Hi, Bruce, I'm wondering where I can get this system-wide FreeSurfer 5.1 download? Also, is there any manual or instruction for installation on multi-user clusters?
Thank you very much! Zheng Wang -----邮件原件----- 发件人: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 freesurfer-request@nmr. mgh.harvard.edu 发送时间: 2012年8月22日 0:00 收件人: freesurfer@nmr.mgh.harvard.edu 主题: Freesurfer Digest, Vol 102, Issue 23 Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. mri_convert introduces flip (Janosch Linkersd?rfer) 2. freesurfer license on multi-user cluster (John Donners) 3. QDEC's clusters and connectivity maps (Antonella Kis) 4. Re: freesurfer license on multi-user cluster (Bruce Fischl) 5. Re: Edits to aparc+aseg.mgz (Sarosh, Cyrus) 6. Convert QDEC clusters on the MNI_152_T1 space (Antonella Kis) ---------------------------------------------------------------------- Message: 1 Date: Tue, 21 Aug 2012 13:42:43 +0200 From: Janosch Linkersd?rfer <notes4ja...@googlemail.com> Subject: [Freesurfer] mri_convert introduces flip To: freesurfer <freesurfer@nmr.mgh.harvard.edu> Message-ID: <bc636725-64b9-4919-b13d-a270261a1...@googlemail.com> Content-Type: text/plain; charset="iso-8859-1" Hi experts, I?m trying to convert original images in native space from the LPBA40-Atlas (http://www.loni.ucla.edu/Atlases/LPBA40/) from img/hdr to nii/nii.gz. Conversion always results in a left/right flip. Also, mri_convert complains that no .mat file is available but there are no mat files provided... Here my command and output: mri_convert S01.native.mri.img S01.native.mri.nii.gz $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from S01.native.mri.img... ----------------------------------------------------------------- INFO: could not find /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in /Users/Januz/Downloads/__Tests/__test/S01.native.mri.mat file ----------------------------------------------------------------- TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 1, 0) k_ras = (0, 0, 1) writing to S01.native.mri.nii.gz... Thanks for your help, Janosch -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20120821/9a 5f1637/attachment-0001.html ------------------------------ Message: 2 Date: Tue, 21 Aug 2012 15:52:00 +0200 From: John Donners <john.donn...@sara.nl> Subject: [Freesurfer] freesurfer license on multi-user cluster To: <freesurfer@nmr.mgh.harvard.edu> Message-ID: <50339280.3020...@sara.nl> Content-Type: text/plain; charset="ISO-8859-1"; format=flowed Dear developers, I just installed freesurfer 5.1.0 system-wide on one of our clusters. All of our users can now access the software, although there is only one license key in the installation directory. Maybe you prefer that every user on our system uses their own license key for your usage statistics? An environment variable FREESURFER_LICENSE could maybe be used for this purpose? Or an additional check for a local license file ~/.freesurfer_license? With regards, John -- John Donners Consultant OSD SARA Science Park 140 1098 XG Amsterdam T +31 (0)20 592 3055 F +31 (0)20 668 3167 M +31 (0)6 1903 9023 E john.donn...@sara.nl www.sara.nl ------------------------------ Message: 3 Date: Tue, 21 Aug 2012 07:04:48 -0700 (PDT) From: Antonella Kis <ator...@yahoo.com> Subject: [Freesurfer] QDEC's clusters and connectivity maps To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <1345557888.55711.yahoomail...@web121701.mail.ne1.yahoo.com> Content-Type: text/plain; charset="iso-8859-1" Dear FS team, I am trying to find what is the? connection between white matter tracts with reduced FA and a number of cortical regions/clusters with significant reduction in cortical thickness from QDEC. Is there a way to overlap my cortical regions with reduced thickness more exactly the clusters from QDEC on the connectivity maps in FSL. How I create a mask of the QDEC clusters and used them in tractography?? The tractography/ connectivity maps has been performed on the MNI standard space. Any suggestion will be greatly appreciated. Antonella -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20120821/9f d028b2/attachment-0001.html ------------------------------ Message: 4 Date: Tue, 21 Aug 2012 10:07:22 -0400 From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freesurfer license on multi-user cluster To: John Donners <john.donn...@sara.nl> Cc: "<freesurfer@nmr.mgh.harvard.edu>" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <d986a7a2-70f1-470a-a117-a5ff7f650...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii Hi John We prefer but don't require that every user download a license Thanks for asking Bruce On Aug 21, 2012, at 9:52 AM, John Donners <john.donn...@sara.nl> wrote: > Dear developers, > > I just installed freesurfer 5.1.0 system-wide on one of our clusters. > All of our > users can now access the software, although there is only one license key > in the installation directory. Maybe you prefer that every user on our > system > uses their own license key for your usage statistics? An environment > variable > FREESURFER_LICENSE could maybe be used for this purpose? > Or an additional check for a local license file ~/.freesurfer_license? > > With regards, > John > > -- > John Donners > Consultant > OSD > SARA > Science Park 140 > 1098 XG Amsterdam > T +31 (0)20 592 3055 > F +31 (0)20 668 3167 > M +31 (0)6 1903 9023 > E john.donn...@sara.nl > www.sara.nl > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > ------------------------------ Message: 5 Date: Tue, 21 Aug 2012 14:44:47 +0000 From: "Sarosh, Cyrus" <csar...@med.umich.edu> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <67b549f7c6690c4ea53a8e63f2eca00d13a29...