Re: [Freesurfer] Hippocampal subfields, stuck? [SOLVED!]
Hi all, It worked! I was setting up the alias in the shell, and it didn't work. I set up now the alias as a global alias in the tcsh profile file (~/.tcshrc) and it worked. No problem this time. Best, MBP On dijous 28 abril 2016 10:47 CEST, BAUTISTA-PERPINYA Maximilià<maximila.bautista-perpi...@etu.unistra.fr> wrote: > Hi Eugenio and all FS experts, > > I tried your suggestion of making an alias 'mv' > 'mv -f', but it still > didn't work. I am working on a tcsh shell. The alias does work when I type on > the terminal, but doesn't seem to be changed when running recon-all. Any > other suggestions? Any help could be greatly appreciated. > > Best, > > Max > > > > On dijous 21 abril 2016 17:09 CEST, Eugenio Iglesias <e.igles...@bcbl.eu> > wrote: > > > Dear Maximilià, > > first of all, sorry for the late response. > > We assume throughout the code that mv a.ext b.ext will overwrite b.ext if > > it exists. If this is not the case in your system, maybe you could create > > an alias from 'mv' -> 'mv -f' before calling recon-all? > > Cheers, > > /Eugenio > > > > Juan Eugenio Iglesias > > Postdoctoral researcher BCBL > > www.jeiglesias.com > > www.bcbl.eu > > > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > > > - Original Message - > > From: "BAUTISTA-PERPINYA Maximilià" > > <maximila.bautista-perpi...@etu.unistra.fr> > > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > > Sent: Monday, April 18, 2016 9:35:05 AM > > Subject: [Freesurfer] Hippocampal subfields, stuck? > > > > Dear all experts, > > > > I am running FS 6dev version. This is my recon-all comand: "recon-all > > -nuintensitycor-3T -i [directory] -s [subjectname] -all > > -hippocampal-subfields-T1". > > > > Everything goes fine until the ''Hippocampal Subfields processing (T1 > > only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It > > doesn't matter whether I say y or n; it seems it gets stuck and doesn't > > progress at all. There is no cpu usage. Any recommendations? I have > > attached the hippocampal subfields log. > > > > More info: > > - > > > > FREESURFER_HOME: /usr/local/freesurfer > > > > Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202 > > > > RedHat release: CentOS release 6.7 (Final) > > > > Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 > > > > - > > > > > > -- > > Maximilià Bautista-Perpinyà, BSc > > Master student at Joint Master in Neuroscience (JMN) > > Université de Strasbourg (in partnership with Universität Freiburg and > > Universität Basel) > > & > > Master Intern at Biological and Personality Psychology Laboratory > > Department of Psychology, Universität Freiburg > > > > (+49) 015759302368 > > maximila.bautista-perpi...@etu.unistra.fr > > maxbau...@gmail.com > > > > ___ > > Freesurfer mailing list > > 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 > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Maximilià Bautista-Perpinyà, BSc > Master student at Joint Master in Neuroscience (JMN) > Université de Strasbourg (in partnership with Universität Freiburg and > Universität Basel) > & > Master Intern at Biological and Personality Psychology Laboratory > Department of Psychology, Universität Freiburg > > (+49) 015759302368 > maximila.bautista-perpi...@etu.unistra.fr > maxbau...@gmail.com > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpi...@etu.unistra.fr maxbau...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfields, stuck?
