Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Re: [Freesurfer] mris_fix_topology
by Douglas N Greve 19 Aug '09

19 Aug '09

Hmmm, not sure what's going on, may have to wait for Bruce. Have you looked at the ?h.orig.nofix in tkmedit/tksurfer? Falk Lüsebrink wrote: > Hi Doug, > > I get the following error: > > rh.orig: face[161898].v[2] = 82472, but face 161898 not in vertex 82472 face > list > > Falk > > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, August 20, 2009 12:12 AM > To: Falk Lüsebrink > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_fix_topology > > > It was not mris_fix_topology that failed but mris_euler_number (but that > might have failed because of something in the topology fix). What > happens if you: > > cd /home/falk/freesurfer/subjects/yv98_05mm_div > mris_euler_number ../surf/rh.orig > > doug > > Falk Lüsebrink wrote: > >> Hi FreeSurfers, >> >> >> >> Attached is a log file containing an error of mris_fix_topology and I >> would like to know how to fix that issue if that is possible. Is it >> possible to view a defect (in that case #33) in tksurfer or freeview >> to identify a possible error in the wm.mgz or filled.mgz to correct it >> manually? >> >> >> >> Thanks in advance, >> >> Falk >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Re: [Freesurfer] mris_fix_topology
by Douglas N Greve 19 Aug '09

19 Aug '09

It was not mris_fix_topology that failed but mris_euler_number (but that might have failed because of something in the topology fix). What happens if you: cd /home/falk/freesurfer/subjects/yv98_05mm_div mris_euler_number ../surf/rh.orig doug Falk Lüsebrink wrote: > > Hi FreeSurfers, > > > > Attached is a log file containing an error of mris_fix_topology and I > would like to know how to fix that issue if that is possible. Is it > possible to view a defect (in that case #33) in tksurfer or freeview > to identify a possible error in the wm.mgz or filled.mgz to correct it > manually? > > > > Thanks in advance, > > Falk > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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mris_fix_topology
by Falk Lüsebrink 19 Aug '09

19 Aug '09

Hi FreeSurfers, Attached is a log file containing an error of mris_fix_topology and I would like to know how to fix that issue if that is possible. Is it possible to view a defect (in that case #33) in tksurfer or freeview to identify a possible error in the wm.mgz or filled.mgz to correct it manually? Thanks in advance, Falk

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Re: [Freesurfer] RAS Conversion
by Douglas N Greve 19 Aug '09

19 Aug '09

Try this: 1. Get vox2ras matrix for volume RAS (Call it T): mri_info --vox2ras-tkr volume.mgz 2. Get vox2ras matrix for scanner RAS (Call it S): mri_info --vox2ras volume.mgz 3. Compute M = S*inv(T) 4. Foreach xyz in label, NewXYZ = M*[X Y Z 1]' doug Joseph Barrington Keller wrote: > Hello, > I'm trying to convert labels in volume RAS to volume scanner RAS in order to use them in another program. How would I accomplish this? Any advice on this subject would be greatly appreciated. Thanks > > > Joe > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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bbregister
by Victoria Williams 19 Aug '09

19 Aug '09

Hello, I used bbregister to create a register.dat file aligning a subject's T2(lowb) dti image to their FreeSurfer orig volume. I am now wondering with what command can I apply this register.dat file to the other diffusion measures such as FA to bring them into alignment with the orig, as they are identical and thus use the same registration as the lowb? I would ideally like to save the transformed diffusion measure volumes as a new volume so I can run segstats to extract the wmparc segmentation means. Thanks in advance!! Tori

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Re: [Freesurfer] (no subject)
by caoaize 19 Aug '09

