Re: [Freesurfer] bvals and bvecs for dt_recon
Anastasia, The thing not clear from me is the format for those files. I did not see an example anywhere in the wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do you have an example? I know how to get those from private dicom tags. Gen -Original 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 should be straightforward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: 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 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] bvals and bvecs for dt_recon
Thxs for all the help. On March 13, 2014 at 2:19:16 PM, Louis Nicholas Vinke (vi...@nmr.mgh.harvard.edumailto:vi...@nmr.mgh.harvard.edu) wrote: Attached are examples of the bvals.dat and bvecs.dat files extracted from siemens dicoms by dt_recon. This was for a 60 dir DTI scan w/ 10 b0s. 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 for those files. I did not see an example anywhere in t he wiki or in the distribution. And I am downing tutorial data now. Hope it is there. BTW, do yo u have an example? I know how to get those from private dicom tags. Gen -Original 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 should be straightfo rward to convert it yourself from 3 rows to 3 columns. On Thu, 13 Mar 2014, Gennan Chen wrote: 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 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator The information in this e-mail is intended only for the person to whom it is addressed. If you be lieve this e-mail was sent to you in error and the e-mail contains patient information, please co ntact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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 prohibite d. If you are not the intended recipient, please contact the sender by reply email and destroy al l copies of the original message. If you are the intended recipient, please be advised that the c ontent of this message is subject to access, review and disclosure by the sender's Email System A dministrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] dt_recon error for Siemens mosaics image
Possible. Can you give me DICOM tag/tags the program looks for?? Gen -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, February 12, 2014 8:24 AM To: freesurfer@nmr.mgh.harvard.edu 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 ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I can confirm it is Siemens mosaics format. Any idea how to by pass 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] dt_recon error for Siemens mosaics image
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 ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header I can confirm it is Siemens mosaics format. Any idea how to by pass 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] algorithm developer position open
Hi! All, We have an algorithm developer position open at Synarc. If you are interested, please send me your resume. Position Description: The algorithm developer engineer works with our scientific groups to come up innovative image processing and data mining/pattern recognition algorithms to maintain scientific lead in all TA areas Responsibilities: Work with Scientists and TA lead on surveying literature /algorithms and existing commercial implementation for specific tasks. Prototype and validating algorithms on large dataset by using in house cluster or Amazon EC2. Prototype related UI elements and addressing integration on Synarc internal proprietary platform. Work with Scientists and TA lead on journal/conference publications and intellectual properties related document. Qualifications: Education: PhD in biomedical engineering, physics, applied math or computer science Experience: Must be expert in ITK and Matlab Familiar with HPC like condor or SGE is a must have Experience with EC2 will be a plus Experience with VTK or QT will be a plus. Experience with Python/Java/SQL will be a plus Skills: Good written and verbal communication skills. 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. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[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 confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 mpsam...@gmail.com wrote: ps: i believe my error is the same as the one in this thread: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg28047.html Mehul On Thu, May 30, 2013 at 12:13 AM, Mehul Sampat mpsam...@gmail.com wrote: Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] position open
Hi! We have an algorithm developer position open. Below is the job description. Although it stats in a very general term, the person will spend most of time working on freesurfer related algorithms and services. Experience in PhD or Post doc did count as long as it is related to algorithm 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 used in clinical trials settings. Responsibilities: * Prototype, Design, develop, unit test and release medical imaging processing algorithms to support Synarc's business. * Work with end users to understand requirements. * Write and contribute to design specifications, installation guides and other technical documentation in accordance with Synarc best practices. * Work with other technical staff to support system installations, upgrades, and configurations of software. * Assist in training of users and creation of user manuals. * Ensure that systems are released in accordance with regulatory and Synarc standards. * Work with end users, other developers, software QA, product managers and software project managers to deliver applications, bug fixes and enhancements. * Use professional experience to provide creative, effective solutions to complex problems. Qualifications: Education: PhD in biomedical engineering, physics or computer science Experience: 4+ years of design and implement complex medical imaging algorithms in related fields such as registration and segmentation. Expert in Matlab and extending Matlab in C/C++ Experience in Freesurfer and related processing stream. Experience with DICOM standard Experience with cloud, cluster and other high performance computation environment. Experience with Java enterprise application development stack Experience with SQL and relational database Skills: Good problem solving, technical troubleshooting, organizational, interpersonal and team skills. Good written and verbal communication skills. 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 that the problem is somewhere in -autorecon2. I've included the system information below, as well as the error message I got, and the recon-all log. I've tried this with another subject as well and the same error occurs. It'd be great if someone could tell me what the problem is and how I can fix it. - FREESURFER_HOME: /home/virtualuser/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Debian version: squeeze/sid Kernel info: Linux 2.6.31-23-generic i686 - The command line: FreeSurfer:~/freesurfer/subjects recon-all -subjid avo0260 -autorecon2 The error message: GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is: gzip -f -c transforms/talairach.m3z GCAMwrite:: the popen error code is: 12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-- #@# CA Reg Inv Fri Nov 18 11:23:25 EST 2011 /home/virtualuser/freesurfer/subjects/avo0260/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FreeSurfer 2.6.31-23-generic #75-Ubuntu SMP Fri Mar 18 18:08:39 UTC 2011 i686 GNU/Linux recon-all -s avo0260 exited with ERRORS at Fri Nov 18 11:23:26 EST 2011 The recon-all.log and recon-all.error files are attached. Thanks for your time and help! Regards, Linda Zhang University of Hong Kong recon-all.logrecon-all.error___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 the region you want to pick. Do you have any insight for how to solve that problem? Anyway, I finally got some free time to work on Osirix. I hope I can integrate freesufer pipeline and its visualization together at the end. Will tackle IO and visualization in next few weeks. if anyone is interested in joining some coding, please let me know. we can coordinate the effort. Gen 2010/8/27 Pedro Paulo de Magalhães Oliveira Junior p...@netfilter.com.br: Some weeks ago Bruce announced the first version of the free brain atlas app for IPhone using FreeSurfer aseg. Today we have a major upgrade and now the app has a native IPad interface. Also Bruce provided high resolution mri segmented so IPhone and IPod touch users will benefit too http://itunes.apple.com/br/app/isurf-brainview/id381072423?mt=8 Suggestions for the upcoming version ate welcome. Cheers Pedro Paulo Jr. -- via iPhone iOS4 ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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-stable-pub-v5.0.0 It shows freesurfer's version and did not copy file at all. I have no idea why scp command will have something to do with freesurfer. Does anyone know anything about this?? 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 intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] scp issue??