Hi Eugenio and all FS experts, I tried your suggestion of making an alias 'mv' > 'mv -f', but it still didn't work. I am working on a tcsh shell. The alias does work when I type on the terminal, but doesn't seem to be changed when running recon-all. Any other suggestions? Any help could be greatly appreciated. Best, Max On dijous 21 abril 2016 17:09 CEST, Eugenio Iglesias <e.igles...@bcbl.eu> wrote: > Dear Maximilià, > first of all, sorry for the late response. > We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it > exists. If this is not the case in your system, maybe you could create an > alias from 'mv' -> 'mv -f' before calling recon-all? > Cheers, > /Eugenio > > Juan Eugenio Iglesias > Postdoctoral researcher BCBL > www.jeiglesias.com > www.bcbl.eu > > Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer > > - Original Message - > From: "BAUTISTA-PERPINYA Maximilià" > <maximila.bautista-perpi...@etu.unistra.fr> > To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> > Sent: Monday, April 18, 2016 9:35:05 AM > Subject: [Freesurfer] Hippocampal subfields, stuck? > > Dear all experts, > > I am running FS 6dev version. This is my recon-all comand: "recon-all > -nuintensitycor-3T -i [directory] -s [subjectname] -all > -hippocampal-subfields-T1". > > Everything goes fine until the ''Hippocampal Subfields processing (T1 > only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't > matter whether I say y or n; it seems it gets stuck and doesn't progress at > all. There is no cpu usage. Any recommendations? I have attached the > hippocampal subfields log. > > More info: > - > > FREESURFER_HOME: /usr/local/freesurfer > > Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202 > > RedHat release: CentOS release 6.7 (Final) > > Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 > > - > > > -- > Maximilià Bautista-Perpinyà, BSc > Master student at Joint Master in Neuroscience (JMN) > Université de Strasbourg (in partnership with Universität Freiburg and > Universität Basel) > & > Master Intern at Biological and Personality Psychology Laboratory > Department of Psychology, Universität Freiburg > > (+49) 015759302368 > maximila.bautista-perpi...@etu.unistra.fr > maxbau...@gmail.com > > ___ > Freesurfer mailing list > 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpi...@etu.unistra.fr maxbau...@gmail.com ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Hippocampal subfields, stuck?
Dear Maximilià, first of all, sorry for the late response. We assume throughout the code that mv a.ext b.ext will overwrite b.ext if it exists. If this is not the case in your system, maybe you could create an alias from 'mv' -> 'mv -f' before calling recon-all? Cheers, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: "BAUTISTA-PERPINYA Maximilià" <maximila.bautista-perpi...@etu.unistra.fr> To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> Sent: Monday, April 18, 2016 9:35:05 AM Subject: [Freesurfer] Hippocampal subfields, stuck? Dear all experts, I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1". Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log. More info: - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 - -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpi...@etu.unistra.fr maxbau...@gmail.com ___ Freesurfer mailing list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Hippocampal subfields, stuck?
