Hi Bruce, Thanks again. I tried the following from the command line to increase thickness estimates to 10mm but get the same error when using both mris_make_surfaces and mris_thickness:
$ recon-all -expert mris_make_surfaces -max 10 Epi003 l lh.thickness ERROR: cannot find mris_make_surfaces Linux ivan 2.6.32-32-generic #62-Ubuntu SMP Wed Apr 20 21:52:38 UTC 2011 x86_64 GNU/Linux recon-all -s exited with ERRORS at Fri Jul 31 10:48:01 PDT 2015 and: $ recon-all -expert mris_thickness -max 10 Epi003 l lh.thickness ERROR: cannot find mris_thickness Linux ivan 2.6.32-32-generic #62-Ubuntu SMP Wed Apr 20 21:52:38 UTC 2011 x86_64 GNU/Linux Thank you for your help, Jesse On Thu, Jul 30, 2015 at 6:33 AM, <freesurfer-requ...@nmr.mgh.harvard.edu> wrote: > 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. Re: recon-all -white does not respect wm edits (Antonin Skoch) > 2. Re: wm parcellation freesurfer (Bruce Fischl) > 3. randmoness flag and aseg.stats measures (Keith Harenski) > 4. Increasing thickness threshold? (Jesse Bledsoe) > 5. Re: Increasing thickness threshold? (Bruce Fischl) > 6. Pial surface in dural sinus in Longitudinal processing > (Justin McKee) > 7. Re: cluster_wise correction (Meiling Li) > 8. Re: dev version of mri_ca_label memory leak? (Chris Adamson) > 9. FreeSurfer Courses 2015 (Charalambous, Thalis) > 10. Re: FreeSurfer Courses 2015 (Christophe Destrieux) > 11. Re: Repost: problem with mri_label2label - large amount of > holes (Caspar M. Schwiedrzik) > 12. Re: dev version of mri_ca_label memory leak? (Bruce Fischl) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 29 Jul 2015 18:08:34 +0200 > From: "Antonin Skoch" <a...@medicon.cz> > Subject: Re: [Freesurfer] recon-all -white does not respect wm edits > To: freesurfer@nmr.mgh.harvard.edu > Cc: a...@medicon.cz > Message-ID: <20150729160834.7ad5a...@posta.medicon.cz> > Content-Type: text/plain; charset="us-ascii" > > Dear Bruce, > > no, both ?h.orig.nofix and ?h.orig are ok (respecting my wm.mgz edits), > but only ?h.white (result of mris_make_surfaces) is not ok (leaking to > regions where wm.mgz has value 1). > > Regards, > > Antonin > > > > > Hi Antonin > > > if it is correct in the orig.nofix but not correct in the orig that means > > it was an incorrectly fixed topological defect that you need to manually > > correct. I'll see if we can find someone here to take a look. > > Bruce > > On Wed, 29 Jul > 2015, Antonin Skoch wrote: > > > Dear experts, > > > > during the manual correction of freesurfer reconstruction I encountered > following > > problem: > > > > White surface did not follow gray / white matter boundary probably > partly due to > > skullstrip error and partly to the insufficient local gray/white matter > contrast. > > I tried to fix it by editing wm.mgz, in some cases it worked well, but > in some > > cases white surface "does not respect" my wm.mgz editing and still leaks > out to > > the areas where wm.mgz has value 1. > > The problem is probably at the level of recon-all -white since > orig.nofix.mgz and > > orig.mgz are OK - does well follow my edits and does not leak to areas > with > > wm.mgz = 1. > > I tried to put some control points to these areas but it still did not > help (the > > brainmask.mgz at most of the problematic areas has intensity 110). > Processing the > > data by development version did not help either.? > > > > I have uploaded 2 examples to your ftp file exchange: > > > > not_corrected_wm_1 > > - slice 96 in coronal view, right hemisphere, at the convexity > > - slices 97-98, 103, 107,108, in coronal view,? left hemisphere, at the > convexity > > > > not_corrected_wm_2 > > - slices 78 in coronal view, right hemisphere, 2 areas at the convexity > > - slices 79-83 in coronal view, two quite large areas in both > hemispheres at the > > convexity > > - slices 88-95 in coronal view, quite large areas at righ hemispheres at > the > > convexity > > > > and other areas in following slices, there are quite large amount of > them in this > > subject. > > > > Could you please look at the data to find where could be the problem? > > > > Thank you very much for all your help. > > > > Best regards, > > > > Antonin Skoch > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/0a8d4c9b/attachment.html > > ------------------------------ > > Message: 2 > Date: Wed, 29 Jul 2015 12:25:02 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] wm parcellation freesurfer > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.11.1507291223320.24...