Re: [Freesurfer] running two versions of fs in the same
is it just the BA labels you want out of the newer version? If so, just change your FREESURFER_HOME to point at the new version after your 5.1 recon-all is done and run the -dobalabels target with the dev recon-all cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: Hi Bruce, The command that we ran is recon-all. Below is the error msg: mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject HMN122 --trglabel ./lh.BA2.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = HMN122 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Invalid argument ERROR reading /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN122 exited with ERRORS at Tue Feb 23 16:40:01 EST 2016 --- --- Hi Fengji you need to give us more details about the problems before we can help you. What commands failed? What was the screen output? Note that there is still no such thing as FS 6.0. We are hoping to have it in the relatively near term, but it doesn't exist yet. cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: > Dear fs developers,? > > we are attempting to use the stable version of fs 5.1 for processing while > also using the most current version for hippocampal segmentation on the same > set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when > the develop version of fs 6 was installed, we began having an issue with the > fsaverage folder linking to the newest version, when we need it to link to > version 5.1 during processing. The label files that we need for processing > in version 5.1 are not accessible in the new version?s fsaverage > folder.?However, before we updated to fs 6.0 dev version on 28-Jan-2016, we > never had this issue. So, we are wondering if the newest develop version of > fs 6.0 does not allow?two versions of fs to be used in the same data.? > > Looking forward to hearing from you and thanks in advance. > > Best, > > - Fengji --- Fengji ___ 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] running two versions of fs in the same
Hi Bruce, The command that we ran is recon-all. Below is the error msg: mri_label2label --srcsubject fsaverage --srclabel /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label --trgsubject HMN122 --trglabel ./lh.BA2.label --hemi lh --regmethod surface No such file or directory mri_label2label: could not open label file /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srclabel = /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label srcsubject = fsaverage trgsubject = HMN122 trglabel = ./lh.BA2.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR/export/data/hippocampus/HMN/data FREESURFER_HOME /cell_root/software/freesurfer/current/sys Loading source label. Invalid argument ERROR reading /export/data/hippocampus/HMN/data/fsaverage/label/lh.BA2.label Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux recon-all -s HMN122 exited with ERRORS at Tue Feb 23 16:40:01 EST 2016 -- Hi Fengji you need to give us more details about the problems before we can help you. What commands failed? What was the screen output? Note that there is still no such thing as FS 6.0. We are hoping to have it in the relatively near term, but it doesn't exist yet. cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: > Dear fs developers,? > > we are attempting to use the stable version of fs 5.1 for processing while > also using the most current version for hippocampal segmentation on the same > set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when > the develop version of fs 6 was installed, we began having an issue with the > fsaverage folder linking to the newest version, when we need it to link to > version 5.1 during processing. The label files that we need for processing > in version 5.1 are not accessible in the new version?s fsaverage > folder.?However, before we updated to fs 6.0 dev version on 28-Jan-2016, we > never had this issue. So, we are wondering if the newest develop version of > fs 6.0 does not allow?two versions of fs to be used in the same data.? > > Looking forward to hearing from you and thanks in advance. > > Best, > > - Fengji --- Fengji ___ 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] running two versions of fs in the same dataset
Hi Fengji you need to give us more details about the problems before we can help you. What commands failed? What was the screen output? Note that there is still no such thing as FS 6.0. We are hoping to have it in the relatively near term, but it doesn't exist yet. cheers Bruce On Tue, 1 Mar 2016, Fengji Geng wrote: Dear fs developers, we are attempting to use the stable version of fs 5.1 for processing while also using the most current version for hippocampal segmentation on the same set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when the develop version of fs 6 was installed, we began having an issue with the fsaverage folder linking to the newest version, when we need it to link to version 5.1 during processing. The label files that we need for processing in version 5.1 are not accessible in the new version’s fsaverage folder. However, before we updated to fs 6.0 dev version on 28-Jan-2016, we never had this issue. So, we are wondering if the newest develop version of fs 6.0 does not allow two versions of fs to be used in the same data. Looking forward to hearing from you and thanks in advance. Best, - Fengji ___ 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] running two versions of fs in the same dataset
Dear fs developers, we are attempting to use the stable version of fs 5.1 for processing while also using the most current version for hippocampal segmentation on the same set of subjects (freesurfer 6.0 dev version on 28-Jan-2016). However, when the develop version of fs 6 was installed, we began having an issue with the fsaverage folder linking to the newest version, when we need it to link to version 5.1 during processing. The label files that we need for processing in version 5.1 are not accessible in the new version’s fsaverage folder. However, before we updated to fs 6.0 dev version on 28-Jan-2016, we never had this issue. So, we are wondering if the newest develop version of fs 6.0 does not allow two versions of fs to be used in the same data. Looking forward to hearing from you and thanks in advance. Best, - Fengji ___ 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.