Dear all experts, I am running FS 6dev version. This is my recon-all comand: "recon-all -nuintensitycor-3T -i [directory] -s [subjectname] -all -hippocampal-subfields-T1". Everything goes fine until the ''Hippocampal Subfields processing (T1 only)''. At some point it says '"mv: overwrite `imageDump.mgz'?". It doesn't matter whether I say y or n; it seems it gets stuck and doesn't progress at all. There is no cpu usage. Any recommendations? I have attached the hippocampal subfields log. More info: - FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos6_x86_64-dev-20160202 RedHat release: CentOS release 6.7 (Final) Kernel info: Linux 2.6.32-573.7.1.el6.x86_64 x86_64 - -- Maximilià Bautista-Perpinyà, BSc Master student at Joint Master in Neuroscience (JMN) Université de Strasbourg (in partnership with Universität Freiburg and Universität Basel) & Master Intern at Biological and Personality Psychology Laboratory Department of Psychology, Universität Freiburg (+49) 015759302368 maximila.bautista-perpi...@etu.unistra.fr maxbau...@gmail.com # #@# Hippocampal Subfields processing (T1 only) left Mon Apr 18 10:49:08 CEST 2016 -- Setting up environment variables --- LD_LIBRARY_PATH is .:/usr/local/freesurfer/MCRv80/runtime/glnxa64:/usr/local/freesurfer/MCRv80/bin/glnxa64:/usr/local/freesurfer/MCRv80/sys/os/glnxa64:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/freesurfer/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64: Warning: application is running on a locale different from the original platform locale. Warning: No display specified. You will not be able to display graphics on the screen. Registering imageDump.mgz to hippocampal mask from ASEG This file does not contain MRI parameters fixedImageFileName: imageDump.mgz movingImageFileName: /usr/local/freesurfer/subjects/B_HA_30_MRI_E_T0/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz degreesOfFreedom: 3 numberOfBins: 20 useDefaultSchedule: 1 initialTranslationMode: 2 extraInputImageFileNames: Initializing the parameters as follows: [0, -0, 0, -54.104, -70.9115, -45.3863, 1, 1, 1, 0, 0, 0] Using fixedShrinkFactors: [4, 4, 4] Shrinking fixed image: 0% 0.999885% 1.99977% 2.99965% 3.99954% 4.99942% 5.99931% 6.99919% 7.99908% 8.99896% 9.99885% 10.9987% 11.9986% 12.9985% 13.9984% 14.9983% 15.9982% 16.998% 17.9979% 18.9978% 19.9977% 20.9976% 21.9975% 22.9973% 23.9972% 24.9971% 25.997% 26.9969% 27.9968% 28.9967% 29.9965% 30.9964% 31.9963% 32.9962% 33.9961% 34.996% 35.9959% 36.9957% 37.9956% 38.9955% 39.9954% 40.9953% 41.9952% 42.995% 43.9949% 44.9948% 45.9947% 46.9946% 47.9945% 48.9944% 49.9942% 50.9941% 51.994% 52.9939% 53.9938% 54.9937% 55.9935% 56.9934% 57.9933% 58.9932% 59.9931% 60.993% 61.9929% 62.9927% 63.9926% 64.9925% 65.9924% 66.9923% 67.9922% 68.9921% 69.9919% 70.9918% 71.9917% 72.9916% 73.9915% 74.9914% 75.9912% 76.9911% 77.991% 78.9909% 79.9908% 80.9907% 81.9906% 82.9904% 83.9903% 84.9902% 85.9901% 86.99% 87.9899% 88.9897% 89.9896% 90.9895% 91.9894% 92.9893% 93.9892% 94.9891% 95.9889% 96.9888% 97.9887% 98.9886% 99.9885% 100% 100% Using movingShrinkFactors: [1, 1, 1] Shrinking moving image: 0% 1% 2% 3% 4% 5% 6% 7% 8% 9% 10% 11% 12% 13% 14% 15% 16% 17% 18% 19% 20% 21% 22% 23% 24% 25% 26% 27% 28% 29% 30% 31% 32% 33% 34% 35% 36% 37% 38% 39% 40% 41% 42% 43% 44% 45% 46% 47% 48% 49% 50% 51% 52% 53% 54% 55% 56% 57% 58% 59% 60% 61% 62% 63% 64% 65% 66% 67% 68% 69% 70% 71% 72% 73% 74% 75% 76% 77% 78% 79% 80% 81% 82% 83% 84% 85% 86% 87% 88% 89% 90% 91% 92% 93% 94% 95% 96% 97% 98% 99% 100% 100% 100% Using fixedSchedule: [4, 4, 4] [1, 1, 1] Using movingSchedule: [4, 4, 4] [1, 1, 1] Using scales: [57.1429, 57.1429, 57.1429, 1, 1, 1, 100, 100, 100, 100, 100, 100] Using parameterOrder: [0, 0, 0, 1, 2, 3, 0, 0, 0, 0, 0, 0] Calculating fixed image pyramid: 0% 50% 100% Calculating moving image pyramid: 0% 50% 100% Doing registration at level 0 of 2 Iteration 0: value = -0.172259 Current position: Rotation: 0 -0 0 Translation: -52.4992 -74.7962 -46.0813 Scaling: 1 1 1 Skewing: 0 0 0 Iteration
