Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
thanks, that solved my problem! Angela Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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 hippocampal-subfields-T1.log Description: Binary data ___ 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.
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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 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
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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 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. run_segmentSubjectT1_autoEstimateAlveusML.sh Description: application/shellscript run_segmentSubjectT1T2_autoEstimateAlveusML.sh Description: application/shellscript run_segmentSubjectT2_autoEstimateAlveusML.sh Description: application/shellscript ___ 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] WM and GM Volume and visual inspection for failure
Hi there, I am using Freesurfer in children which means lots of manual editing. I got very nice results with doing the recommended reconstruction (https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) . However, I got a problem with the volumes: Gray Matter and White Matter: When I want to check the segmentation, which overlay do I have to choose for visual check? As WM and GM are calculated from both, surface-based volume calculations and voxel counts (http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats), I am not sure if I have to even edit bad segmentation (tkmedit -aseg). Is there tutorial for it? I only found the following: http://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/TkMeditSegmentations But there I cannot see which kind of failure have to be corrected. Cheers, Kristina ___ 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.
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/Desktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. 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: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
[Freesurfer] extracting cluster surface area measurements for individual subjects from qdec output
I’m trying to extract the surface area measurements for each subject from clusters generated by Monte Carlo analysis within qdec. From previous posts I came up with the following command: mri_segstats --annot fsaverage lh mc-z.abs.th20.sig.ocn --i y.mgh --avgwf lh-Diff-HV-WAGR-Intercept-area.dat As an aside, the only way that this command would work was by copying the mc-z.abs.th20.sig.ocn.annot file within the contrast directory lh-Diff-HV-WAGR-Intercept-area to the fsaverage/label directory and renaming it to lh.mc-z.abs.th20.sig.ocn.annot. If I enter the absolute path of the annotation file into the command as follows: mri_segstats --annot fsaverage lh /Users/flalonde/Desktop/WAGR_freesurfer5.3/qdec/lh_10_area_WAGR_HV/lh-Diff-HV-WAGR-Intercept-area/mc-z.abs.th20.sig.ocn.annot --i y.mgh --avgwf lh-Diff-HV-WAGR-Intercept-area_full_path.dat I get the following error: Reading annotation could not read annot file /Users/flalonde/Desktop/WAGR_freesurfer5.3/fsaverage/label/lh./Users/flalonde/Desktop/WAGR_freesurfer5.3/qdec/lh_10_area_WAGR_HV/lh-Diff-HV-WAGR-Intercept-area/mc-z.abs.th20.sig.ocn.annot.annot No such file or directory ... trying local annot reading colortable from annotation file... colortable with 6 entries read (originally none) Successfully read local annot Oddly enough I get the same results in the avgwf file with either command. Pardon what might be a silly question but what are the values in the avgwf file? The columns seem to refer to individual clusters and the rows to individual subjects (presumably in the same order as the original qdec table used to generate the analysis) but the numbers range from 0 to 1. Thanks, François ___ 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.
Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation
Hi all, I am also running hippocampal subfields segmentation with V6 develop version, and I got the error as following: # #@# Hippocampal Subfields processing (T1 only) left Tue Jun 30 23:06:21 PDT 2015 /home/xzhuang/Downloads/freesurfer/bin/segmentSF_T1.sh /home/xzhuang/Downloads/freesurfer/MCRv80 /home/xzhuang/Downloads/freesurfer 1 /home/xzhuang/Downloads/freesurfer/subjects left See log file: /home/xzhuang/Downloads/freesurfer/subjects/1/scripts/hippocampal-subfields-T1.log Linux localhost.localdomain 3.10.0-123.8.1.el7.x86_64 #1 SMP Mon Sep 22 19:06:58 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1 exited with ERRORS at Tue Jun 30 23:06:21 PDT 2015 For more details, see the log file /home/xzhuang/Downloads/freesurfer/subjects/1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting; And inside log file is following: # #@# Hippocampal Subfields processing (T1 only) left Tue Jun 30 23:06:21 PDT 2015 Is there any suggestions, thoughts or similar experience? Best, Xiaowei. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Eugenio Iglesias Sent: Wednesday, July 1, 2015 4:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Sorry, I forgot to mention that you should change the permissions of the files. Please run the following command: chmod u+x $FREESURFER_HOME/bin/run_segmentSubject*.sh 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 1:07:31 PM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Thank you Eugenio, but the problem is still present (attached the log). Thank you for any help! Angela #@# Hippocampal Subfields processing (T1 only) left Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects left \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. # #@# Hippocampal Subfields processing (T1 only) right Wed Jul 1 13:04:47 CEST 2015 \n /Users/angelafavaro/Desktop/prova/freesurfer/bin/segmentSF_T1.sh /Users/angelafavaro/Desktop/prova/freesurfer/MCRv80 /Users/angelafavaro/Desktop/prova/freesurfer subj001 /Users/angelafavaro/Desktop/prova/subjects right \n See log file: /Users/angelafavaro/Desktop/prova/subjects/subj001/scripts/hippocampal-subfields-T1.log /Users/angelafavaro/Desktop/prova/freesurfer/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: Permission denied. #-- Started at Wed Jul 1 13:04:45 CEST 2015 Ended at Wed Jul 1 13:04:47 CEST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s subj001 finished without error at Wed Jul 1 13:04:47 CEST 2015 Hi Angela, I think this is a problem I fixed in the development version a couple of days ago. Can you please just try saving the attached 3 files in the directory $FREESURFER_HOME/bin/ replacing the ones that are there? 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, July 1, 2015 5:42:07 AM Subject: Re: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hi all, I have tried to run the new hippocampal segmentation module (after running the dev version of FS 6. The module did not work and this message error appears (please find attached the log). DYLD_LIBRARY_PATH is /Users/angelafavaro/Desktop/prova/freesurfer/lib/gcc/lib:.:/Users/ange lafavaro/Desktop/prova/freesurfer/MCRv80/runtime/maci64:/Users/angelaf avaro/Desktop/prova/freesurfer/MCRv80/bin/maci64:/Users/angelafavaro/D esktop/prova/freesurfer/MCRv80/sys/os/maci64 Warning: application is running on a locale different from the original platform locale. is it due to something wrong in my path specification? how can I solve this? thank you! Angela Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data
Re: [Freesurfer] [FreeSurfer] aparc+aseg.mgz unkown voxels
Hi Joe what FS version are you using? That certainly looks like a bug, but maybe it's one we've fixed already? Bruce On Wed, 1 Jul 2015, joseph veliz wrote: Hello Freesrufers, There are voxels in random areas of the aparc+aseg.mgz that are categorized as 'unknown'. I read an earlier email stating that aparc+aseg.mgz should not be directly edited by filling in voxels. Correct? A specific example of this is shown on the attatched images. aseg.mgz categorizes this area as cortex, yet the aparc+aseg.mgz does not even though it is within pial boundary and is adjacent to other (categorized) cortical and sub cortical regions. How could we go about correcting this? Thank so much Joe ___ 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.
Re: [Freesurfer] unique label from volume / surface ROIs
How did you create the ROIs? On 07/01/2015 12:25 PM, Martin Hebart wrote: Dear members of the list, I'm new to Freesurfer, so please excuse me asking possibly basic questions. I have spent quite some time on the wiki and searching through the emails before writing to the list, but I might have missed some important information. I would like to work on anatomical ROIs created based on Freesurfer's surface-based and volumetric ROIs and continue working with them in nifti format (e.g. for SPM). If I understand it correctly, the surface-based ROIs should take into account the individual subject's anatomy better than the volumetric ROIs would. At the same time, for subcortical regions it is necessary to use volumetric ROIs. I did recon -all, followed by extracting all surface ROIs using mri_label2vol --annot aparc.a2009s.annot and the volumetric ROIs using mri_label2vol --seg aparc.a2009s+aseg.mgz . Finally, I manually removed all cortical labels from the volumetric ROIs. Now when looking at the ROIs, they overlap slightly, both between left and right hemisphere (roughly 150 voxels), and between the hemispheres and the subcortical regions (roughly 300 voxels). Is there a way I can assign the masks volumes a unique label? I was considering removing these voxels, but ideally I would just keep them in and use the label with the highest probability. Or is there an alternative suggestion that makes more sense (e.g. rather attributing overlapping regions to subcortical regions)? Thanks a lot in advance for your reply! Martin ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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.