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > Hi Owais > > do you mean the wmparc.mgz or the aparc+aseg.mgz? You can use > mris_divide_parcellation or mris_make_face_parcellation to subdivide or > make an isotropic finer scale one if you want. I believe that you can then > create a new aparc+aseg from one of those and then the wmparc from that to > get a finer one > cheers > Bruce > > > On Tue, 28 Jul 2015, > Owais Syed wrote: > > > Hi, > > Is it possible to increase the number of parcellations when making the > aparc+aseg > > file? I have a high resolution MRI, and one parcellation will match > every three > > slides, but I want a better match overall. > > > > Thanks, > > > > Owais > > > > > > > ------------------------------ > > Message: 3 > Date: Wed, 29 Jul 2015 11:48:43 -0600 > From: Keith Harenski <kharen...@mrn.org> > Subject: [Freesurfer] randmoness flag and aseg.stats measures > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: > < > cagdev2u02pa+zbovgvquehm3i7k06vviafq8vg8_gavftn0...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > Similar to the thread below we ran several subjects through the freesurfer > (v5.3.0) using the -randomess flag and noticed no differences in the > volumes in aseg.stats across the runs. Is this by design? This thread ended > here. > > >Pernille, > > Can you send me the recon-all.log file of one of the subjects? > > Nick > > > On Fri, 2009-08-21 at 15:19 +0200, Pernille Iversen wrote: > >* Dear Nick, > *>* I have now used version 4.5.0 and the -randomness flag no longer gives > *>* errors, however, after 10 parallel runs of a subject with the > *>* -randomness flag set, I observe that the stats are completely > *>* identical. In the logs I can see that the line "setting seed for > *>* random number generator to 1234" is no longer there. In the earlier > *>* versions where the random initialisation was default I observed > *>* differences in the stats when I made the 10 parallel runs on the same > *>* subject as I have used this time - so it would seem that the random > *>* initialisation is not turned on when I use the flag. Can you please > *>* comment on this :) > *> >* Thanks, > *>* Pernille* > > > I also came across this thread separately which seems to indicate that the > -randomness flag only changes the cortical measures (which were different > across runs for the subjects): > > >Hi Andreia, > > >> > >> Then I would guess that your error comes from the fact that you > >> didn't rerun the autorecon3 at that stage for these 2 subjects. *As > >> the randomness flag changes the number of vertices when recreating > >> the surfaces*, that explains the error. > > > I'd appreciate any clarification. > > > Thanks, > > > Keith > > > -- > Keith Harenski > Mobile MRI Manager > Mobile MRI Core and Clinical Cognitive Neuroscience Laboratory > > The Mind Research Network > 1101 Yale Blvd NE Albuquerque, NM 87106-4188 > Office: 505.504.1338 | Fax: 505.272.8002 > kharen...@mrn.org | www.mrn.org | www.lrri.org > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/c989432e/attachment.html > > ------------------------------ > > Message: 4 > Date: Wed, 29 Jul 2015 12:32:29 -0700 > From: Jesse Bledsoe <bleds...@msu.edu> > Subject: [Freesurfer] Increasing thickness threshold? > To: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CAL6n2hM0y77-povyGkSv= > wo1h16nycioyp352-maxe_y3xk...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi FreeSurfer community, > > I would like to see if FreeSurfer could be used to improve clinical > detection of cortical dysplasia. Given that dysplasias can be several mm > thicker than typical cortex, are there ways to increase the thickness > thresholds to improve detection of cortex that may be up to 10mm thick? Is > it possible to increase the thickness measurements beyond 5mm? > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > Thank you, > Jesse > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/9ba33e30/attachment.html > > ------------------------------ > > Message: 5 > Date: Wed, 29 Jul 2015 15:35:05 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Increasing thickness threshold? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.11.1507291534370.24...@gate.nmr.mgh.harvard.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > yes, specify -max <something biggger than 5> on the command line > to mris_thickness and mris_make_surfaces (you can do this in recon-all with > expert options) > > cheers > Bruce > > > On Wed, 29 Jul 2015, Jesse > Bledsoe wrote: > > > Hi FreeSurfer community, > > > > I would like to see if FreeSurfer could be used to improve clinical > detection of > > cortical dysplasia. Given that dysplasias can be several mm thicker than > typical > > cortex, are there ways to increase the thickness thresholds to improve > detection > > of cortex that may be up to 10mm thick? Is it possible to increase the > thickness > > measurements beyond 5mm? > > > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > > > > Thank you, > > Jesse > > > > > > > ------------------------------ > > Message: 6 > Date: Wed, 29 Jul 2015 19:47:57 +0000 > From: Justin McKee <justin.mc...@ndcn.ox.ac.uk> > Subject: [Freesurfer] Pial surface in dural sinus in Longitudinal > processing > To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <93c6d798f9bf054a9382c81e1cbcdecc21b05...@mbx07.ad.oak.ox.ac.uk> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, > > Sorry if this is basic- I'm a bit of a novice. > > I'm running the longitudinal pipeline on patients with three time points. > For one of the time points the .long pail surface has included some of the > superior sagital sinus as it ascends between the occipital hemispheres. The > white matter mask is good, the base image pial surface is good, and the > original "cross" image for this time point also doesn't have this artefact. > > Reading the longitudinal edits on the wiki it seems to advice agains > editing the .long brainmask -even though I think it would resolve this > situation if this was in a "cross" image/subject? I wondered about editing > the brain.finalsurfs.mgz image? but the wiki is quite specific about this > only being for cerebellar problems. > > The occipital lobes are are a region of interest in my study so keen to > get accurate surfaces. > > Could you advise on where to go from here to edit this? > > I hope the above makes sense and thanks for your help! > > Cheers > > Justin > > Dr Justin McKee > > Clinical Research Fellow in Multiple Sclerosis, > > Nuffield Department of Clinical Neurosciences, > > University of Oxford > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150729/9db0e874/attachment.html > > ------------------------------ > > Message: 7 > Date: Thu, 30 Jul 2015 09:12:06 +0800 (CST) > From: "Meiling Li" <limeilingch...@163.com> > Subject: Re: [Freesurfer] cluster_wise correction > To: freesurfer-help <freesurfer@nmr.mgh.harvard.edu> > Cc: gr...@nmr.mgh.harvard.edu > Message-ID: > <558f0681.14b41.14edc842ccc.coremail.limeilingch...@163.com> > Content-Type: text/plain; charset="gbk" > > Hi doug > Thanks for your response! > I do the FC analysis in the volume. The seed I selected to do the FC is > from freesurfer-nonlinear space. > I try to do the correction according to the steps from Wiki. I got > results, but i am still a little confused. Can you help me to make sure the > following steps i used are right? > 1. Copy all the FC images(for example: *corcoef_zfrm.nii.gz, 100 subjects, > the dimention for one FC file is 128*128*128) into one file, such as > /autofs/cluster/Meiling/Correction_test/mgz > 2. Concanate all the FC files into one VOLUME File, I named it as > All_Concanated.mgz(the dimention is 128*128*128*100) > 3.Create g2v0.fsgd(I just want to do two-sample t-test, no covariates are > included) > 4. GLM model to fit. > mri_glmfit --glmdir g2v0 --y All_Concanated.mgz --fsgd g2v0.fsgd --C > group.diff.mtx --C High.mtx --C Low.mtx > > > 5. Do correction using GRF(set the voxel-wise and cluster-wise as 1.3 and > 0.05 ) > mri_glmfit-sim --glmdir g2v0 --grf 1.3 pos --cwp .05 > mri_glmfit-sim --glmdir g2v0 --grf 1.3 neg --cwp .05 > > > Then I got the corrected results : > /autofs/cluster/Meiling/Correction_test/g2v0/group.diff/grf.th1.3.pos.sig.cluster.mgh > > > /autofs/cluster/Meiling/Correction_test/g2v0/group.diff/grf.th1.3.neg.sig.cluster.mgh > To