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. MarcosThe 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.