Re: [Freesurfer] Overlaying .nii
Is it registered to the surface? If so, you can use mri_vol2surf to sample it onto the surface then display it as an overlay. cheers Bruce On Wed, 1 Jul 2015, Worker, Amanda wrote: Hi, I am trying to find a way to overlay a .nii file for a single blob of activation - simply to visualise the region of the blob with the cortical surface. Is there a way to do this in either freeview or tksurfer? The blob is in nifti format and the surface is in the usual .mgh format. Thanks, Amanda ___ 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] Overlaying .nii
Hi, I am trying to find a way to overlay a .nii file for a single blob of activation - simply to visualise the region of the blob with the cortical surface. Is there a way to do this in either freeview or tksurfer? The blob is in nifti format and the surface is in the usual .mgh format. Thanks, Amanda ___ 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] unique label from volume / surface ROIs
Dear members of the list, I'm new to Freesurfer, so please excuse me asking possibly basic questions. I have spent quite some time on the wiki and searching through the emails before writing to the list, but I might have missed some important information. I would like to work on anatomical ROIs created based on Freesurfer's surface-based and volumetric ROIs and continue working with them in nifti format (e.g. for SPM). If I understand it correctly, the surface-based ROIs should take into account the individual subject's anatomy better than the volumetric ROIs would. At the same time, for subcortical regions it is necessary to use volumetric ROIs. I did recon -all, followed by extracting all surface ROIs using mri_label2vol --annot aparc.a2009s.annot and the volumetric ROIs using mri_label2vol --seg aparc.a2009s+aseg.mgz . Finally, I manually removed all cortical labels from the volumetric ROIs. Now when looking at the ROIs, they overlap slightly, both between left and right hemisphere (roughly 150 voxels), and between the hemispheres and the subcortical regions (roughly 300 voxels). Is there a way I can assign the masks volumes a unique label? I was considering removing these voxels, but ideally I would just keep them in and use the label with the highest probability. Or is there an alternative suggestion that makes more sense (e.g. rather attributing overlapping regions to subcortical regions)? Thanks a lot in advance for your reply! Martin ___ 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.
Re: [Freesurfer] mri_label2label problem revisited
Michael, can you send me the label in fsaverage space?
doug
On 06/16/2015 05:00 PM, Michael Kranz wrote:
Hi guys,
I have created a custom surface label in the fsaverage template. I
then used mri_label2label to map onto an individual subject. Despite
the fsaverage label looking ok, the label mapped onto the individual
subject is not as the label is spotty and has holes. On the free
surfer archive it seems that some people have had this problem and
described it as eroded or islands (see
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15125.html),
but it wasn't clear to me that this issue has been solved.
The above link recommended using one of the predefined labels to see
if the problem persisted. I used rh.BA45.label and there was were no
problems.
I also used mri_surfcluster (as was done in the above link) to make my
label. Below is the 1.) command 2.) the fsaverage label in tksurfer
3.) a pic of the same label mapped onto a subject in tksurfer
Do you have an idea of what the issue is? Let me know if you need more
info!
