Hello Ali, I looked at the data and its not surprising talairach failed. Parts of the temporal lobes and cerebellum are missing, so a manual alignment might be a good idea.
However, I have discovered how to get around the perl error on Ubuntu machines. You will need to install "perlbrew" then use it to install perl version 5.14 onto your machine. To instal perlbrew type the following: $> sudo apt-get install perlbrew Then use perlbrew to install perl version 5.14.14 $> perlbrew install perl-5.14.4 $> perlbrew switch perl-5.14.4 Once complete type "which perl" to see where perl 5.14 was installed. Replace the top line of $FREESURFER_HOME/mni/bin/mritotal with the output of the "which perl" command: replace: #!/usr/bin/perl -w with: #!<output_from_which_perl> This will resolve the shellwords.pl error message. I ran your example case and recon-all has been running for several hours (but still not yet complete). Best, -Zeke On 09/02/2015 01:53 AM, Ali Radaideh wrote: > Dear Z K, > > I have put them in transfer/incoming folder. The file name is example.tar.gz > > Thanks in advance, > Ali > > On Tue, Sep 1, 2015 at 1:33 PM, Z K <zkauf...@nmr.mgh.harvard.edu > <mailto:zkauf...@nmr.mgh.harvard.edu>> wrote: > > Hello Ali, > > As you have observed, when there is an alignment failure using the > talairach method, freesurfer reverts to the mni tool "mritotal". The mni > tools will error out with mritotal because mritotal references > "shellwords.pl <http://shellwords.pl>" which no longer ships with > new version of perl (starting > around 5.14). In order to solve this error the user either needs to > manually align the data or use an older version of perl. > > One possible work around is to use tkregister to manually align the > image, such that mritotal is not run, and the rest of recon-all should > run properly. > > If you can upload the data for a subject that fails to our ftp server I > will take a look: > > https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange > > Let me know once you have uploaded the file. > > -Zeke > > > > > On 09/01/2015 01:04 AM, Ali Radaideh wrote: > > Thanks Bruce, > > > > Could you please suggest something for me t sort out this issue for > > future projects. All PCs will have UBUNTU 14.04 and not of them > was able > > to run the 8 subjects. If I install an older version of UBUNTU > then Ii > > dont get and update and so can not install tcsh and csh. > > > > Today I am running subject number 5 of those who failed to run > before. > > It is running fine on that PC with UBUNTU 13.1. > > > > I want also to provide you with this info. > > > > All the 8 subjects did not pass the talairach step. and went to the > > MRITOTAL stage where they all failed to run on any PC with UBUNTU > 14.01. > > However, when running them on the PC with UBUNTU 13.1, they also dont > > pass the talairach stage and go to MRITOTAL and then the pass > this step > > and carry on. > > > > I thought this may help you figuring out the problem. > > > > Many thanks in advance, > > Ali > > > > On Mon, Aug 31, 2015 at 10:31 AM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>>> wrote: > > > > Hi Ali > > > > it's not that I know that the quality is fine. It might be > (or not), > > but this seems to be a perl error that doesn't have to do > with quality > > Bruce > > On Mon, 31 Aug 2015, Ali Radaideh wrote: > > > > Dear Bruce and Jürgen, > > > > Now I see something important which may help solving the > problem. > > > > I have 31 PCs in my lab and all of them are installed with > > UBUNTU 14.04. 30 > > PCs were able to process all 47 subjects successfully. But > > failed to process > > the remaining 8 subjects. Fortunately, one PC is > installed with > > UBUNTU > > 13.01. I managed to installed the tcsh and csh after > update and > > then run two > > of the failed subjects so far successfully. I concluded > it is the > > installation version of UBUNTU. So 13.01 works fine but > not 14.04. > > > > I tried to re-install 13.01 on another PC, and I did that > > successfully. > > However, but when I come to install the tcsh, after update it > > fails and it > > says it is unable to locate the package tcsh (the reason > is that > > 13.01 has > > not longer packages to download. > > > > As a summary, > > > > one PC with 13.01 UBUNTU is running OK (but with the tcsh > installed) > > another OC with 13.01 is not running because I was not > able to > > install tcsh > > after update > > > > I am now think of copying the