From fischl@nmr.mgh.harvard.edu Tue Oct 8 09:00:28 2013 From: Bruce Fischl To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_smooth issue with gaussian parameters Date: Tue, 08 Oct 2013 09:00:22 -0400 Message-ID: In-Reply-To: <1381182953.3668.14.camel@alien> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3623896244958496638==" --===============3623896244958496638== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi Marcos 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. cheers Bruce On Mon, 7 Oct 2013, Marcos Martins da=20 Silva wrote: > Hi, Bruce > I proceeded as explained at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFil= eExchange . > 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 bu= t 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.<= /p> >

Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 8= 0

> >=20 > So I am not sure you received the file. You should find a suj46.zip corresp= onding 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 u= sual 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 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 > >=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 following > >=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 volumes) > >=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 from 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 segmented > >=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 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, 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 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 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.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 u= sing Gaussian curvature smoothing with norm 5.00 with 2 smooth 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 like: > >=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 quality 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 left > >=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 completes > >=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= 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 > > >=20 >=20 >=20 > --===============3623896244958496638==--