visualize, i concanted the two results > mri_convert grf.th1.3.neg.sig.cluster.mgh grf.th1.3.neg.sig.cluster.nii.gz > mri_convert grf.th1.3.pos.sig.cluster.mgh grf.th1.3.pos.sig.cluster.nii.gz > fslmaths grf.th1.3.neg.sig.cluster.nii.gz -add > grf.th1.3.pos.sig.cluster.nii.gz grf.th1.3.sig.cluster.nii.gz > > > Finally, I project the grf.th1.3.sig.cluster.nii.gz onto fsaverage4 for > visualization. It seems that the results are corrected because a few > clusters are kept, but some of the clusters are so small. I think we do the > correction in the volume, so there maybe some transform erros when project > the results on to fsaverage4? We should check the results in the volume? > Attached file is part of the results i did. Please help me to correct the > steps and the test results. Thank you very much! > > > Meiling > > > > > > > How did you do the FC analysis? In the volume or on the surface? > doug > > On 07/23/2015 11:00 AM, Meiling Li wrote: > > Hello Freesurfer Experts > > I am emailing to ask aome questions about cluster_wise correction on > > surf. I hope some experts here could help me... > > The seed_based functional connectivity maps are generated in two > > groups, such as Patient and HC. I do the functional connectivity > > comparison between the two groups using two-sample t-test in Matlab, > > uncorrected P map(the value is -log10(p) exactly) was finally created, > > which named > > Patient-smaller-HC_P.nii.gz. I projected the P map onto fsaverage4 > > for visualization, we name it as > > 'Patient-smaller-HC_P_on_fsaverage4_lh.mgh'. Now i want to do the > > cluster_wise correction with p<0.05., or do the FDR correction. Could > > you please give me some suggestions how to do it? I do appreciate any > > help! > > > > Meiling > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150730/a72f1465/attachment.html > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: Correction_testimg.jpg > Type: image/jpeg > Size: 315010 bytes > Desc: not available > Url : > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150730/a72f1465/attachment.jpg > > ------------------------------ > > Message: 8 > Date: Thu, 30 Jul 2015 05:06:23 +0000 > From: Chris Adamson <chris.adam...@mcri.edu.au> > Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > < > 43a4603348d2ac409b1b958efe5c8b940166e72...@mitsmxmbx01v.mcri.edu.au> > Content-Type: text/plain; charset="utf-8" > > Ok how can I send you the files and commands? > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > Sent: Thursday, 30 July 2015 12:03 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak? > > Hi Chris > > if you send me all the inputs to mri_ca_label and your exact command line > I'll see if I can replicate it and either fix it or send you a new version. > Or you can try the current dev version and see if it fixes things > > cheers > Bruce > On Wed, 29 Jul 2015, Chris Adamson wrote: > > > > > Devs, > > > > ? > > > > I?m running the CVS version of Freesurfer, checked out on 28/7/2015 > > (7/28/2015 for US people). I get to the ?calabel step and mri_ca_label > > takes a *long* time > > (400 minutes) and uses a *lot* of memory. After it outputs ?saving > > sequentially combined intensity scales to > > aseg.auto_noCCseg.label_intensities.txt? the memory consumption > continues to increase. Currently it is at 8.9GB. > > > > ? > > > > Can I send output to help debug this? > > > > ? > > > > Chris. > > > > ? > > > > Dr?Chris Adamson > > Research Officer, Developmental Imaging,?Murdoch Childrens Research > > Institute Murdoch Childrens Research Institute Royal Children?s > > Hospital Flemington Road,?Parkville, Victoria??3052,?Australia > > www.mcri.edu.au > > > > E ??chris.adam...@mcri.edu.au > > T???03 9936 6780 > > > > ? > > > > > > ______________________________________________________________________ > > This email has been scanned by the Symantec Email Security.cloud service. > > For more information please visit http://www.symanteccloud.com > > ______________________________________________________________________ > > > > > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > > If you have any questions, please contact MCRI IT Servicedesk for further > assistance. > ______________________________________________________________________ > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ > > > > ------------------------------ > > Message: 9 > Date: Thu, 30 Jul 2015 08:22:22 +0000 > From: "Charalambous, Thalis" <thalis.charalambous...