Re: [Freesurfer] Hippocampal segmentation doubts
Thank you so much for your answer Koen,I understand, but now I'm having some trouble when running the command on one subject, hope you can help me.I have tried to perform the hippocampal subfields segmentation by running:recon-all -s MySubject -hippo-subfields and also:kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults But I always get the following error:maximalDeformation: 75.1793Transforming meshDone transforming meshRasterizing Levenberg-Marquardt...numberOfEntries: 24131/root/trabajo/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 23175 Segmentation fault kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtfailed to do kvlSegmentWithoutGUI configurationFileDeformableRegistration.txtLinux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul 3 15:54:39 CEST 2012For more details, see the log file /root/trabajo/freesurfer/subjects/MySubject/scripts/recon-all.logTo report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReportingThe recon-all.log says:##@# Hippocampal Subfields processing Tue Jul 3 15:48:33 CEST 2012 mkdir -p /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults kvlSegmentHippocampalSubfields.sh MySubject left /root/trabajo/freesurfer/subjects /root/trabajo/freesurfer/subjects/MySubject/tmp/subfieldResults Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linuxrecon-all -s MySubject exited with ERRORS at Tue Jul 3 15:54:39 CEST 2012To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting This error occurres only on this subject and for the left hemisphere, not like this for the right hemisphere, which ends perfectly when running the second command. I'm sending you the configurationFileDeformation for the left hemisphere, in case it may help. Any help will be so appreciatedBest Regards,GabrielEl 04/07/12, Koen Van Leemput k...@nmr.mgh.harvard.edu escribió:Hi Gabriel,1. Using pre-processed data obtained with an older version ofFreeSurfer should be OK, as long as you remember that the obtainedresults might/will be different from the ones you'd get if you had runthe whole analysis from scratch.2. The generic label hippocampus is used to denote the tail of thehippocampus, where no attempt is made to further subdivide between thedifferent subfields. This is admittedly not a great naming convention- sorry for the confusion.3. You should not do any correction on the obtained volumes: partialvolume here merely means the effect of voxels containing a mix ofdifferent subfields simultaneously. The non-partial volume resultshere only indicate that this effect is not explicitly modeled when youcall the hippocampal subfield segmentation routine with its defaultsettings.Hope this helps,KoenOn Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamillaggon...@upo.es wrote: Dear Freesurfer experts I'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts... If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields? I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right? second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e. volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissure c_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626 and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced, Gabriel -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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
Re: [Freesurfer] Hippocampal segmentation doubts
Hi Gabriel, 1. Using pre-processed data obtained with an older version of FreeSurfer should be OK, as long as you remember that the obtained results might/will be different from the ones you'd get if you had run the whole analysis from scratch. 2. The generic label hippocampus is used to denote the tail of the hippocampus, where no attempt is made to further subdivide between the different subfields. This is admittedly not a great naming convention - sorry for the confusion. 3. You should not do any correction on the obtained volumes: partial volume here merely means the effect of voxels containing a mix of different subfields simultaneously. The non-partial volume results here only indicate that this effect is not explicitly modeled when you call the hippocampal subfield segmentation routine with its default settings. Hope this helps, Koen On Thu, Jun 28, 2012 at 5:29 AM, Gabriel Gonzalez Escamilla ggon...@upo.es wrote: Dear Freesurfer experts I'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts... If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields? I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right? second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e. volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissure c_12_hipo3789.973215.082654.657705.2336.8574841.63 4158.49356.626 and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced, Gabriel -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Seville - Spain - Email: ggon...@upo.es http://www.upo.es/neuroaging/es/ ___ 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 segmentation doubts
Dear Freesurfer expertsI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the -hippo-subfields recon seems to not modify the whole brain segmentation, am I right?second, when I apply the kvlQuantifyHippocampalSubfieldSegmentations.sh I do obtain two txt files containing such segmentation of the 8 hippocampal subfields, but at the beggining it appear a field for the left and right hippocampus, but I don't know exactly what does this column represents, because if I sum the other colums the subfield sums are so much bigger than the hippocampus field; i.e.volume_in_number_of_voxels Left-Hippocampus left_presubiculum left_CA1 left_CA2-3 left_fimbria left_subiculum left_CA4-DG left_hippocampal_fissurec_12_hipo 3789.97 3215.08 2654.65 7705.2 336.857 4841.63 4158.49 356.626and last. Do I need to somehow do some partial volume corrections to this output volumes? Because the txt file sais nonPartialVolumeStats, and I'd saw on the page that the output is 0.5*0.5*0.5mm^3. Many thanks in advanced,Gabriel -- --PhD. student Gabriel González-EscamillaLaboratory of Functional NeuroscienceDepartment of Physiology, Anatomy, and Cell BiologyUniversity Pablo de OlavideCtra. de Utrera, Km.141013 - Seville- Spain -Email: ggon...@upo.eshttp://www.upo.es/neuroaging/es/ ___ 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.
