Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

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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Slow Processing
by Marlisa Isom 11 Jun '08

11 Jun '08

Hi All, We have 3 Mac Pros with Leopard which we use to process data (version 4). Two of them process a brain in 30-36 hours, but one takes a week to process ONE brain if not more. While the processors are slightly different (3GHz vs 2.6), not amazingly so. This is seemingly the only difference. Does anyone have any ideas? All the machines are updated etc. Marlisa

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Fixing Bad Output From the Talairach Registration
by skgtgac＠ucl.ac.uk 11 Jun '08

11 Jun '08

Hi, my name is giovanni, hope you can help me... i started the command recon-all -s patient_lyp -all on a folder containing the data of one of my patients... after few minutes I got this error message: ########################################################################### Thu Jun 5 08:13:09 BST 2008 talairach_avi done cp transforms/talairach.auto.xfm transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Thu Jun 5 08:13:10 BST 2008 /home/gacocco/freesurfer/subjects/patient_lyp/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.5852, pval=0.2817 >= threshold=0.0050) awk -f /home/gacocco/freesurfer/bin/extract_talairach_avi_QA.awk /home/gacocco/freesurfer/subjects/patient_lyp/mri/transforms/talairach_avi.log TalAviQA: 0.95959 z-score: -4 ERROR: Talairach QA check failed! z-score = -4 <= -4 = threshold Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux pc244-174 2.6.24-17-generic #1 SMP Thu May 1 14:31:33 UTC 2008 i686 GNU/Linux recon-all exited with ERRORS at Thu Jun 5 08:13:11 BST 2008 ############################################################################ I went to the page indicated by the message http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach and followed the instructions... so I typed in the terminal: gacocco@pc244-174:~/freesurfer/subjects$ tkmedit control_dr orig.mgz and i got this message: ############################################################################ Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % gacocco@pc244-174:~/freesurfer/subjects$ tksurfer control_dr rh pial surfer: current subjects dir: /home/gacocco/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/gacocco/freesurfer/subjects surfer: Reading header info from /home/gacocco/freesurfer/subjects/control_dr/mri/T1.mgz surfer: vertices=108452, faces=216900 Loading /home/gacocco/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: single buffered window surfer: tkoInitWindow(control_dr) surfer: using interface /home/gacocco/freesurfer/lib/tcl/tksurfer.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... % reading colortable from annotation file... colortable with 35 entries read (originally /space/amaebi/26/users/buckner_cortical_atlas/scripts/colortable_final.txt) Found embedded color table in annotation. surfer: dmin=12.2021, vno=73320, x=45.2575, y=-2.4731, z=41.6030 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73320 marked (curv=0.000000, stat=0.000000) x = (45.3, -2.5, 41.6), n = (-0.3, 0.9, 0.4). surfer: dmin=0.3104, vno=76989, x=36.2031, y=1.3400, z=30.5769 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76989 marked (curv=0.000000, stat=0.000000) x = (36.2, 1.3, 30.6), n = (0.7, 0.5, 0.5). surfer: dmin=0.4661, vno=76851, x=33.4849, y=1.2373, z=45.7916 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 76851 marked (curv=0.000000, stat=0.000000) x = (33.5, 1.2, 45.8), n = (0.3, 0.9, -0.4). surfer: dmin=0.2625, vno=71233, x=20.1145, y=-4.2706, z=67.2250 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 71233 marked (curv=0.000000, stat=0.000000) x = (20.1, -4.3, 67.2), n = (0.4, 0.9, -0.0). surfer: dmin=0.6131, vno=66208, x=37.6014, y=-9.3269, z=62.7725 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 66208 marked (curv=0.000000, stat=0.000000) x = (37.6, -9.3, 62.8), n = (0.9, 0.3, -0.3). surfer: dmin=0.6404, vno=70561, x=57.4662, y=-4.9873, z=31.2062 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 70561 marked (curv=0.000000, stat=0.000000) x = (57.5, -5.0, 31.2), n = (0.8, 0.4, 0.4). surfer: dmin=0.6560, vno=73265, x=44.8697, y=-2.3008, z=44.3611 % surfer: curv=0.000000, fs=0.000000 % surfer: val=0.000000, val2=0.000000 % surfer: amp=0.000000, angle=0.000000 deg (0.000000) % surfer: vertex 73265 marked (curv=0.000000, stat=0.000000) x = (44.9, -2.3, 44.4), n = (0.1, 0.9, -0.4). gacocco@pc244-174:~/freesurfer/subjects$ tkmedit patient_lyp brainmask.mgz Reading /home/gacocco/freesurfer/lib/tcl/tkm_common.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/gacocco/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/gacocco/freesurfer/lib/tcl/tkUtils.tcl gacocco@pc244-174:~/freesurfer/subjects$ tkregister2 --mgz --s patient_lyp --fstal --surf origsurfname set to orig INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume (null) reg file (null) LoadVol 1 ZeroCRAS 1 $Id: tkregister2.c,v 1.86.2.2 2008/03/10 14:02:35 nicks Exp $ Diagnostic Level -1 % tkregister2 talairach.xfm --------------------- 1.263 -0.018 -0.037 1.562; 0.062 1.083 0.453 4.335; 0.041 -0.467 1.180 20.571; 0.000 0.000 0.000 1.000; INFO: loading target /home/gacocco/freesurfer/subjects/patient_lyp/mri/orig.mgz Zeroing CRAS of target new xfm ----------------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000; --------------------- INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable /home/gacocco/freesurfer/average/mni305.cor.mgz INFO: changing move type to float Tmov: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; mkheaderreg = 0, float2int = 0 ---- Input registration matrix -------- 1.263 -0.018 -0.037 4.634; 0.062 1.083 0.453 5.415; 0.041 -0.467 1.180 -14.586; 0.000 0.000 0.000 1.000; subject = patient_lyp Reading lh surface orig MRISread(/home/gacocco/freesurfer/subjects/patient_lyp/surf/lh.orig): could not open file No such file or directory tkregister2.bin: could not read surface orig No such file or directory gacocco@pc244-174:~/freesurfer/subjects$ ############################################################################ So I typed: tkregister2 --mgz --s patient_lyp --fstal This time the utility starts, according to waht it says in the tutorial, but i do not see the green lines that should help me to stretch, translate, and rotate my MOVEABLE volume. Where am i wrong? best regards giovanni antonio cocco

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Re: [Freesurfer] wiki problem
by Liat Levita 11 Jun '08

11 Jun '08

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 >

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Re: [Freesurfer] wiki problem
by Liat Levita 11 Jun '08

11 Jun '08

No, it is really strange, I don't get it. I am not sure if it is a problem with our own network at Cornell. Safari could not open the page http://surfer.nmr.mgh.harvard.edu/fswiki because the server is not responding. Safari could not open the page https://surfer.nmr.mgh.harvard.edu/fswiki because the server is not responding. ----- Original Message ----- From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Date: Wednesday, June 11, 2008 8:33 am Subject: Re: [Freesurfer] wiki problem > so you can't get to: > > https://surfer.nmr.mgh.harvard.edu/fswiki > > or > > http://surfer.nmr.mgh.harvard.edu/fswiki > > I have no problem with either site... > Bruce > > > On Wed, 11 Jun 2008, 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 >

1 0

wiki problem
by Liat Levita 10 Jun '08

10 Jun '08

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

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