From fischl@nmr.mgh.harvard.edu Tue Oct 8 08:24:27 2013 From: Bruce Fischl To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_smooth issue with gaussian parameters Date: Tue, 08 Oct 2013 08:24:23 -0400 Message-ID: In-Reply-To: <1381204905.2072.13.camel@alien> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============3361883439608519446==" --===============3361883439608519446== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable ok, I just downloaded it and am trying to replicate your problem now On Tue,=20 8 Oct 2013, Marcos Martins da Silva wrote: > Hi, Bruce > Filedrop worked great and fast! Thank you for the tip. > It follows the bath I run for each subject: > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippo lh.surfHippo > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoHead lh.surfHipp= oHead > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHipp= oBody > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoTail lh.surfHipp= oTail > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippo rh.surfHippo > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippoHead rh.surfHip= poHead > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippoBody rh.surfHip= poBody > =C2=A0=C2=A0 mris_smooth -nw -g 5 2 -a 1 -n 1 surfRightHippoTail rh.surfHip= poTail >=20 > 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 as 20:47 -0400, Bruce Fischl escreveu: >=20 > 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 b > ut > > 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 as 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 a > ll > >=C2=A0 subjects, except > > > the 3 files (surfaces) mris_smooth seems to enter a loop. When I tried t > o=20 > > smooth > > > surfLeftHippobody I waited for more than 4 hours. Comparing to the total > t > > ime I needed to > > > process all files I concluded something was wrong and esed control + C t > o=20 > > interrupt the > > > process. I tested on 2 machines (mine is running CentOS 6 and the second > i > > s a Mac, both using > > > Freesurfer 5.3) and got the same result. Including they seem to stop at= =20 > 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 hippoc > am > > pus (the problem > > > only appears when processing the body segment), I guess I could get a si > mi > > lar and perhaps > > > better result if I could make a label from each of the binary masks of t > he > >=C2=A0 3 segments (head, > > > body, tail), merge them in an annot file and finally load the whole surf > ac > > e and the annot file > > > so I get the 3 segments discriminated by color. I found on Freesurfer Wi > ki > >=C2=A0 how to merge the > > > labels into an annot file but not how to make the labels from the binary > m > > asks. > > > 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= Hi, 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=20 > fo > > llowing > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= 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= 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 > v > > olumes) > > >=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 > f > > rom 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= into 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= Using freeview I got a screenshot showing both hippocampi se > gm > > ented > > >=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= This approach worked well for 16 subjects up to step 5. Step > 6 > >=C2=A0 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= completed > > >=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 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= The only problem was during left hippocampal body smoothing=20 > in > >=C2=A0 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= 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= (all the other surfaces from all 16 subjects in were smoothe > d=20 > > 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= problem). For these 3 surfaces, mris_smooth simply freezes,=20 > wi > > th 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= error > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= message. I must press control + C to quit the program. Durin > g=20 > > 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= freezing 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= noticed 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= It 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= mris_smooth -nw -g 5 2 -a 1 -n 1 surfLeftHippoBody lh.surfHi > pp > > oBody > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= using Gaussian curvature smoothing with norm 5.00 with 2 smo > ot > > h 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= averaging 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= smoothing 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= smoothing 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= If I supress the gaussian parameters and run just something=20 > li > > ke: > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= mris_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= or 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= mris_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 qual > it > > y 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= good 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 c > an > >=C2=A0 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=20 > le > > ft > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= hippocampus > > >=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 co > mp > > letes > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= without > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= error > > >=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0= Thank 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= Marcos > > >=20 > > >=20 > > >=20 > > >=20 > > >=20 > > > The information in this e-mail is intended only for the person to whom i > t=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 Hel > pL > > ine at > > > http://www.partners.org/complianceline . If the e-mail was sent to you i > n=20 > > error > > > but does not contain patient information, please contact the sender and= =20 > pr > > operly > > > dispose of the e-mail. > > >=20 > > >=20 > > >=20 > > > > >=20 > >=20 > >=20 > > >=20 >=20 >=20 > --===============3361883439608519446==--