mri_label2label \
--srcsubject fsaverage \
--srclabel ${srclabelpwd}/${rhROI} \
--trgsubject $subbase \
--trglabel ${SUBJECTS_DIR}/${subbase}/label/${rhROI} \
--hemi rh \
--regmethod surface
Inline image 1
Inline image 2
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
[Freesurfer] Preproc-sess failed
Yes, the sudo prefix is optional, but may be required otherwise you get a 'not authorized' message (i.e. you need administrative privileges to install software and libraries); note 'libXp' is case-sensitive! sudo yum install libXp.x86_64 The library will be installed at /usr/lib64/libXp.so.6, a symbolic link to /usr/lib64/libXp.so.6.2.0 And try Zeke's advice as well, just to be sure export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH You would have to run that command at every new terminal you open, or add it to the configuration file of your terminal. P.S. I removed libXp on my machine, and yes, 3dvolreg.afni complains about missing libXp.so.6. After installing it again with the first command, it works again. On Jul 01, 2015, at 06:47 AM, Thục Trinh thuctrinh...@gmail.com wrote: Is the command line like this: yum install libXp.so.6.x86_64 because I did run yum install libXp.so.6 before and it did not work. 2015-07-01 11:28 GMT+07:00 Z K zkauf...@nmr.mgh.harvard.edu: Yes, and when it is done installing, determine exactly what directory the libXp.so.6 file was installed into. That is the directory you want to add to your LD_LIBRARY_PATH environment variable. -Zeke On Jun 30, 2015, at 11:39 PM, Thục Trinh thuctrinh...@gmail.com wrote: Hi, I did exactly what you said, and the error still remain: 3dvolreg.afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory I cannot find any folder name libXp.so.6,should I re-download libXp.so.6 64 bits ? 2015-06-29 18:15 GMT+07:00 Jalmar Teeuw jal...@me.com: Sorry, I didn't have access to my CentOS machine, the 32-bit libraries use the suffix i686 instead of i386, so try sudo yum remove libXp.i686 By removing the 32-bit version you essential ensure only the 64-bit version is available when the application tries to load libXp. Hope that works. My machine only has the 64-bit version installed. Although technically, it should not matter if you have both installed on the system as it should automatically pick the correction version. If it doesn't work, you could try to run find / -type f -iname libXp.so* -print to check if the libXp libraries might be installed somewhere else. It may take some time to scan the entire system and any mounted volumes. You can use the `file file` command to check if the library is 32 or 64-bit, and remove any 32-bit or even 64-bit version outside /usr/lib64 (BEWARE: removing libraries is at risk of breaking functioning of other application that depend on that particular library. If necessary, you can always run `sudo yum install libXp.i686` to install the 32-bit version again) On Jun 29, 2015, at 08:10 AM, Thục Trinh thuctrinh...@gmail.com wrote: Hi, yum remove libXp.i386 command returns with No Packages marked for removal This is my output for:'file $FREESURFER_HOME/bin/3dvolreg.afni' /usr/local/freesurfer/bin/3dvolreg.afni: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, stripped 2015-06-26 16:19 GMT+07:00 Jalmar Teeuw jal...@me.com: Have you tried removing the 32-bit version of the libraries? I believe it is yum remove libXp.i386 What is the output of file $FREESURFER_HOME/bin/3dvolreg.afni Maybe you could try locate all the libXp.so on your system and see if there is a local 32-bit copy find / -type f -iname libXp.so* On 25 Jun 2015, at 09:45, Thục Trinh thuctrinh...@gmail.com wrote: the lib files are now in /usr/lib64, the ERROR still the same after I set a new path for shared lib with this command in .bashrc file export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH the Error still the same. 3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32 output of uname -a on my system is: Linux localhost.localdomain 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux 2015-06-25 14:15 GMT+07:00 Jalmar Teeuw jal...@me.com: Is still gives you the same error? I'm not certain about libXpm; I recall having to install certain libraries on a slimmed down version of Centos 6.5, libXp and libXpm were amongst those libraries. For me, the lib files are stored in /usr/lib64 Try find /usr/lib64 -type f -iname libXp* -print This will search for the files. What is the output uname -a On your system? On 25 Jun 2015, at 09:01, Thục Trinh thuctrinh...@gmail.com wrote: Hi, After complete install the suitable version of shared library as you suggested, I cannot find any file name libXpm.x86_64 to set the new path for shared library. Ps: Is there any differences between libXpm.x86_64 and libXp.x86_64 2015-06-24 16:03 GMT+07:00 Jalmar Teeuw jal...@me.com: That sounds more like you have only the 32-bit version of the libXp installed when 64-bit is required. Are you using the 64-bit version of Freesurfer 5.3.0 for CentOS 6 that is available on the downloads page? Have you tried sudo yum install libXp.x86_64
[Freesurfer] Processing problem in Freesurfer
Dear Freesurfer team: I am here want to ask for your help for some problems in Freesurfer when I was processing my data. As described below, Freesurfer report : ERROR! FOV=320.000 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. so regarding this type of problem, how could I solve it? It seems that the FOV of my NIFT image is 320, and it is bigger than 256, which cannot be readed and written by orig.mgz. I have tried to open the org.mgz file, but it was unaccessible. so, there are any solutions to deal with this problem? if yes, please delivery some instructions to me. Thank you. -- Best regards, Guo Bin/ ___ 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.
