From marcosm@hucff.ufrj.br Tue Oct 8 00:01:51 2013 From: Marcos Martins da Silva To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_smooth issue with gaussian parameters Date: Tue, 08 Oct 2013 01:01:45 -0300 Message-ID: <1381204905.2072.13.camel@alien> In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============2861773284254456681==" --===============2861773284254456681== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Hi, Bruce Filedrop worked great and fast! Thank you for the tip. It follows the bath I run for each subject: mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippo lh.surfHippo mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoHead lh.surfHippoHead mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHippoBody mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoTail lh.surfHippoTail mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippo rh.surfHippo mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippoHead rh.surfHippoHead mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippoBody rh.surfHippoBody mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippoTail rh.surfHippoTail The only file with the problem I reported is surfLeftHippoBody (3rd line). If I could generate an annotation file from surfLeftHippoHead, surfLeftHippoBody and surfLeftHippoTail or the binary masks I used mri_tessellate to make these surfaces it would be a good alternative. Perhaps, even better because I would get a faster processing (smoothing 2 surfaces, surfLeftHippo and surfRightHippo, per subject instead of 8). Thank you again. Em Seg, 2013-10-07 =C3=A0s 20:47 -0400, Bruce Fischl escreveu: > sorry, I don't think it completed as unzip can't find the end of directory = > mark in the file. Try our filedrop instead: >=20 > https://gate.nmr.mgh.harvard.edu/filedrop2/ >=20 > cheers > Bruce >=20 >=20 > On=20 > Mon, 7 Oct 2013, Marcos Martins da=20 > Silva wrote: >=20 > > 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 tota= l 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 secon= d 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 hippo= cam > > pus (the problem > > > only appears when processing the body segment), I guess I could get a s= imi > > 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 sur= fac > > e and the annot file > > > so I get the 3 segments discriminated by color. I found on Freesurfer W= iki > > how to merge the > > > labels into an annot file but not how to make the labels from the binar= y m > > asks. > > > Thank you for your attention. > > >=20 > > >=20 > > > 2013/10/4 Bruce Fischl > > > how long have you waited? > > > > > > On Fri, 4 Oct 2013, Marcos Martins da Silva wrote: > > >=20 > > > > > > Hi, Freesurfers > > > I am getting some interesting hippocampal surfaces with the= fo > > llowing > > > steps: > > > 1- recon-all -all -hippo-subfields > > > 2- mri-concat (only CA1, CA23, CA4DG and the tail complemen= t v > > olumes) > > > 3- a custom OCTAVE script to segment the concatenated volum= e f > > rom 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 s= egm > > ented > > > (hipposurf3d.png is attached). > > > This approach worked well for 16 subjects up to step 5. Ste= p 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 smooth= ed=20 > > with no > > > problem). For these 3 surfaces, mris_smooth simply freezes,= wi > > th no > > > error > > > message. I must press control + C to quit the program. Duri= ng=20 > > 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.surfH= ipp > > oBody > > > using Gaussian curvature smoothing with norm 5.00 with 2 sm= oot > > h steps > > > averaging curvature for 1 iterations > > > smoothing for 1 iterations > > > smoothing surface tessellation for 1 iterations... > > > ------------------------------------------------------ > > > ------------------------------------------------------ > > > ------------------ pass 1 (num=3D2853) ------------------ > > > ------------------------------------------------------ > > > ------------------------------------------------------ > > > > > > If I supress the gaussian parameters and run just something= li > > ke: > > > 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 qua= lit > > y 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= le > > ft > > > hippocampus > > > (including head, problematic body and tail and) smoothing c= omp > > letes > > > without > > > error > > > Thank you very much for any help. > > > Marcos > > >=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 He= lpL > > 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 > > --===============2861773284254456681== Content-Type: text/html Content-Transfer-Encoding: base64 Content-Disposition: attachment; filename="attachment.html" MIME-Version: 1.0 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDQuMCBUUkFOU0lUSU9OQUwv L0VOIj4KPEhUTUw+CjxIRUFEPgogIDxNRVRBIEhUVFAtRVFVSVY9IkNvbnRlbnQtVHlwZSIgQ09O VEVOVD0idGV4dC9odG1sOyBDSEFSU0VUPVVURi04Ij4KICA8TUVUQSBOQU1FPSJHRU5FUkFUT1Ii IENPTlRFTlQ9Ikd0a0hUTUwvNC42LjYiPgo8L0hFQUQ+CjxCT0RZPgpIaSwgQnJ1Y2U8QlI+CkZp bGVkcm9wIHdvcmtlZCBncmVhdCBhbmQgZmFzdCEgVGhhbmsgeW91IGZvciB0aGUgdGlwLjxCUj4K SXQgZm9sbG93cyB0aGUgYmF0aCBJIHJ1biBmb3IgZWFjaCBzdWJqZWN0OjxCUj4KJm5ic3A7Jm5i c3A7IDxCPm1yaXNfc21vb3RoIC1udyAtZyA1IDIgLWEgMSAtbiAxIHN1cmZMZWZ0SGlwcG8gbGgu 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