19 Aug '09

Hello Bruce, The sequence we used is called Turbo field Echo, I need to check it again. I checked our scanning protocol, found that we did have marker on the subjects' forehead. I generate the right hippocampus from freesurfer, overlay with orig.nii (from orig.mgz), the overlay shows that the subject's right side is the right side in freesurfer's statistical report. It means that our left side is bigger than the right side. This result consitently appears on our other subjects data. I extract the hippocampus left side mask in this way: mri_binarize --i aseg.mgz --match 17 --o hippo_left.nii The label for right side is 53. Anything wrong for what I used? Also, I used asegstats2table --subject s1 s2... --meas volume --tablefile stats.txt to get the statistical report. If we accept the low corelation between manual and auto segmentation, how can we explain that the left side is bigger than the right side? I hope your help. Thanks a lot. Best Regards, Aize > Date: Mon, 17 Aug 2009 13:51:26 -0400 > From: fischl(a)nmr.mgh.harvard.edu > To: caoaize(a)hotmail.com > Subject: RE: [Freesurfer] (no subject) > > wow, I don't think I've ever seen a T1-weighted MR with gray matter this > dark. The gray/csf contrast is very low. What kind of sequence is it? > > On Tue, 18 Aug 2009, caoaize wrote: > > > > > Hi, Bruce, > > > > > > > > Here is the aseg.mgz and norm.mgz files. Thanks. > > > > > > > > Aize > > > >> Date: Mon, 17 Aug 2009 13:27:07 -0400 > >> From: fischl(a)nmr.mgh.harvard.edu > >> To: caoaize(a)hotmail.com > >> Subject: RE: [Freesurfer] (no subject) > >> > >> Hi Aize, > >> > >> I need the aseg.mgz as well (and probably the norm.mgz). Differences in > >> the definitions of what is hippocampus and what isn't will reduce the > >> correlation coefficient. They should still be somewhat correlated, but even > >> a perfect pair of segmentations under each protocol for each subject will > >> not have a perfect correlation, so it's hard to assess what it means, since > >> the protocols are different. > >> Bruce > >> > >> > >> On Tue, 18 Aug 2009, caoaize wrote: > >> > >>> > >>> Our data is 3T, the manual segmentation follow the McConnell protocol described in "Volumetry of hippocampus and amygdala with high-resolution MRI and three-dimensional analysis software: minimizing the discrpancies between laboratories". I do not know what is the difference between yours and theirs. But, if both method are consistant, then the correlation coeffienct should be high. Here is one image that has bad segmention on happocampus. > >>> > >>> > >>> > >>> I am appreciate for your help. > >>> > >>> > >>> > >>> Aize > >>> > >>> > >>>> Date: Mon, 17 Aug 2009 11:52:19 -0400 > >>>> From: fischl(a)nmr.mgh.harvard.edu > >>>> To: caoaize(a)hotmail.com > >>>> CC: nicks(a)nmr.mgh.harvard.edu; freesurfer(a)nmr.mgh.harvard.edu > >>>> Subject: RE: [Freesurfer] (no subject) > >>>> > >>>> it lost interior voxels? That doesn't sound right. Can you send us an > >>>> image? If your manual protocol is different than the one we used then the > >>>> DICE overlap is somewhat irrelevant. > >>>> > >>>> cheers, > >>>> Bruce > >>>> > >>>> On Mon, 17 Aug 2009, caoaize wrote: > >>>> > >>>>> > >>>>> Hi, Bruce, > >>>>> > >>>>> > >>>>> > >>>>> I am not clear what manual segmentation protocol we are using, it was done by a trained RA. Currently we just calculate the volumes correlation between manual segmentation and the auto one, but not your DICE method. Our aquisitions are: Philips 3D sense, T1TFE, TR 7.9ms. > >>>>> > >>>>> > >>>>> > >>>>> In 27 subjects, we have two hippocampus volumes from Freesurfer auto segmentation around 1700, it keeps the edge, but lost lots of inside voxels. I am thinking to manual edit these two volumes, but do not know what happened. > >>>>> > >>>>> > >>>>> > >>>>> Aize > >>>>> > >>>>>> Date: Sat, 15 Aug 2009 09:14:30 -0400 > >>>>>> From: fischl(a)nmr.mgh.harvard.edu > >>>>>> To: caoaize(a)hotmail.com > >>>>>> CC: nicks(a)nmr.mgh.harvard.edu; freesurfer(a)nmr.mgh.harvard.edu > >>>>>> Subject: RE: [Freesurfer] (no subject) > >>>>>> > >>>>>> Hi Aize, > >>>>>> > >>>>>> you are using the CMA manual segmentation protocol? We have not found a > >>>>>> bias in volumes, and our DICE is usually close to .9 for hippocampus. > >>>>>> What acquisitions are you using? > >>>>>> > >>>>>> cheers, > >>>>>> Bruce > >>>>>> On Sat, 15 Aug 2009, caoaize wrote: > >>>>>> > >>>>>>> > >>>>>>> Hi, Bruce, > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> Our