@ucl.ac.uk> > Subject: [Freesurfer] FreeSurfer Courses 2015 > To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu> > Message-ID: <213c75be-482a-420c-ab51-9e489ea50...@live.ucl.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > To whom it may concern, > > My name is Thalis and I am about to start my PhD at University College > London (UCL). FreeSurfer is going to be a very useful tool and for this > reason I am thinking of attending the course that will take place in Boston > between the 28/09/2015-1/10/2015. > However, I would like to ask whether there are any other courses taking > place in Europe in the next couple of months that would be more convenient > for me to attend. > > Regards, > > Thalis Charalambous > > > > > ------------------------------ > > Message: 10 > Date: Thu, 30 Jul 2015 13:05:02 +0200 > From: Christophe Destrieux <christophe.destri...@univ-tours.fr> > Subject: Re: [Freesurfer] FreeSurfer Courses 2015 > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: <f2b0275a-39ca-4a59-bfaf-6fc3c5a1e...@univ-tours.fr> > Content-Type: text/plain; charset="utf-8" > > Hi > we will organize one in Tours, Loire Valley France next may, with the > Boston team > sincerely > > Christophe Destrieux, > Unit? ? Imagerie et Cerveau ? UMRS INSERM U930, Universit? Fran?ois > Rabelais de Tours > http://www.u930.tours.inserm.fr/ <http://www.u930.tours.inserm.fr/> > > Service de Neurochirurgie > et Laboratoire d'Anatomie - Facult? de M?decine - 10 Bd Tonnell? - 37032 > Tours - France > tel (33) 2 47 36 61 36 - fax (33) 2 47 36 62 07 > > > > > > > > Le 30 juil. 2015 ? 10:22, Charalambous, Thalis < > thalis.charalambous...@ucl.ac.uk> a ?crit : > > > > To whom it may concern, > > > > My name is Thalis and I am about to start my PhD at University College > London (UCL). FreeSurfer is going to be a very useful tool and for this > reason I am thinking of attending the course that will take place in Boston > between the 28/09/2015-1/10/2015. > > However, I would like to ask whether there are any other courses taking > place in Europe in the next couple of months that would be more convenient > for me to attend. > > > > Regards, > > > > Thalis Charalambous > > > > > > _______________________________________________ > > 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. > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150730/543de692/attachment.html > > ------------------------------ > > Message: 11 > Date: Thu, 30 Jul 2015 08:17:39 -0400 > From: "Caspar M. Schwiedrzik" <cschwie...@mail.rockefeller.edu> > Subject: Re: [Freesurfer] Repost: problem with mri_label2label - large > amount of holes > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <CA+bX-3-kK--qr= > 35pmyraflbbfwqfxyb0c4ukdu62r2legr...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce and Doug, > thanks for looking into this and sorry for the delay. > The command line we are using is: > > mri_label2label --srclabel > > /Volumes/Macintosh_HD/Applications/freesurfer/subjects/y$1/label/lh.v1.predict0p8.label > --srcsubject y$1 --trglabel > > /Volumes/Macintosh_HD/Applications/freesurfer/subjects/yx$1/label/yx$1_av1_lh_tp2.label > --trgsubject yx$1 --regmethod surface --hemi lh > > We have several anatomies from the same subject, acquired on different > occasions. We defined labels based on results of an fMRI experiment, and > tried to use mri_label2label to map them within subjects from one anatomy > to another. As a control, we also wanted to map the Hinds V1 from one > anatomy to another, but this is where we ran into these holes. > We will make an example subject available for debugging later today. > > Thanks! Caspar > > > > > > 2015-07-24 12:33 GMT-04:00 Douglas Greve <gr...@nmr.mgh.harvard.edu>: > > > what is your command line? What do you mean by one anatomy to another? > > > > > > On 7/24/15 9:26 AM, Caspar M. Schwiedrzik wrote: > > > > > > > > ---------- Forwarded message ---------- > > From: *Caspar M. Schwiedrzik* <cschwie...