@uhexmbspr11.umhs.med.umich.edu> Content-Type: text/plain; charset="us-ascii" Doug, Thanks for the update and not much time was wasted so no worries. I edited the brainmask.mgz file and ran the new recon-all command with autorecon-pial, which created a new brain.finalsurfs.mgz with the dura edited out and correct surfs. New stat files were created, but no new aparc+aseg.mgz file. Loading this file still shows the segmentation including dura in the cortex and the modification date is the original recon-all date. Is there any way to create a new aparc+aseg.mgz file with this new surf data? Thanks, Cyrus -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr. mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, August 20, 2012 2:18 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz Hi Cyrus, my apologies, I told you to edit the wrong file. You should edit brainmask.mgz, not brainmask.finalsurfs.mgz. Sorry about, I hope you did not waste too much time. doug On 08/20/2012 09:31 AM, Sarosh, Cyrus wrote: > Doug, > > I edited the dura from the brain.finalsurfs.mgz file using the command tkmedit (subject ID) brain.finalsurfs.mgz -aux T1.mgz -surfs and going through the necessary slices that need fixing and erase the dura. I then ran this subject with the command recon-all -subjid (subject ID) -autorecon-pial. Looking at the date modified information it appears that new stat files were created, but no new aparc+aseg.mgz file was created. I loaded the brain.finalsurfs.mgz file, which contained a modify date of when I ran the new recon-all command and it looked identical to the original brain.finalsurfs.mgz file, so all of my edits were gone and all of the surfs were incorrect just like before. Also, loading the aparc+aseg.mgz file it looks identical to the previous aparc+aseg.mgz, so no changes were made. Looking at the log it appears my edits were useless because the first step that runs is the -maskbfs step which appears to generate the brain.finalsurfs.mgz file. So, do I need to edit a different file or was my command line incorrect? > > Thanks, > > Cyrus > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Tuesday, August 14, 2012 1:43 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz > > > For GM volume and thickness, you will certainly want to fix it. Given how big the PET voxels are, it might not be such a big deal for that. To fix it, you would edit the dura from the brain.finalsurfs.mgz and run recon-all with -autorecon-pial. This will fix aparc+aseg and re-generate the stats files. > doug > > > On 08/14/2012 01:40 PM, Sarosh, Cyrus wrote: >> Doug, >> >> Well we want to use the stats information for gray matter volume and thickness of certain vois and we want to use the aparc+aseg file to run PET image analysis to collect data from certain vois. Would performing the given actions correct any incorrect data in the stats files and create a new aparc+aseg.mgz file or will this require separate actions? >> >> Thanks, >> >> Cyrus >> >> -----Original Message----- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >> N Greve >> Sent: Tuesday, August 14, 2012 11:28 AM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz >> >> >> Depending upon how bad it is and what you are going to do with it, it may be a good idea to edit the brain.finalsurfs.mgz to remove the dura, then run recon-all -autorecon-pial ... >> doug >> >> >> On 08/14/2012 11:18 AM, Sarosh, Cyrus wrote: >>> Doug, >>> >>> I looked at the surface files by using the command -tkmedit (subject ID) brainmask.mgz -surfs -aseg. I also viewed the same surfs using the T1.mgz file. The pial surface (red line) does identify the dura as part of the cortex, but it doesn't look as bad as the aseg.mgz vois made it appear. >>> >>> Cyrus >>> >>> -----Original Message----- >>> From: freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas >>> N Greve >>> Sent: Monday, August 13, 2012 4:13 PM >>> To: freesurfer@nmr.mgh.harvard.edu >>> Subject: Re: [Freesurfer] Edits to aparc+aseg.mgz >>> >>> Hi Cyrus, this may or may not be a problem. The cortical label in >>> aseg.mgz is not used for this reason. Usually, the surface-based >>> method will exclude the dura in these situations. Are the surfaces >>> accurate or are they including dura as well? BTW, you should not be >>> editing the >>> aparc+aseg.mgz. >>> doug >>> >>> On 08/13/2012 01:04 PM, Sarosh, Cyrus wrote: >>>> Hello FreeSurfer Users, >>>> >>>> I looked for a possible solution to my problem in the Mail Archive and found this article referring to almost the exact same problem I am having: >>>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06314. >>>> h t ml. Basically,pieces of the subarachnoid space/pia >>>> mater/arachnoid/dura mater/skull are being segmented as the cortex >>>> in certain slices and this occurs when it is physically adjacent to the gray matter. Besides this point everything else seems to be running smooth. >>>> In the related article I found that this may be caused by the MR parameters so I will give you the acquisition information that I know. >>>> Theacquisitions are SPGRs, taken on either a GE 3T or 1.5T and the >>>> resolution is 1mm isotropic. Any solutions besides going through >>>> each series slice by >>>> slice and making corrections would be greatly appreciated. >>>> >>>> Thanks, >>>> >>>> Cyrus >>>> >>>> ********************************************************** >>>> Electronic Mail is not secure, may not be read every day, and >>>> should not be used for urgent or sensitive issues >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> _______________________________________________ >>> 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. >>> >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should >>> not be used for urgent or sensitive issues >>> >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should >> not be used for urgent or sensitive issues >> >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues > > > _______________________________________________ > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues ------------------------------ Message: 6 Date: Tue, 21 Aug 2012 08:06:46 -0700 (PDT) From: Antonella Kis <ator...@yahoo.com> Subject: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Message-ID: <1345561606.93798.yahoomail...@web121705.mail.ne1.yahoo.com> Content-Type: text/plain; charset="us-ascii" Dear All, Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template? Thank you. Antonella -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20120821/63 6cffe1/attachment-0001.html ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 102, Issue 23 ******************************************* _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