segmentation protocol is the same one as Freesurfer's auto segmentation, I used recon-all -s subject -all, command. I do not know in this protocol, whether fimbria and alveus are included. We do not have skin fiducial to tell right or left side. The interesting thing the mean volume for auto is less than manual segmentation. > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> Aize > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>> > >>>>>>>> Subject: Re: [Freesurfer] (no subject) > >>>>>>>> From: nicks(a)nmr.mgh.harvard.edu > >>>>>>>> To: fischl(a)nmr.mgh.harvard.edu > >>>>>>>> CC: caoaize(a)hotmail.com; freesurfer(a)nmr.mgh.harvard.edu > >>>>>>>> Date: Fri, 14 Aug 2009 18:53:41 -0400 > >>>>>>>> > >>>>>>>> just to add a factoid, from the ADNI data set, 793 subjects processed by > >>>>>>>> freesurfer: > >>>>>>>> Volume Mean: StdDev: > >>>>>>>> ------------------- ----- ------- > >>>>>>>> Left-Hippocampus 3184.335 604.930 > >>>>>>>> Right-Hippocampus 3233.753 621.896 > >>>>>>>> > >>>>>>>> seems pretty symmetric, with the right being slightly larger (but within > >>>>>>>> std). this subject set is a mix of controls, MCI and AD patients. > >>>>>>>> > >>>>>>>> n. > >>>>>>>> > >>>>>>>> On Fri, 2009-08-14 at 17:53 -0400, Bruce Fischl wrote: > >>>>>>>>> is your segmentation protocol the same as the one we base our automated > >>>>>>>>> segmentation on? For example, are fimbria and alveus considered part of > >>>>>>>>> the hippocampus? > >>>>>>>>> > >>>>>>>>> As far as left/right switches go, do you have any fiducial markers (e.g. > >>>>>>>>> vitamin E tablets) in the images? > >>>>>>>>> > >>>>>>>>> cheers > >>>>>>>>> Bruce > >>>>>>>>> On Sat, 15 Aug 2009, caoaize wrote: > >>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> Hi, there, > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> I have some problem for the hippocampus segmentation results. > >>>>>>>>>> > >>>>>>>>>> 1. My structural data are originally in par-rec file. I used r2agui to > >>>>>>>>>> convert them into .nii format, then use recon-all -i to convert the .nii > >>>>>>>>>> data into freesurfer .mgz format. Based on these operations, I run > >>>>>>>>>> recon-all -all on all my data, the statistical report show that the mean > >>>>>>>>>> left hippocampus volume is bigger than the right one, while literature > >>>>>>>>>> shows that the right one should be bigger. This problem continuously > >>>>>>>>>> appeared in our different studies. I am not sure whether it is r2agui's > >>>>>>>>>> problem, which changed the oritation of the structural data. Do you have > >>>>>>>>>> any idea? > >>>>>>>>>> > >>>>>>>>>> 2. After autosegmentation, we did a statistical comparison analysis > >>>>>>>>>> between automatic segmentation and manual segmentation, and the > >>>>>>>>>> correlation is quite low, less than 80%, which is not acceptable for us. > >>>>>>>>>> > >>>>>>>>>> 3. Can I edit the auto segmentation results in Freesurfer if we think the > >>>>>>>>>> auto segmentation is not good enough in some area? > >>>>>>>>>> > >>>>>>>>>> I will be really appreciated for your help. > >>>>>>>>>> > >>>>>>>>>> Aize > >>>>>>>>>> > >>>>>>>>>> > >>>>>>>>>> _________________________________________________________________ > >>>>>>>>>> Messenger°²È«±£»¤ÖÐÐÄ£¬Ãâ·ÑÐÞ¸´ÏµÍ³Â©¶´£¬±£»¤Messenger°²È«£¡ > >>>>>>>>>> http://im.live.cn/safe/ > >>>>>>>>> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>>>>>>> > >>>>>>> > >>>>>>> _________________________________________________________________ > >>>>>>> ÿÿWindows Live ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿMessengerÿÿ > >>>>>>> http://www.windowslive.cn > >>>>> > >>>>> _________________________________________________________________ > >>>>> ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > >>>>> http://www.microsoft.com/china/windows/windowslive/products/photos-share.as… > >>> > >>> _________________________________________________________________ > >>> ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > >>> http://www.microsoft.com/china/windows/windowslive/products/photos-share.as… > > > > _________________________________________________________________ > > ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿ > > http://www.microsoft.com/china/windows/windowslive/products/photos-share.as… _________________________________________________________________ Messenger安全保护中心，免费修复系统漏洞，保护Messenger安全！ http://im.live.cn/safe/