Sorry. I figure it out what went wrong. It has nothing to do with freesurfer installed. The problem is the machine I tried to scp to also has freesurfer's settings in .bashrc. Somehow source those .sh create a problem. Anyway, nothing to do with freesurfer. Gen On Thu, Aug 26, 2010 at 8:11 AM, Gennan Chen gnc...@gmail.com 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_dsa.pub sdg.zip macpro:~/tmp freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0 It shows freesurfer's version and did not copy file at all. I have no idea why scp command will have something to do with freesurfer. Does anyone know anything about this?? 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 intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ftp server down??
Working now. Gen On Tue, Aug 24, 2010 at 8:49 PM, Gennan Chen gnc...@gmail.com wrote: Will do. Gen On Tue, Aug 24, 2010 at 8:10 PM, Paul Raines rai...@nmr.mgh.harvard.edu 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, 2010 at 6:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu 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 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 intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- --- Paul Raines email: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] ftp server down??
No. Still down. Gen On Tue, Aug 24, 2010 at 6:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu 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 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 intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] ftp server down??
Will do. Gen On Tue, Aug 24, 2010 at 8:10 PM, Paul Raines rai...@nmr.mgh.harvard.edu 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, 2010 at 6:30 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu 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 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 intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- --- Paul Raines email: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129 USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 linux box with single NVIDIA FX card and macpro snow leopard box with dual NVIIDA GT 120. Does CUDA support work for both OS? If they do, any idea what the speed up will be?? Gen 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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 cld2...@columbia.edu wrote: Hi, again (I've emailed once before), I am trying to test my freesurfer installation and everything goes fine (tksurfer, qdec, etc). However, once I get to: recon-all -s bert -autoreco1 i get: FREESURFER_HOME: Undefined variable. However, I believe I've set it up properly with: setenv FREESURFER_HOME Desktop/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh And I get back: Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Desktop/freesurfer FSFAST_HOME Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii SUBJECTS_DIRDesktop/freesurfer/subjects MNI_DIR Desktop/local/freesurfer/mni With no errors. When I give the command: echo $FREESURFER_HOME I also get back: Desktop/freesurfer Any suggestions? Thanks, Carl 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] CUDA support in 5.0
Thx. Nick. Will give it a shot. BTW, is there also a plan for using OPENMP, MKL or ATLAS to speed it up a bit? A lot of off the shelf rack mounted servers cannot put those cards in. Gen On 8/17/10 10:03 AM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: i forgot to add: make sure you have the latest nvidia driver, which has support for cuda 3. n. On Tue, 2010-08-17 at 13:00 -0400, Nick Schmansky wrote: currently the _cuda binaries are distributed only in the centos4 and centos4_x86_64 distributions. however, those should work in centos5, and i've made a tarball of the _cuda binaries downloadable from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc look for the file 'fscudabins-linux-centos4_x86_64.tgz' and untar in your freesurfer/bin dir. ! note ! this is a beta release of these binaries! they havent been fully tested across a wide subject set, so don't use the -use-gpu flag in any kind of important group analysis yet. please let of us know though of any problems you encounter. we need to learn what kind of gpu cards people have out there in order to gauge how far we can optimize our routines. n. On Tue, 2010-08-17 at 11:35 -0500, joel bruss wrote: Not to hijack your question, but I have similar questions. I have CUDA toolkit 3.1 installed, cudadetect returns: Detecting CUDA... 32767 CUDA enabled device(s) detected. but, when I run recon-all, e.g.: recon-all -subjid PC -all -use-gpu I get the following errors at the mri_em_register_cuda step: /lcn2/lesion_warp.dir/MAP3_Nifti/freesurfer_subs.dir/PC/mri mri_em_register_cuda -skull nu.mgz /usr/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta mri_em_register_cuda: Command not found. Linux linux-lvmb 2.6.34-12-desktop #1 SMP PREEMPT 2010-06-29 02:39:08 +0200 x86_64 x86_64 x86_64 GNU/Linux A quick peak in /usr/freesurfer/bin shows that there is no mri_em_register_cuda binary. Are cuda binaries supposed to be bundled with the 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 11:14:35 CDT 2010 On Tue, Aug 17, 2010 at 11:07 AM, Gennan Chen gennan.c...@synarc.com wrote: 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 linux box with single NVIDIA FX card and macpro snow leopard box with dual NVIIDA GT 120. Does CUDA support work for both OS? If they do, any idea what the speed up will be?? Gen __ 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo
[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 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, please contact the sender by reply email and destroy all copies of the original message. If you are the intended recipient, please be advised that the content of this message is subject to access, review and disclosure by the sender's Email System Administrator ___ 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 is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
