Freesurfer June 2008

freesurfer@nmr.mgh.harvard.edu

58 participants
77 discussions

Prob:Software Download Tiger version \
by Liat Levita 16 Jun '08

16 Jun '08

Hi, I am trying to download the updated FreeSurfer - Mac OS X Tiger (10.4.11) PowerPC stable v4.0.5 15 June 2008 - freesurfer-Darwin-tiger-ppc-stable-pub-v4.0.5-full.dmg However, when I do so I keep getting the zipped Leopard package. I wonder if something is wrong with the link to the tiger version? Liat

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Re: [Freesurfer] HBM 2008
by Pedro Paulo de Magalhães Oliveira Junior 16 Jun '08

16 Jun '08

There is a very interesting poster using FreeSurfer (174-M) from Marije Jansen (Univ. Nottingham) - "Cortical Thickness and depression in a population-based sample of adolescents." The statistic method used there is very interesting to possibly be added in QDEC. 2008/6/15 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>: > he's there somewhere :) > > On Sun, 15 Jun 2008, Pedro Paulo de Magalhães Oliveira Junior wrote: > > Hi, >> I think some of us are in Melbourne these days in the HBM. >> >> If somebody is interested in exchanging experiences in FreeSurfer usage we >> can meet somewhere in this event. >> >> Actually I was looking for Doug :) >> >> Regards, >> >> Pedro Paulo Oliveira Jr >> >

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HBM 2008
by Pedro Paulo de Magalhães Oliveira Junior 15 Jun '08

15 Jun '08

Hi, I think some of us are in Melbourne these days in the HBM. If somebody is interested in exchanging experiences in FreeSurfer usage we can meet somewhere in this event. Actually I was looking for Doug :) Regards, Pedro Paulo Oliveira Jr

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question
by Valentina.Durastanti＠uniroma1.it 14 Jun '08

14 Jun '08

Hi, I'm starting to use Freesurfer to analyze SPGRs images and my question is: Do I have to use the average of two images (invol1 + invol2) or I just can use one SPGRs? Thanks Valentina

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Re: [Freesurfer] wiki problem
by Liat Levita 13 Jun '08

13 Jun '08

Hello, hope this helps. The quote from our security engineer regarding this issue. "That Harvard machine was doing what appeared to be shellcode NOPs, which is indicative of someone/something trying an exploit. Our policy on such things is that if we feel this to be a valid threatand we did at the timewe block the IP." Liat ----- Original Message ----- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Friday, June 13, 2008 8:35 am Subject: Re: [Freesurfer] wiki problem > good to know it wasn't something on our end. Any idea what > constituted > "suspicious traffic"? It might be useful for us to know. > > cheers, > Bruce > > > On Fri, 13 Jun 2008, Liat Levita wrote: > > > Dear all, thank you so much for all your help. Problem solved. > Cornell > was blocking the site for a security reasons, our network guys said > they > noticed suspicious traffic from that i.p address (the mind boggles > ...). > They have now unblocked it : ) > Liat > > > > > > > > ----- Original Message ----- > > From: Joe Paxton <jpaxton(a)wjh.harvard.edu> > > Date: Wednesday, June 11, 2008 9:34 am > > Subject: Re: [Freesurfer] wiki problem > > > >> Perhaps it is a DNS issue? You could try bypassing DNS by replacing > >> > >> the hostname with the ip in the URL: > >> > >> http://132.183.202.158/fswiki > >> or > >> https://132.183.202.158/fswiki > >> > >> If that works, then the problem is likely with DNS at Cornell, in > >> which case you'll need to contact your network helpdesk. > >> > >> On Jun 11, 2008, at 8:31 AM, Liat Levita wrote: > >> > >>> Hi Krish, > >>> > >>> I am afraid we had no joy with either option. > >>> > >>> No one in lab can get access, we have used both Mozilla Firefox, > >> and > >>> Internet Explorer, neither can establish a connection. > >>> > >>> We never had a problem before. I have tried making changes to my > >>> computer firewall, again no joy. > >>> > >>> Liat > >>> > >>> > >>> ----- Original Message ----- > >>> From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > >>> Date: Tuesday, June 10, 2008 8:01 pm > >>> Subject: Re: [Freesurfer] wiki problem > >>> > >>>> Liat, > >>>> > >>>> Could you tell us the browser you are using? Because we have been > >>>> using the fswiki without problems. ( and I can access fswiki from > >>>> my > >>>> home, hence we can rule out the case that fswiki is not available > >>>> external to our center ) > >>>> > >>>> https://surfer.nmr.mgh.harvard.edu/fswiki > >>>> > >>>> and > >>>> > >>>> http://surfer.nmr.mgh.harvard.edu/fswiki > >>>> > >>>> both should work with the first one asking you to accept a > >>>> certificate. ( secure http connection ) > >>>> > >>>> -Krish > >>>> > >>>> On Jun 10, 2008, at 6:52 PM, Liat Levita wrote: > >>>>> I am sure you are aware of this problem, but since last week we > >>>> have > >>>>> been unable to access the FreeSurfer wiki > >>>> (http://surfer.nmr.mgh.harvard.edu/docs/index.html > >>>>> ). Is it down for maintenance? and if so when will it be up > again?>>>>> > >>>>> I have just started using FreeSurfer, hence having major > >>>> problems > >>>>> without the freesurfer wiki to guide me along. > >>>>> > >>>>> Thank you so much for you help. > >>>>> > >>>>> L > >>>>> > >>>>> > >>>>> _______________________________________________ > >>>>> Freesurfer mailing list > >>>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>> > >>>>> > >>>> > >>>> _______________________________________________ > >>>> Freesurfer mailing list > >>>> Freesurfer(a)nmr.mgh.harvard.edu > >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>> > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > >

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Re: [Freesurfer] wiki problem
by Liat Levita 13 Jun '08

13 Jun '08

Dear all, thank you so much for all your help. Problem solved. Cornell was blocking the site for a security reasons, our network guys said they noticed suspicious traffic from that i.p address (the mind boggles ...). They have now unblocked it : ) Liat ----- Original Message ----- From: Joe Paxton <jpaxton(a)wjh.harvard.edu> Date: Wednesday, June 11, 2008 9:34 am Subject: Re: [Freesurfer] wiki problem > Perhaps it is a DNS issue? You could try bypassing DNS by replacing > > the hostname with the ip in the URL: > > http://132.183.202.158/fswiki > or > https://132.183.202.158/fswiki > > If that works, then the problem is likely with DNS at Cornell, in > which case you'll need to contact your network helpdesk. > > On Jun 11, 2008, at 8:31 AM, Liat Levita wrote: > > > Hi Krish, > > > > I am afraid we had no joy with either option. > > > > No one in lab can get access, we have used both Mozilla Firefox, > and > > Internet Explorer, neither can establish a connection. > > > > We never had a problem before. I have tried making changes to my > > computer firewall, again no joy. > > > > Liat > > > > > > ----- Original Message ----- > > From: Krish Subramaniam <krish(a)nmr.mgh.harvard.edu> > > Date: Tuesday, June 10, 2008 8:01 pm > > Subject: Re: [Freesurfer] wiki problem > > > >> Liat, > >> > >> Could you tell us the browser you are using? Because we have been > >> using the fswiki without problems. ( and I can access fswiki from > >> my > >> home, hence we can rule out the case that fswiki is not available > >> external to our center ) > >> > >> https://surfer.nmr.mgh.harvard.edu/fswiki > >> > >> and > >> > >> http://surfer.nmr.mgh.harvard.edu/fswiki > >> > >> both should work with the first one asking you to accept a > >> certificate. ( secure http connection ) > >> > >> -Krish > >> > >> On Jun 10, 2008, at 6:52 PM, Liat Levita wrote: > >>> I am sure you are aware of this problem, but since last week we > >> have > >>> been unable to access the FreeSurfer wiki > >> (http://surfer.nmr.mgh.harvard.edu/docs/index.html > >>> ). Is it down for maintenance? and if so when will it be up again? > >>> > >>> I have just started using FreeSurfer, hence having major > >> problems > >>> without the freesurfer wiki to guide me along. > >>> > >>> Thank you so much for you help. > >>> > >>> L > >>> > >>> > >>> _______________________________________________ > >>> Freesurfer mailing list > >>> Freesurfer(a)nmr.mgh.harvard.edu > >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>> > >>> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Segmentation of MRI with cortical lesions
by Martti Ilvesmäki 13 Jun '08

13 Jun '08

Hi, I'm using Freesurfer to segment MRI from patients with cortical lesions. The automatic segmentation does not work correctly, so I edited the wm.mgz manually and filled the missing white matter according to the tutorial. After this I ran recon-all with the -autorecon2-wm parameter. In some cases this works fine, but in a few cases the segmentation is still not correct. The wm surface forms a hole at the lesion despite the fact that I have manually filled the wm.mgz at that region. The pial surface forms an even deeper hole at the same spot, so that the surfaces cross. I have filled the gap from end to end but still the segmentation does not work correctly. What would be the correct approach to this problem? Thanks in advance, Martti Ilvesmäki

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qdec color scale
by Sky Raptentsetsang 11 Jun '08

11 Jun '08

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green lines in tkregister2
by karlkarl 11 Jun '08

11 Jun '08

Hi, I started to use Freesufer and finished the first step of recon-all. When I checked the talairach transform, the tutorial said there should be green lines which can be turned on or off by clicking the image window and hitting the s key. But it didn't work for me. Is this because the green lines only appear when you finally finish the surface reconstruction? At this point, what details in the target and moveable volums in the tkregester2 images should i pay attention to before moving to the next step? thanks _________________________________________________________________ 用手机MSN聊天写邮件看空间，无限沟通，分享精彩！ http://mobile.msn.com.cn/

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Patient Orientation and mri_convert
by James Kyle 11 Jun '08

11 Jun '08

I've been wrapping mri_convert for use with some of my lab's scripts. I appreciate the work that's been done with this utility and its flexibility in regard to wide support for many formats...the main incentive for moving over to it. However, recently I've been getting reports of my conversions not behaving well with fsl. I've read the freesurfer archives and am sure the issue is not with mri_convert itself, but with the way I'm using it. I'll use dcm2nii as a comparison as another lab is using this utility are reports everything appears to work fine. Example mri_convert: $ mri_convert mprage.dcm mprage.nii.gz This command very faithfully converts the dicom to nifti. Inspecting the headers shows that nothing is changed whatsoever. $ dcm2nii mprage.dcm This command changes the Patient Orientation header field. In the case of a MPRAGE scan, it is changed from an orientation of PIL (posterior, inferior, left) to PAL. These PAL oriented images are said to be the ones desired. I can replicate this by using: $ mri_convert --out_orientation PAL mprage.dcm mprage.nii.gz Of course, the flip made by dcm2nii for different scan types are themselves different. The dcm2nii script performs patient orientation changes on all of the scan types I've checked so far (3-5 or so). What I am somewhat perplexed over (and what no one in my lab has been able to answer) is by what "rule" and why are these conversions made? If I knew this, I could ensure mri_convert did them when appropriate. Would this be the "flipping" from radiological to neurological? Or is this a question I should be posing to the FSL team on the requirements of their images? Many thanks for any input, and thank you for patience with my newness to this area. Cheers, James A. Kyle

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Freesurfer June 2008