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Convert to original orientation
by Renske de Boer 19 Aug '09

19 Aug '09

Hi, I would like to register a FreeSurfer segmentation (or actually the corresponding T1 image) to another scan of the same subject. In order to perform this registration, the mri/T1.mgz file needs to have the same orientation as the original T1 scan (mri/orig/001.mgz). Resampling is not necessary since I want to prevent multiple interpolations and resampling is already necessary in the registration/transformation. How can I convert mri/T1.mgz to the same orientation as the original T1 scan? Thanks! Renske -- _____________________________________ Ms. Renske de Boer, MSc Biomedical Imaging Group Rotterdam Erasmus MC, University Medical Center Rotterdam, the Netherlands www.bigr.nl ______________________________________

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None
by None 19 Aug '09

19 Aug '09

by outgoing.mit.edu (8.13.6/8.12.4) with ESMTP id n7JKRD4b007003 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for <freesurfer(a)nmr.mgh.harvard.edu>; Wed, 19 Aug 2009 16:27:14 -0400 (EDT) Received: from oc11exhub1.exchange.mit.edu (18.9.3.11) by w92exedge4.exchange.mit.edu (18.7.73.16) with Microsoft SMTP Server (TLS) id 8.1.393.1; Wed, 19 Aug 2009 16:26:56 -0400 Received: from w92expo3.exchange.mit.edu ([18.7.49.69]) by oc11exhub1.exchange.mit.edu ([18.9.3.11]) with mapi; Wed, 19 Aug 2009 16:27:13 -0400 From: Joseph Barrington Keller <jkeller1(a)MIT.EDU> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Date: Wed, 19 Aug 2009 16:25:06 -0400 Thread-Topic: RAS Conversion Thread-Index: AQHKIQtuio/Y5oVpNkupRyicCi/ROA== Message-ID: <1250713634.cE8F1a.25757DEC7EF6FBF97BB488FC479FE6AE8930237A6369A9A(a)w92expo3.exchange.mit.edu> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: acceptlanguage: en-US Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 X-Scanned-By: MIMEDefang 2.42 X-Spam-Flag: NO X-Spam-Score: 0.00 X-NMR-MGH-MailScanner-Information: Please contact the ISP for more information X-NMR-MGH-MailScanner-ID: n7JKRGA7002157 X-NMR-MGH-MailScanner: Not scanned: please contact your Internet E-Mail Service Provider for details X-NMR-MGH-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=0.001, required 5, autolearn=disabled, UNPARSEABLE_RELAY 0.00) X-NMR-MGH-MailScanner-From: jkeller1(a)mit.edu X-Spam-Status: No Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by mail.nmr.mgh.harvard.edu id n7JKRGA7002157 Subject: [Freesurfer] RAS Conversion X-BeenThere: freesurfer(a)nmr.mgh.harvard.edu X-Mailman-Version: 2.1.9 Precedence: list List-Id: <freesurfer.nmr.mgh.harvard.edu> List-Unsubscribe: <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>, <mailto:freesurfer-request@nmr.mgh.harvard.edu?subject=unsubscribe> List-Archive: <http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer> List-Post: <mailto:freesurfer@nmr.mgh.harvard.edu> List-Help: <mailto:freesurfer-request@nmr.mgh.harvard.edu?subject=help> List-Subscribe: <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>, <mailto:freesurfer-request@nmr.mgh.harvard.edu?subject=subscribe> X-List-Received-Date: Wed, 19 Aug 2009 20:27:17 -0000 Hello, I'm trying to convert labels in volume RAS to volume scanner RAS in order to use them in another program. How would I accomplish this? Any advice on this subject would be greatly appreciated. Thanks Joe

