Hi David - The fact that it's taking so many tries to initialize the left
ILF tells me that something has gone wrong with the data, either with the
T1 to DWI registration, or with the mask, or something like that. Have you
looked at any of the output files of the pre-processing? The FA map, the
aparc+aseg, etc?
a.y
On Wed, 7 Aug 2013, Soto, David wrote:
Hi Anastasia, I checked the becs and bvals files,
there was a bug in the transposition of the columns into
3 rows in the bvecs. But i still have problems..
I rerun trac-all -prep and seemed fine but ended
with a Segmentation fault (core dumped)
which however is not present in the last line of the
trac-all.log (Attached).
Writing output files to
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_*
Writing spline volume to
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_cpts_5.nii.gz
Segmentation fault (core dumped)
Just in case I tried trac-all -bedp complains like these below, any advise
appreciated, cheers - ds
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/tracula02ST.txt -bedp
INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui
Actual FREESURFER_HOME /usr/local/freesurfer
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri
/usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh:
Syntax error: "(" unexpected
http://www1.imperial.ac.uk/medicine/people/d.soto/
________________________________________
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 07 August 2013 17:22
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
Hi David - Every time you run trac-all, the results get appended to this
file, so you need to look for error messages only in the more recent
invocation of trac-all. The first error there seems to be:
Error: bvecs and bvals don't have the same number of entries
Do you have the same number of b-values and gradient vectors and volumes
in your DWI series?
a.y
On Tue, 6 Aug 2013, Soto, David wrote:
hi
I upgraded to FS 5.3 but still encountering issues with
trac-all prep.
The log is attached, things I noted after inspecting it
1) INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Current Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
2) Error: input image /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb
not valid
3) Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/lowb_brain
4) Image Exception : #22 :: ERROR: Could not open image
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/White-Matter++.
5) ERROR: Could not read
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dtifit_FA.nii.gz
but despite all this it says:
trac-preproc finished without error at Tue Aug 6 21:27:30 BST 2013
thanks for your help
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
________________________________________
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 06 August 2013 19:30
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] trac-all inquiry
I see, you're using the old version of tracula (from freesurfer 5.1). In
that version, you had to define the number of low-b images in the
configuration file. I strongly recommend updating to freesurfer 5.3. A lot
of things have improved in tracula since then.
Also, in the future please attach any log files as separate attachments
instead of pasting them into the body of your email - this causes the body
of the email to exceed the limit allowable on the list.
Thanks,
a.y
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.
