From fischl@nmr.mgh.harvard.edu Mon Oct 7 20:47:06 2013 From: Bruce Fischl To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_smooth issue with gaussian parameters Date: Mon, 07 Oct 2013 20:47:04 -0400 Message-ID: In-Reply-To: <1381182953.3668.14.camel@alien> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3593043391084537061==" --===============3593043391084537061== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable sorry, I don't think it completed as unzip can't find the end of directory=20 mark in the file. Try our filedrop instead: https://gate.nmr.mgh.harvard.edu/filedrop2/ cheers Bruce On=20 Mon, 7 Oct 2013, Marcos Martins da=20 Silva wrote: > 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

> >=20 > 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. > 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= =20 > smooth > > surfLeftHippobody I waited for more than 4 hours. Comparing to the total t > ime I needed to > > process all files I concluded something was wrong and esed control + C to= =20 > interrupt the > > process. I tested on 2 machines (mine is running CentOS 6 and the second i > s a Mac, both using > > Freesurfer 5.3) and got the same result. Including they seem to stop at th > e 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 hippocam > pus (the problem > > only appears when processing the body segment), I guess I could get a simi > lar 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 surfac > e and the annot file > > so I get the 3 segments discriminated by color. I found on Freesurfer Wiki > how to merge the > > labels into an annot file but not how to make the labels from the binary m > asks. > > Thank you for your attention. > >=20 > >=20 > > 2013/10/4 Bruce Fischl > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 how long have you waited? > > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 On Fri, 4 Oct 2013, Marcos Martins da= Silva wrote: > >=20 > > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 H= i, Freesurfers > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I= am getting some interesting hippocampal surfaces with the fo > llowing > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 s= teps: > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 1= - recon-all -all -hippo-subfields > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 2= - mri-concat (only CA1, CA23, CA4DG and the tail complement v > olumes) > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 3= - a custom OCTAVE script to segment the concatenated volume f > rom step > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 2 > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 i= nto Head, Body and Tail > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 4= - mri_binarize Head, Body and Tail volumes from step 3 > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 5= - mri_tessellate the binary masks from step 4 > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 6= - mri_smooth the surfaces from step 5 > > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 U= sing freeview I got a screenshot showing both hippocampi segm > ented > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (= hipposurf3d.png is attached). > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 T= his approach worked well for 16 subjects up to step 5. Step 6 > was > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 c= ompleted > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 a= s well in 13 out 16 subjects. > > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 T= he only problem was during left hippocampal body smoothing in > 3 > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 s= ubjects > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (= all the other surfaces from all 16 subjects in were smoothed=20 > with no > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 p= roblem). For these 3 surfaces, mris_smooth simply freezes, wi > th no > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 e= rror > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 m= essage. I must press control + C to quit the program. During=20 > the > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 f= reezing I > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 n= oticed high CPU use. > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I= t follows the exactly command I used and the screen output. > > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 m= ris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHipp > oBody > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 u= sing Gaussian curvature smoothing with norm 5.00 with 2 smoot > h steps > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 a= veraging curvature for 1 iterations > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 s= moothing for 1 iterations > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 s= moothing surface tessellation for 1 iterations... > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -= ----------------------------------------------------- > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -= ----------------------------------------------------- > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -= ----------------- pass 1 (num=3D2853) ------------------ > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -= ----------------------------------------------------- > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 -= ----------------------------------------------------- > > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I= f I supress the gaussian parameters and run just something li > ke: > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 m= ris_smooth -nw -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 o= r even > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 m= ris_smooth -nw=C2=A0 surfLeftHippoBody lh.surfHippoBody > > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I= got the smoothed surface with no errors but the final qualit > y is not > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 as > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 g= ood as when I use the gaussian parameters. > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 I= am attaching one of the problematic surface files so you can > check > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 it > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (= surfLeftHippobody). Intersting if I use a surface with all le > ft > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 h= ippocampus > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 (= including head, problematic body and tail and) smoothing comp > letes > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 w= ithout > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 e= rror > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 T= hank you very much for any help. > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 M= arcos > >=20 > >=20 > >=20 > >=20 > >=20 > > The information in this e-mail is intended only for the person to whom it= =20 > is > > addressed. If you believe this e-mail was sent to you in error and the e-m > ail > > contains patient information, please contact the Partners Compliance HelpL > ine at > > http://www.partners.org/complianceline . If the e-mail was sent to you in= =20 > error > > but does not contain patient information, please contact the sender and pr > operly > > dispose of the e-mail. > >=20 > >=20 > >=20 > > >=20 >=20 >=20 > --===============3593043391084537061==--