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[Fwd: Re: ROI reliability]
by jentis＠nmr.mgh.harvard.edu 19 Aug '09

19 Aug '09

Hi Nick, It appears mri_compute_seg_overlap only works with .mgz files and not .label files, which is how I saved the ROIs. I tried renaming the labels as .mgz files, but that did not work. Any suggestions? Thanks. > the utility for comparing segs is 'mri_compute_seg_overlap', included > with freesurfer. it compares two arbitrary segs. we use it to compare > the manual seg with the auto seg to get Jaccard and Dice coefficients. > > On Mon, 2009-08-17 at 12:03 -0400, Bruce Fischl wrote: >> if all you want is reliability on the same volume then you don't need >> any >> reconstructions. Just manually label them in something like freeview and >> directly compute the overlap (Nick has some tools for this if you don't >> - >> it's pretty straightforward) >> >> cheers, >> Bruce >> On Mon, 17 Aug 2009 jentis(a)nmr.mgh.harvard.edu >> wrote: >> >> > Hi Bruce, >> > >> > Essentially, for this ROI reliability problem we've asked you about, >> we >> > want to use the high-res volumetric data to make a refined >> segmentation >> > of the amygdala. We can't do this by using the 1mm data because of >> its >> > visual integrity. But, maybe what we can do (as per your email) is >> make >> > the labels in the .38 volume data, map that to the 1mm data and then >> > compare the reliability of those labels? Basically, this is a similar >> > project to Brad Dickerson's high-res manual hippocampus segmentation. >> We >> > just need to confirm that we can trace it twice with a high amount of >> > overlap and accuracy. >> > Thanks so much for your help! >> > >> > Best, >> > Jon >> > >> > >> > >> > >> >> Hi Jon, >> >> >> >> I would use the 1mm data to create the surfaces then map them to the >> >> hires data and do your tracing that way. You can then use the >> surfaces for >> >> various things like inter-subject registration. I'd need more details >> to >> >> give better advice, but generating surfaces from highres data is >> hard, and >> >> usually not necessary. >> >> >> >> cheers, >> >> Bruce >> >> >> >> On Mon, 10 Aug 2009 >> >> jentis(a)nmr.mgh.harvard.edu wrote: >> >> >> >>> Hi Bruce, >> >>> >> >>> Yes, we have the 1mm data. However, the project is designed to >> >>> manually trace an ROI based on the increased visibility in the >> high-res >> >>> scans. We need to do reliability to test our method of manual >> >>> segmentation. Perhaps I am misunderstanding, but it seems like >> using >> >>> the 1mm surface data would defeat our purpose. Any suggestions? >> >>> Thanks again! >> >>> >> >>> Best, >> >>> Jon >> >>> >> >>> >> >>>> can't you get 1mm data to go with your highres data? For many >> reasons >> >>>> the high resolution data is usually quite poor for generating >> surface >> >>>> models. >> >>>> >> >>>> cheers, >> >>>> Bruce >> >>>> On Sun, 9 Aug 2009 jentis(a)nmr.mgh.harvard.edu wrote: >> >>>> >> >>>>> Hi Freesurfer team, >> >>>>> I am trying to get intra-rater reliability statistics on an ROI >> >>>>> manually traced twice (blindly). The scans are anisotropic (.38 x >> .38 >> >>>>> x .8 mm) and so I have not run them automatically through the >> >>>>> Freesurfer segmentation because they fail after autorecon1. I >> tried >> >>>>> to >> >>>>> use the following command but have had problems: >> >>>>> mris_anatomical_stats -a ${s}/label/${h}.aparc.annot -f >> >>>>> cortical_thickness_stats/${h}_${s}.txt $s $h >> >>>>> >> >>>>> It seems this command requires certain data from the autorecon >> process >> >>>>> such as wm.mgz and other surface information that I cannot get >> because >> >>>>> autorecon fails on these types of scans. >> >>>>> >> >>>>> I have only traced one hemisphere (the Left) and the ROIs are >> saved as >> >>>>> label files; >> >>>>> an example is: >> >>>>> /autofs/space/phrenic_007/users/jon/hires_amy/Round_2/HRDEV126/ >> >>>>> whole_amygdala.label >> >>>>> >> >>>>> Is there another way to get reliability (pixel overlap, total >> number >> >>>>> of >> >>>>> pixels, etc.) for two ROIs? Would you suggest another command or >> is >> >>>>> there >> >>>>> a way to bypass those requirements for the mri_anatomical_stats >> >>>>> command? >> >>>>> >> >>>>> Thanks! >> >>>>> _______________________________________________ >> >>>>> 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] a "redraw failed: no gl window open" problem
by Guang Zeng 19 Aug '09