tcsh from one pc to the > 13.01 PC > > to make it > > running but still trying. > > > > I think as Bruce said, it is something wrong with the > > installation as the > > quality is fine. > > > > I hope I was able to clarify the problem and hope to > receive any > > helpful > > answer. > > > > Many thanks in advance > > > > Ali > > > > > > > > On Sun, Aug 30, 2015 at 4:05 PM, Bruce Fischl > > <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu> > <mailto:fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>> > > wrote: > > Hi > > Jürgen and Ali > > > > I don't think it has anything to do with the quality of the > > data, but > > we are also happy to take a look if you upload one > subject. This > > seems > > more like an installation issue, and I would think it would > > happen on > > every subject. Did someone upgrade perl at somepoint? Or > just some > > paths? > > > > > > cheers > > Bruce > > > > On Sun, 30 Aug 2015, Jürgen Hänggi wrote: > > > > Dear Ali > > > > instead of downgrading perl you can use the > perlbrew tool > > that allow to > > install several perls in parallel and switch > between perl > > versions. > > if you are able to install perl 5.12 (perlbrew install > > 5.12, you can see the > > available perl versions with perlbrew available) > and then > > use > > perlbrew use 5.12 before running recon-all in the > > terminal. > > > > Does it work? > > > > Cheers > > Jürgen > > > > > > > > --------------------------------------------------------------------------- > > > > Jürgen Hänggi, Ph.D. > > > > Division Neuropsychology > > > > Institute of Psychology > > > > University of Zurich > > > > Binzmuehlestrasse 14, PO Box 25 > > > > 8050 Zurich, Switzerland > > > > 0041 44 635 73 97 (phone office) > > > > 0041 76 445 86 84 (phone mobile) > > > > 0041 44 635 74 09 (fax office) > > > > BIN 4.D.04 (office room number) > > > > j.haenggi[at]psychologie.uzh.ch > <http://psychologie.uzh.ch> > > <http://psychologie.uzh.ch> (email) > > > > http://www.psychologie.uzh.ch/neuropsy/ (website) > > > > http://www.juergenhaenggi.ch (private website) > > > > > > This e-mail (and any attachment/s) contains > confidential > > > > and/or privileged information. If you are not the > intended > > > > recipient (or have received this e-mail in error) > please > > notify > > > > the sender immediately and destroy this e-mail. Any > > > > unauthorised copying, disclosure or distribution > of the > > > > material in this e-mail is strictly forbidden. > > > > > > --------------------------------------------------------------------------- > > > > > > > > > > Von: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>> on behalf of > > Ali Radaideh > > <ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo> <mailto:ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo>>> > > Antworten an: Freesurfer Mailinglist > > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > Datum: Samstag, 29. August 2015 15:56 > > An: Freesurfer Mailinglist > > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > Betreff: Re: [Freesurfer] MRITOTAL > > > > Dear Jürgen, > > > > Thanks for your reply. Could you please guide me > on how to > > downgrade > > it? I need to try everything with these 8 subjects to > > finish the whole > > cohort of subjects. > > > > Your help is so appreciated. > > > > Thanks, > > Ali > > > > On Sat, Aug 29, 2015 at 4:16 PM, Jürgen Hänggi > > <j.haen...@psychologie.uzh.ch > <mailto:j.haen...@psychologie.uzh.ch> > > <mailto:j.haen...@psychologie.uzh.ch > <mailto:j.haen...@psychologie.uzh.ch>>> wrote: > > Dear Ali > > > > > > if Talairach alignment is not of good quality, then > > mritotal is > > used and the shellwords.pl <http://shellwords.pl> > <http://shellwords.pl> problem > > is related to the fact > > that > > you have a newer version of perl that no longer > contain > > shellwords.pl <http://shellwords.pl> <http://shellwords.pl>. > > > > you can downgrade perl to 5.12 or so, which > however, is > > not a > > good idea. > > > > > > I have no other solution > > > > > > Cheers > > > > Jürgen > > > > > > > > Von: <freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>> on behalf of > > Ali > > Radaideh <ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo> > > <mailto:ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo>>> > > Antworten an: Freesurfer Mailinglist > > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > Datum: Samstag, 29. August 2015 13:41 > > An: Freesurfer Mailinglist > > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>> > > Betreff: [Freesurfer] MRITOTAL > > > > Dear FreeSurfer experts, > > > > I have sent email 10 days ago asking for a help with > > processing 8 out of 55 subjects who failed to pass the > > Talairach phase and gave me the following error: > > > > tmpdir is transforms/tmp.talairach.5272 > > > > /media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FILES/ > > > > MS_patients/freesurfer_test/Images_test/Samer/mri > > mri_convert orig_nu.mgz > > transforms/tmp.talairach.5272/src.mnc > > mri_convert orig_nu.mgz > > transforms/tmp.talairach.5272/src.mnc > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 > mreuter > > Exp $ > > reading from orig_nu.mgz... > > TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to transforms/tmp.talairach.5272/src.mnc... > > -------------------------------------------- > > mritotal -verbose -debug -clobber -modeldir > > /usr/local/freesurfer/mni/bin/../share/mni_autoreg > > -protocol icbm transforms/tmp.talairach.5272/src.mnc > > transforms/talairach.auto.xfm > > Can't locate shellwords.pl <http://shellwords.pl> > <http://shellwords.pl> in @INC > > (@INC contains: > > /usr/local/freesurfer/mni/bin/../lib/mni_autoreg > > /usr/local/freesurfer/mni/lib/perl5/5.8.5 /etc/perl > > /usr/local/lib/perl/5.18.2 > /usr/local/share/perl/5.18.2 > > /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 > > /usr/share/perl/5.18 /usr/local/lib/site_perl .) at > > /usr/local/freesurfer/mni/bin/mritotal line 460. > > ERROR: mritotal failed, see transforms/talairach.log > > Linux ali-XPS-L501X 3.19.0-27-generic > #29~14.04.1-Ubuntu > > SMP Sun Aug 16 01:51:13 UTC 2015 x86_64 x86_64 x86_64 > > GNU/Linux > > > > recon-all -s Samer exited with ERRORS at Sat Aug 29 > > 07:27:06 EDT 2015 > > > > For more details, see the > > > > logfile/media/ali/HU_Research/HU_Research/HU/MS_Project/MS_analysis/ANALYZE_FI > > LES/ > > > > > MS_patients/freesurfer_test/Images_test/Samer/scripts/recon-all.log > > To report a problem, see > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > Please, is there any way I can force this phase to > run? I > > have checked the images and they look fine but I > dont know > > why they failed. > > > > Please your response is so important to my project as > > everything is pending. > > > > Many thanks in advance > > > > Ali > > > > -- > > Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo> <mailto:ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo>> > > webpage: > http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= > > > > _______________________________________________ > Freesurfer > > > > > > mailinglistfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/ > <http://mail.nmr.mgh.harvard.edu/mailman/> > > <http://mail.nmr.mgh.harvard.edu/mailman/> > > list > > info/freesurfer 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. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > > > -- > > Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo> <mailto:ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo>> > > webpage: > http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= > > > > _______________________________________________ > Freesurfer > > mailing > > list Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > 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. > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > > > -- > > Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo> <mailto:ali.radai...@hu.edu.jo > <mailto:ali.radai...@hu.edu.jo>> > > webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM= > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > 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. > > > > > > > > > > -- > > /Ali M. Al-Radaideh. PhD > > Head of Department of Medical Imaging > > Vice Dean of the Faculty of Allied Health Sciences > > The Hashemite University, > > Zarqa, Jordan > > W.phone +962 5 3903333 ext.5422, 5355, 5364 > > Email: ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo> > <mailto:ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo>> > > / > > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > -- > /Ali M. Al-Radaideh. PhD > Head of Department of Medical Imaging > Vice Dean of the Faculty of Allied Health Sciences > The Hashemite University, > Zarqa, Jordan > W.phone +962 5 3903333 ext.5422, 5355, 5364 > Email: ali.radai...@hu.edu.jo <mailto:ali.radai...@hu.edu.jo> > / > /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
