Hi Marcos I've fixed this problem, which is a bug in one of the open source math libraries we use. If you email us the details of your hardware/software environment we'll get you a patch. cheers Bruce On Mon, 7 Oct 2013, Marcos Martins da 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"> > <html><head> > <title>405 Method Not Allowed</title> > </head><body> > <h1>Method Not Allowed</h1> > <p>The requested method PUT is not allowed for the URL /transfer/incoming.</p> > <hr> > <address>Apache/2.2.15 (CentOS) Server at surfer.nmr.mgh.harvard.edu Port 80</address> > </body></html> > > 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 às 09:21 -0400, Bruce Fischl escreveu: > > hmmm, I guess you should upload the subject so that we can track it down > On > Mon, 7 Oct 2013, Marcos Martins da Silva wrote: > > > 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 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 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 hippocampus (the problem > > only appears when processing the body segment), I guess I could get a similar 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 surface 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 masks. > > Thank you for your attention. > > > > > > 2013/10/4 Bruce Fischl <fischl@nmr.mgh.harvard.edu> > > how long have you waited? > > > > On Fri, 4 Oct 2013, Marcos Martins da Silva wrote: > > > > > > 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 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 segmented > > (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 in 3 > > subjects > > (all the other surfaces from all 16 subjects in were smoothed with no > > problem). For these 3 surfaces, mris_smooth simply freezes, with 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.surfHippoBody > > using Gaussian curvature smoothing with norm 5.00 with 2 smooth steps > > averaging curvature for 1 iterations > > smoothing for 1 iterations > > smoothing surface tessellation for 1 iterations... > > ------------------------------------------------------ > > ------------------------------------------------------ > > ------------------ pass 1 (num=2853) ------------------ > > ------------------------------------------------------ > > ------------------------------------------------------ > > > > 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 quality 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 completes > > without > > error > > Thank you very much for any help. > > Marcos > > > > > > > > > > > > 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. > > > > > > > > > > > >