19 Aug '09

yeah, it didn't work From: ppj(a)netfilter.com.br Date: Tue, 18 Aug 2009 19:46:02 -0300 Subject: Re: [Freesurfer] a "redraw failed: no gl window open" problem To: freesurfer_zg(a)hotmail.com I suppose you have tried the trick bellow setenv doublebuffer_flag 1----------------------------------------------------------- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- Novo Netfilter 3.0 www.Netfilter.com.br --- New Netfilter Small Business 2009/8/18 Guang Zeng <freesurfer_zg(a)hotmail.com> Hi, there, I am still facing the problem of "redraw failed: no gl window open", I got another linux machine with Nvidia graphic card, I ran the tksurfer command "tksurfer bert lh inflated", it still gave me the "redraw failed: no gl window open" error. surfer: current subjects dir: /home/m047599/freesurfer-install/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/m047599 surfer: Reading header info from /home/m047599/freesurfer-install/freesurfer/subjects/bert/mri/T1.mgz surfer: vertices=131369, faces=262734 Loading /home/m047599/freesurfer-install/freesurfer/surface_labels.txt surfer: ### redraw failed: no gl window open surfer: double buffered window surfer: tkoInitWindow(bert) surfer: using interface /home/m047599/freesurfer-install/freesurfer/lib/tcl/tksurfer.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_common.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkm_wrappers.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/fsgdfPlot.tcl Reading /home/m047599/freesurfer-install/freesurfer/lib/tcl/tkUtils.tcl Successfully parsed tksurfer.tcl reading white matter vertex locations... I read a previously posted thread by Nick, it looks like we can download a new tksurfer.bin file to solve this problem at ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/cento… But I clicked the link, the file has been removed. Does any one can help me get the new link of this file? Thanks a lot! Guang Windows Live: Keep your friends up to date with what you do online. Find out more. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _________________________________________________________________ Hotmail® is up to 70% faster. Now good news travels really fast. http://windowslive.com/online/hotmail?ocid=PID23391::T:WLMTAGL:ON:WL:en-US:…

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