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.
> 
> 
> 
>