@rockefeller.edu> > > Date: Thursday, July 16, 2015 > > Subject: problem with mri_label2label - large amount of holes > > To: "Freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > > > > > > Hi! > > We are doing some analyses in which we map custom labels from one > anatomy > > to another, within subjects. As a control, we also tried to map > > anatomically defined V1s according to the method by Hinds within subject > > from one anatomy to another. However, as you can see in the attachment, > > there are very many holes in the labels after using mri_label2label. This > > does not happen with smaller labels. Why is this happening and is there a > > solution? > > Thanks, Caspar > > > > > > > > > > > > > > > > _______________________________________________ > > Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps:// > 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 > > > > > > 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. > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20150730/6730a600/attachment.html > > ------------------------------ > > Message: 12 > Date: Thu, 30 Jul 2015 09:33:20 -0400 (EDT) > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak? > To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> > Message-ID: > <alpine.lrh.2.11.1507300932570.24...@gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > you can probably just email them to me as they aren't terribly big. Make > sure you get every file that is on the mri_ca_label command line > > cheers > Bruce > On Thu, 30 > Jul 2015, Chris Adamson wrote: > > > Ok how can I send you the files and commands? > > > > -----Original Message----- > > From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto: > freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > > Sent: Thursday, 30 July 2015 12:03 AM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] dev version of mri_ca_label memory leak? > > > > Hi Chris > > > > if you send me all the inputs to mri_ca_label and your exact command > line I'll see if I can replicate it and either fix it or send you a new > version. Or you can try the current dev version and see if it fixes things > > > > cheers > > Bruce > > On Wed, 29 Jul 2015, Chris Adamson wrote: > > > >> > >> Devs, > >> > >> ? > >> > >> I?m running the CVS version of Freesurfer, checked out on 28/7/2015 > >> (7/28/2015 for US people). I get to the ?calabel step and mri_ca_label > >> takes a *long* time > >> (400 minutes) and uses a *lot* of memory. After it outputs ?saving > >> sequentially combined intensity scales to > >> aseg.auto_noCCseg.label_intensities.txt? the memory consumption > continues to increase. Currently it is at 8.9GB. > >> > >> ? > >> > >> Can I send output to help debug this? > >> > >> ? > >> > >> Chris. > >> > >> ? > >> > >> Dr?Chris Adamson > >> Research Officer, Developmental Imaging,?Murdoch Childrens Research > >> Institute Murdoch Childrens Research Institute Royal Children?s > >> Hospital Flemington Road,?Parkville, Victoria??3052,?Australia > >> www.mcri.edu.au > >> > >> E ??chris.adam...@mcri.edu.au > >> T???03 9936 6780 > >> > >> ? > >> > >> > >> ______________________________________________________________________ > >> This email has been scanned by the Symantec Email Security.cloud > service. > >> For more information please visit http://www.symanteccloud.com > >> ______________________________________________________________________ > >> > >> > > > > ______________________________________________________________________ > > This email has been scanned by the Symantec Email Security.cloud service. > > For more information please visit http://www.symanteccloud.com > > > > If you have any questions, please contact MCRI IT Servicedesk for > further assistance. > > ______________________________________________________________________ > > > > ______________________________________________________________________ > > This email has been scanned by the Symantec Email Security.cloud service. > > For more information please visit http://www.symanteccloud.com > > ______________________________________________________________________ > > > > _______________________________________________ > > 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 > > End of Freesurfer Digest, Vol 137, Issue 41 > ******************************************* >
_______________________________________________ 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.
