfer] ftp server down??

Hi! I cannot download anything from ftp://surfer.nmr.mgh.harvard.edu/pub. Is it down? Gen ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intende

Re: [Freesurfer] CUDA support in 5.0

e new 5.0 release, or > > are they created on the fly by FreeSurfer, or are they just plain > > missing? FWIW, I have CentOS 5 x86_64 version of FreeSurfer > > installed, running on OpenSuse 11.3 > > > > > > recon-all -s PC exited with ERRORS at Tue Aug 17

Re: [Freesurfer] recon-all error

Carl, Looks like you only use relative path. You need to put in absolute path. Something like setenv FREESURFER_HOME /home/carl/Desktop/freesurfer Gen On 8/17/10 9:14 AM, "Carl Dambkowski" wrote: Hi, again (I've emailed once before), I am trying to test my freesurfer installation and everyt

[Freesurfer] CUDA support in 5.0

Hi! I will like to try the beta CUDA support in 5.0. And I have some questions here 1. Are all needed libraries bundled in the release? Or I need to go to CUDA's site to get those dependency? And if I need to, what are those dependency I need to grab and install? 2. I have RH 5 64 bit lin

[Freesurfer] mri_convert sort dicom files??

Hi! Does mri_convert sort dicom files in a different way for Siemens' dicom file? I have dicom files from GE, Philips and Siemens. They have the same ImagePositionPatient and SliceLocation tags. But volume from Siemens flip in the 3rd dimension? Why is it?? I know it doesn't matter as long as

[Freesurfer] mapping surface file??

Hi! I was able to use mri_convert to reslice aprc+aseg.mgz to the original dicom coordinates/space. However, I wonder if I need to do the same for all surface files, i.e. mapping vertex coordinate to different one. If I need to do that, which utility should I use? Gen