Re: [Freesurfer] Preproc-sess failed
Yay !!! It works finally. So the problem in the first place is: I got the wrong version of shared library :) Thank you so much. 2015-07-01 14:58 GMT+07:00 Jalmar Teeuw jal...@me.com: Yes, the sudo prefix is optional, but may be required otherwise you get a 'not authorized' message (i.e. you need administrative privileges to install software and libraries); note 'libXp' is case-sensitive! sudo yum install libXp.x86_64 The library will be installed at /usr/lib64/libXp.so.6, a symbolic link to /usr/lib64/libXp.so.6.2.0 And try Zeke's advice as well, just to be sure export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH You would have to run that command at every new terminal you open, or add it to the configuration file of your terminal. P.S. I removed libXp on my machine, and yes, 3dvolreg.afni complains about missing libXp.so.6. After installing it again with the first command, it works again. On Jul 01, 2015, at 06:47 AM, Thục Trinh thuctrinh...@gmail.com wrote: Is the command line like this: yum install libXp.so.6.x86_64 because I did run yum install libXp.so.6 before and it did not work. 2015-07-01 11:28 GMT+07:00 Z K zkauf...@nmr.mgh.harvard.edu: Yes, and when it is done installing, determine exactly what directory the libXp.so.6 file was installed into. That is the directory you want to add to your LD_LIBRARY_PATH environment variable. -Zeke On Jun 30, 2015, at 11:39 PM, Thục Trinh thuctrinh...@gmail.com wrote: Hi, I did exactly what you said, and the error still remain: *3dvolreg.afni: error while loading shared libraries: libXp.so.6: cannot open shared object file: No such file or directory* I cannot find any folder name libXp.so.6,should I re-download libXp.so.6 64 bits ? 2015-06-29 18:15 GMT+07:00 Jalmar Teeuw jal...@me.com: Sorry, I didn't have access to my CentOS machine, the 32-bit libraries use the suffix i686 instead of i386, so try sudo yum remove libXp.i686 By removing the 32-bit version you essential ensure only the 64-bit version is available when the application tries to load libXp. Hope that works. My machine only has the 64-bit version installed. Although technically, it should not matter if you have both installed on the system as it should automatically pick the correction version. If it doesn't work, you could try to run find / -type f -iname libXp.so* -print to check if the libXp libraries might be installed somewhere else. It may take some time to scan the entire system and any mounted volumes. You can use the `file file` command to check if the library is 32 or 64-bit, and remove any 32-bit or even 64-bit version outside /usr/lib64 (BEWARE: removing libraries is at risk of breaking functioning of other application that depend on that particular library. If necessary, you can always run `sudo yum install libXp.i686` to install the 32-bit version again) On Jun 29, 2015, at 08:10 AM, Thục Trinh thuctrinh...@gmail.com wrote: Hi, yum remove libXp.i386 command returns with *No Packages marked for removal* This is my output for:'file $FREESURFER_HOME/bin/3dvolreg.afni' */usr/local/freesurfer/bin/3dvolreg.afni: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, stripped* 2015-06-26 16:19 GMT+07:00 Jalmar Teeuw jal...@me.com: Have you tried removing the 32-bit version of the libraries? I believe it is yum remove libXp.i386 What is the output of file $FREESURFER_HOME/bin/3dvolreg.afni Maybe you could try locate all the libXp.so on your system and see if there is a local 32-bit copy find / -type f -iname libXp.so* On 25 Jun 2015, at 09:45, Thục Trinh thuctrinh...@gmail.com wrote: the lib files are now in /usr/lib64, the ERROR still the same after I set a new path for shared lib with this command in .bashrc file *export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH* the Error still the same. *3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32* output of uname -a on my system is: *Linux localhost.localdomain 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux* 2015-06-25 14:15 GMT+07:00 Jalmar Teeuw jal...@me.com: Is still gives you the same error? I'm not certain about libXpm; I recall having to install certain libraries on a slimmed down version of Centos 6.5, libXp and libXpm were amongst those libraries. For me, the lib files are stored in /usr/lib64 Try find /usr/lib64 -type f -iname libXp* -print This will search for the files. What is the output uname -a On your system? On 25 Jun 2015, at 09:01, Thục Trinh thuctrinh...@gmail.com wrote: Hi, After complete install the suitable version of shared library as you suggested, I cannot find any file name libXpm.x86_64 to set the new path for shared library. Ps: Is there any differences between libXpm.x86_64 and libXp.x86_64 2015-06-24 16:03 GMT+07:00 Jalmar Teeuw jal...@me.com: That
