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
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