we install freesurfer 5.3 when we run trac-all -prep -c dmrirc
the process ends with the error:
tkreg2FSL: mov det = -64, ref det = 1 INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. Tue Dec 3 13:32:26 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data flirt.fsl -ref /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/refvol.fslregister.nii -in /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/reg.init.dat.fsl.mat0 flirt.fsl: Command not found. ERROR: flirt Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Tue Dec 3 13:32:26 CST 2013
flirt.fsl is not in the $FREESURFER_HOME/bin directory
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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.
Hi Jon - See here for this error: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30262.html
a.y
On Tue, 3 Dec 2013, Jon Wieser wrote:
we install freesurfer 5.3 when we run trac-all -prep -c dmrirc
the process ends with the error:
tkreg2FSL: mov det = -64, ref det = 1 INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, applying LR flip to registration matrix. Tue Dec 3 13:32:26 CST 2013 /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data flirt.fsl -ref /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/refvol.fslregister.nii -in /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/movvol.fslregister.nii -bins 256 -cost corratio -dof 6 -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -verbose 0 -omat /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/fslregister/fslmat0.trans.mat -schedule /usr/local/fsl/etc/flirtsch/xyztrans.sch -init /BrainLabDocs/Studies/Nicotine_MJ_Ecstasy_Study/data/MRI/N1006/data//freesurfer/dmri/xfms/tmp.bbregister.29768/reg.init.dat.fsl.mat0 flirt.fsl: Command not found. ERROR: flirt Darwin cerebrum.uwm.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
trac-preproc exited with ERRORS at Tue Dec 3 13:32:26 CST 2013
flirt.fsl is not in the $FREESURFER_HOME/bin directory
Jon
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, December 3, 2013 1:19:55 AM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - I would *highly* recommend using the version of tracula in 5.3, as there have been improvements in both performance and speed.
You can check the DWI to anatomical registration by overlaying the aparc+aseg from the dlabel/diff directory (which is in diffusion space) on the FA map. Does that look ok?
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi Anastasia,
We're using 5.1. It's likely poor registration. The aparc+aseg. looked fine. Is there anything to do about poor registration?
Thank you for the fast reply. Truly appreciated. Skyler
----- Original Message ----- From: "Anastasia Yendiki" ayendiki@nmr.mgh.harvard.edu To: "Skyler Gabriel Shollenbarger" shollen2@uwm.edu Cc: Freesurfer@nmr.mgh.harvard.edu Sent: Monday, December 2, 2013 4:27:37 PM Subject: Re: [Freesurfer] DTI - tracula - satisfactory cntrl pnts
Hi Skyler - Are you using freesurfer 5.1 or 5.3?
Most likely this issue is due to poor registration, either from the individual DWI to the individual T1, or from the individual T1 to the template space. Or it could be that there is a problem with the aparc+aseg.
a.y
On Mon, 2 Dec 2013, Skyler Gabriel Shollenbarger wrote:
Hi all,
I've been running DTI using tracula (fs version 5) for over 1 week on 2 subjects. It appears that it is having difficulty finding satisfactory control point fit and has attempted over 1600 tries. Any help is greatly appreciated. See error below:
INFO: Distances between consecutive points are 25 24 25 26 WARN: Could not find satisfactory control point fit - try 1665 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels INFO: Length of center streamline is 96 voxels Selecting 5 points on center streamline INFO: Step is 4 voxels WARN: Defaulting to equidistant control points INFO: Selected control points are 108 193 84 112 173 72 98 153 75 74 157 75 74 184 86 INFO: Distances between consecutive points are 24 25 24 29 WARN: Could not find satisfactory control point fit - try 1666 Finding center streamline INFO: Step is 4 voxels WARN: Turning off FA check for center streamline INFO: Step is 4 voxels WARN: Turning off deviation check for center streamline INFO: Step is 4 voxels
Best, Skyler
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.
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
Jon Wieser