Re: [Freesurfer] Need vertex in 2D template space
Hi Bruce, Thank you so much, sorry to replay so late. I also read your conversation with Jonathan regarding 3D to 2D transformation, it is very helpful. On 06/22/2015 11:45 AM, Bruce Fischl wrote: sure, the average subject has a sphere and you can do it there. Or you can flatten and use euclidean coordinates On Mon, 22 Jun 2015, xtong wrote: Hi Bruce, Thanks to your advise, the combination of mri_surf2surf my_subject - fsaverage(paint features to average brain) + mris_convert -c *.ascii(output features to ascii) works well, all my subjects can have the same number of vertice. And it looks like the original xyz coordinate of my_subject can also be passed to the average brain's vertices by mri_surf2surf2 --sval_xyz --tval_xyz, which is terrific. But beside vertex alignment another reason of wanting a 2D representation of the surface features (hence my ridiculous idea of creating template for each single subject), is to facilitate the random sampling of tiny sheets from the whole surface for my simulation study, since cutting a small rectangular (or other shape) from a picture is much easier than working on vertices in 3D. I found a solution by randomly selecting one vertex and retrieve it's k-neighbour using the neighbour vertex table returned by mris_convert -v fsaverage, it's still quite bit of work to be done though. Is there any possibility to paint surface features to a picture in 2D Longitude and Latitude coordinate? Thank you so much. On 06/20/2015 05:46 PM, Bruce Fischl wrote: You probably don't need to create your own template - just use mri_surf2surf to map the data (thickness, area, whatever) to fsaverage and they will all have the same number of vertices cheers Bruce On Sat, 20 Jun 2015, xiaoran tong wrote: Dear FreeSurfer team: I'm trying to model the cortical surface features with a artificial neural network. I need a uniformed number of input features but it turns out the vertices count varies from subject to subject. Is that possible to map the vertices in the Talairach space of XYZ to the sphere template space of theta and phi, so I can work on 2D pictures of uniformed length and width? Probably 251 x 256 like the FreeSurfer *.tif template files. According to https://surfer.nmr.mgh.harvard.edu/fswiki/TemplateTifImageFiles and https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates , I tried to create one registration template per subject with make_average_subject command in this manner: make_average_subject --subjects sbj_i --out sbj_i_template , in the hope that I could at least extract the mean curvature and convexity of that subject in 2-D theta phe space from the resulting sbj_i_template.tif files. It sounds ridiculous to call make_average_subject on just every single subject, but I couldn't think of any way to extract vertex measures and in the them 2D (theta, phi) space. I'm not sure this is correct. Beside curvatures, how should I extract other type of vertex features, like area, volume, and thickness in the 2D template space? I'll be thankful for any suggestions. ___ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail. ___ 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 The information in this e-mail is intended only for the person to whom it is
Re: [Freesurfer] [FreeSurfer] aparc+aseg.mgz unkown voxels
leopard i686 stable pub v5.1.0 As an aside I watched your introductory videos and found you to be very knowledgeable, well-spoken and very helpful in understanding some of the amazing things you guys are doing for analysis. Really cool to be emailing you and getting help from the pros. Thanks Joe On Wed, Jul 1, 2015 at 1:12 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Joe what FS version are you using? That certainly looks like a bug, but maybe it's one we've fixed already? Bruce On Wed, 1 Jul 2015, joseph veliz wrote: Hello Freesrufers, There are voxels in random areas of the aparc+aseg.mgz that are categorized as 'unknown'. I read an earlier email stating that aparc+aseg.mgz should not be directly edited by filling in voxels. Correct? A specific example of this is shown on the attatched images. aseg.mgz categorizes this area as cortex, yet the aparc+aseg.mgz does not even though it is within pial boundary and is adjacent to other (categorized) cortical and sub cortical regions. How could we go about correcting this? Thank so much Joe ___ 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 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.
