From marcosm@hucff.ufrj.br Tue Oct 8 11:37:45 2013 From: Marcos Martins da Silva To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_smooth issue with gaussian parameters Date: Tue, 08 Oct 2013 12:37:35 -0300 Message-ID: <1381246655.1817.4.camel@alien> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============6341289076574494449==" --===============6341289076574494449== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Wow! That was fast. I am running FreeSurfer 5.3 on top of CentOS6 (64-bit). My hardware is a PC powered by Intel=C2=AE Core=E2=84=A2 i5 CPU M 520 @ 2.40GHz =C3=97 4 Thank you for all help. Cheers Marcos. Em Ter, 2013-10-08 =C3=A0s 09:00 -0400, Bruce Fischl escreveu: > Hi Marcos >=20 > I've fixed this problem, which is a bug in one of the open source math=20 > libraries we use. If you email us the details of your hardware/software=20 > environment we'll get you a patch. >=20 > cheers > Bruce > On Mon, 7 Oct 2013, Marcos Martins da=20 > Silva wrote: >=20 > > Hi, Bruce > > I proceeded as explained at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpF= ileExchange . > > Using ftp method, it started at good rate but after I transferred about 3= /4 of the file the transfer rate decreased to some bytes (not Kbytes) per > > second. Tried using curl -T and it seemed to complete after about 50 min = but I got this message on terminal: > > DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN"> > > > > 405 Method Not Allowed > > > >

Method Not Allowed

> >

The requested method PUT is not allowed for the URL /transfer/incoming= .

> >

Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port= 80

> > > >=20 > > So I am not sure you received the file. You should find a suj46.zip corre= sponding to the complete folder from my subject 46. You will find the > > usual structure created by recon-all. At mri folder you will find all the= usual volumes, the posterior* files generated by hippo-subfield > > processing and the files I created on my analysis. Please, could you chec= k if you really received the file? If not, I will try again using plain > > ftp. > > Thank you again for your help. > > Marcos. > > Em Seg, 2013-10-07 =C3=A0s 09:21 -0400, Bruce Fischl escreveu: > >=20 > > hmmm, I guess you should upload the subject so that we can track it down > > On=20 > > Mon, 7 Oct 2013, Marcos Martins da Silva wrote: > >=20 > > > Hi, Bruce. > > > Thank you for your fast answer. > > > I used a script and It took less than 15 min to process all files from = all subjects, except > > > the 3 files (surfaces) mris_smooth seems to enter a loop. When I tried = to smooth > > > surfLeftHippobody I waited for more than 4 hours. Comparing to the tota= l time I needed to > > > process all files I concluded something was wrong and esed control + C = to interrupt the > > > process. I tested on 2 machines (mine is running CentOS 6 and the secon= d is a Mac, both using > > > Freesurfer 5.3) and got the same result. Including they seem to stop at= the same point. Do you > > > think it could need more time to finnish processing? > > > Alternatively, as I can use mris_smooth to process the whole left hippo= campus (the problem > > > only appears when processing the body segment), I guess I could get a s= imilar and perhaps > > > better result if I could make a label from each of the binary masks of = the 3 segments (head, > > > body, tail), merge them in an annot file and finally load the whole sur= face and the annot file > > > so I get the 3 segments discriminated by color. I found on Freesurfer W= iki how to merge the > > > labels into an annot file but not how to make the labels from the binar= y masks. > > > Thank you for your attention. > > >=20 > > >=20 > > > 2013/10/4 Bruce Fischl > > > how long have you waited? > > > > > > On Fri, 4 Oct 2013, Marcos Martins da Silva wrote: > > >=20 > > > > > > Hi, Freesurfers > > > I am getting some interesting hippocampal surfaces with the= following > > > steps: > > > 1- recon-all -all -hippo-subfields > > > 2- mri-concat (only CA1, CA23, CA4DG and the tail complemen= t volumes) > > > 3- a custom OCTAVE script to segment the concatenated volum= e from step > > > 2 > > > into Head, Body and Tail > > > 4- mri_binarize Head, Body and Tail volumes from step 3 > > > 5- mri_tessellate the binary masks from step 4 > > > 6- mri_smooth the surfaces from step 5 > > > > > > Using freeview I got a screenshot showing both hippocampi s= egmented > > > (hipposurf3d.png is attached). > > > This approach worked well for 16 subjects up to step 5. Ste= p 6 was > > > completed > > > as well in 13 out 16 subjects. > > > > > > The only problem was during left hippocampal body smoothing= in 3 > > > subjects > > > (all the other surfaces from all 16 subjects in were smooth= ed with no > > > problem). For these 3 surfaces, mris_smooth simply freezes,= with no > > > error > > > message. I must press control + C to quit the program. Duri= ng the > > > freezing I > > > noticed high CPU use. > > > It follows the exactly command I used and the screen output. > > > > > > mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfH= ippoBody > > > using Gaussian curvature smoothing with norm 5.00 with 2 sm= ooth steps > > > averaging curvature for 1 iterations > > > smoothing for 1 iterations > > > smoothing surface tessellation for 1 iterations... > > > ------------------------------------------------------ > > > ------------------------------------------------------ > > > ------------------ pass 1 (num=3D2853) ------------------ > > > ------------------------------------------------------ > > > ------------------------------------------------------ > > > > > > If I supress the gaussian parameters and run just something= like: > > > mris_smooth -nw -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody > > > or even > > > mris_smooth -nw surfLeftHippoBody lh.surfHippoBody > > > > > > I got the smoothed surface with no errors but the final qua= lity is not > > > as > > > good as when I use the gaussian parameters. > > > I am attaching one of the problematic surface files so you = can check > > > it > > > (surfLeftHippobody). Intersting if I use a surface with all= left > > > hippocampus > > > (including head, problematic body and tail and) smoothing c= ompletes > > > without > > > error > > > Thank you very much for any help. > > > Marcos > > >=20 > > >=20 > > >=20 > > >=20 > > >=20 > > > 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 He= lpLine 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. > > >=20 > > >=20 > > >=20 > > > > >=20 > >=20 > >=20 > > --===============6341289076574494449== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.html" MIME-Version: 1.0 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUUkFOU0lUSU9OQUwv L0VOIj4KPEhUTUw+CjxIRUFEPgogIDxNRVRBIEhUVFAtRVFVSVY9IkNvbnRlbnQtVHlwZSIgQ09O VEVOVD0idGV4dC9odG1sOyBDSEFSU0VUPVVURi04Ij4KICA8TUVUQSBOQU1FPSJHRU5FUkFUT1Ii IENPTlRFTlQ9Ikd0a0hUTUwvNC42LjYiPgo8L0hFQUQ+CjxCT0RZPgpXb3chIFRoYXQgd2FzIGZh c3QuPEJSPgpJIGFtIHJ1bm5pbmcgRnJlZVN1cmZlciA1LjMgb24gdG9wIG9mIENlbnRPUzYgKDY0 LWJpdCkuIE15IGhhcmR3YXJlIGlzIGEgUEMgcG93ZXJlZCBieSBJbnRlbCYjMTc0OyBDb3JlJiM4 NDgyOyBpNSBDUFUgTSA1MjAgQCAyLjQwR0h6ICYjMjE1OyA0PEJSPgpUaGFuayB5b3UgZm9yIGFs 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