From marcosm@hucff.ufrj.br Mon Oct 7 17:56:06 2013 From: Marcos Martins da Silva To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_smooth issue with gaussian parameters Date: Mon, 07 Oct 2013 18:55:53 -0300 Message-ID: <1381182953.3668.14.camel@alien> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============9045627885592518800==" --===============9045627885592518800== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi, Bruce I proceeded as explained at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange . 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

So I am not sure you received the file. You should find a suj46.zip corresponding 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 check if you really received the file? If not, I will try again using plain ftp. Thank you again for your help. Marcos.=20 Em Seg, 2013-10-07 =C3=A0s 09:21 -0400, Bruce Fischl escreveu: > 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 al= l 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 total = 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 second = is a Mac, both using > > Freesurfer 5.3) and got the same result. Including they seem to stop at t= he 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 hippoca= mpus (the problem > > only appears when processing the body segment), I guess I could get a sim= ilar and perhaps > > better result if I could make a label from each of the binary masks of th= e 3 segments (head, > > body, tail), merge them in an annot file and finally load the whole surfa= ce and the annot file > > so I get the 3 segments discriminated by color. I found on Freesurfer Wik= i how to merge the > > labels into an annot file but not how to make the labels from the binary = 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 f= ollowing > > steps: > > 1- recon-all -all -hippo-subfields > > 2- mri-concat (only CA1, CA23, CA4DG and the tail complement = volumes) > > 3- a custom OCTAVE script to segment the concatenated volume = 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 seg= mented > > (hipposurf3d.png is attached). > > This approach worked well for 16 subjects up to step 5. Step = 6 was > > completed > > as well in 13 out 16 subjects. > > > > The only problem was during left hippocampal body smoothing i= n 3 > > subjects > > (all the other surfaces from all 16 subjects in were smoothed= with no > > problem). For these 3 surfaces, mris_smooth simply freezes, w= ith no > > error > > message. I must press control + C to quit the program. During= 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.surfHip= poBody > > using Gaussian curvature smoothing with norm 5.00 with 2 smoo= th 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 l= ike: > > 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 quali= ty is not > > as > > good as when I use the gaussian parameters. > > I am attaching one of the problematic surface files so you ca= n check > > it > > (surfLeftHippobody). Intersting if I use a surface with all l= eft > > hippocampus > > (including head, problematic body and tail and) smoothing com= pletes > > 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 Help= Line 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 p= roperly > > dispose of the e-mail. > >=20 > >=20 > >=20 > > --===============9045627885592518800== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.html" MIME-Version: 1.0 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUUkFOU0lUSU9OQUwv L0VOIj4KPEhUTUw+CjxIRUFEPgogIDxNRVRBIEhUVFAtRVFVSVY9IkNvbnRlbnQtVHlwZSIgQ09O VEVOVD0idGV4dC9odG1sOyBDSEFSU0VUPVVURi04Ij4KICA8TUVUQSBOQU1FPSJHRU5FUkFUT1Ii IENPTlRFTlQ9Ikd0a0hUTUwvNC42LjYiPgo8L0hFQUQ+CjxCT0RZPgpIaSwgQnJ1Y2U8QlI+Ckkg cHJvY2VlZGVkIGFzIGV4cGxhaW5lZCBhdCA8QSBIUkVGPSJodHRwOi8vc3VyZmVyLm5tci5tZ2gu aGFydmFyZC5lZHUvZnN3aWtpL0Z0cEZpbGVFeGNoYW5nZSI+aHR0cDovL3N1cmZlci5ubXIubWdo LmhhcnZhcmQuZWR1L2Zzd2lraS9GdHBGaWxlRXhjaGFuZ2U8L0E+IC48QlI+ClVzaW5nIGZ0cCBt ZXRob2QsIGl0IHN0YXJ0ZWQgYXQgZ29vZCByYXRlIGJ1dCBhZnRlciBJIHRyYW5zZmVycmVkIGFi 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