Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
Hi Fernando - I looked at your data and changing the sign of the z coordinate in your gradient table gave me eigenvectors that looked fine in both fslview and freeview. Why you would get eigenvectors that look different in freeview and fslview before flipping z but not after is still a mystery to me, but at this point I'd just try starting clean, changing the sign in the 3rd column of your gradient table, and testing the whole pipeline on a test subject to see if that fixes things. Let me know how it goes! a.y Dear Anastasia, When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions actually are OK, but when I open them with FSLview they are similar to your screen-shot. Here I also send a screen-shot with the comparison between the two softwares in each monitor. Best, Fernando El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar ___ 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] FW: TRACULA some fiber volumes being too small
Fantastic, thanks! On Fri, 30 Nov 2012, Fernando Ventrice wrote: Dear Anastasia, now it worked perfectly well changing the Z gradient with *(-1)! Here I send you a screenshot. Best, Fernando -Mensaje original- De: Fernando Ventrice Enviado el: 29 November 2012 11:39 Para: Anastasia Yendiki Asunto: RE: [Freesurfer] FW: TRACULA some fiber volumes being too small Hi Anastasia, I'll rerun all steps changing the Z gradient with *(-1). Thanks and I'll write with the results. Best, Fernando -Mensaje original- De: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] En nombre de Anastasia Yendiki Enviado el: 28 November 2012 15:30 Para: Fernando Ventrice CC: freesurfer@nmr.mgh.harvard.edu Asunto: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small Hi Fernando - I looked at your data and changing the sign of the z coordinate in your gradient table gave me eigenvectors that looked fine in both fslview and freeview. Why you would get eigenvectors that look different in freeview and fslview before flipping z but not after is still a mystery to me, but at this point I'd just try starting clean, changing the sign in the 3rd column of your gradient table, and testing the whole pipeline on a test subject to see if that fixes things. Let me know how it goes! a.y Dear Anastasia, When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions actually are OK, but when I open them with FSLview they are similar to your screen-shot. Here I also send a screen-shot with the comparison between the two softwares in each monitor. Best, Fernando El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar El contenido del presente mensaje y el de sus adjuntos, es confidencial, privado y de uso exclusivo de los destinatarios a los cuales está dirigido, pudiendo contener información legalmente protegida. Queda prohibida la revisión, divulgación, publicación, modificación, copia, distribución o acción en relación con esta información, por personas o entidades distintas al destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son exclusivas de su autor, y no representa necesariamente, la opinión de FLENI. http://www.fleni.org.ar ___ 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] FW: TRACULA some fiber volumes being too small
Hi Fernando - Thank you for your kind words. You can indeed try the reinit
option as Christofer suggested when one of the pathways looks like a
single curve and not like a volume.
However, because some of your other pathways in the screenshots look a bit
funky too, I would also check that there was nothing wrong with the
gradient directions. An easy way to check that is by looking at the
eigenvectors from the tensor fit (dmri/dtifit_V1.nii.gz). Although tracula
itself doesn't use tensors, if there's something wrong with the gradient
directions, it'll show up in the tensor fit.
If you're not sure how to check, you can upload all tracula-related
directories of your subject here and I'll take a look:
http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
Hope this helps,
a.y
On Thu, 18 Oct 2012, Fernando Ventrice wrote:
Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what it can
do automatically. These are the commands I used:
export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
-v
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
&
All finished without errors, but there seems to be a problem with CC Forceps
Mayor volume, which gave very small values. Is this OK or I made some mistake?
First I tested with some patient and other fiber tracks also gave very small
volumes. I attached some pictures and the dmrirc and trac-all log files.
Best,
Fernando Ventrice
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
___
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] FW: TRACULA some fiber volumes being too small
Hi Fernando - Thanks for uploading your data. Looking at the primary
directions from tensor fit on the data that you sent me (see screenshot),
they seem to be off by a 90 degree angle from what you'd expect them. This
means that your gradient table is probably off as well.
Hope this helps,
a.y
On Thu, 18 Oct 2012, Fernando Ventrice wrote:
Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what it can
do automatically. These are the commands I used:
export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
-v
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
&
All finished without errors, but there seems to be a problem with CC Forceps
Mayor volume, which gave very small values. Is this OK or I made some mistake?
First I tested with some patient and other fiber tracks also gave very small
volumes. I attached some pictures and the dmrirc and trac-all log files.
Best,
Fernando Ventrice
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
___
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] FW: TRACULA some fiber volumes being too small
If FSL isn't happy with the directions, that's going to be fatal b/c
trac-all relies on bedpostx running properly. I'm going to look into this
further to try to figure out what it is about this data that's causing
the discrepancy.
On Wed, 31 Oct 2012, Fernando Ventrice wrote:
Dear Anastasia,
When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions
actually are OK, but when I open them with FSLview they are similar to your
screen-shot. Here I also send a screen-shot with the comparison between the two
softwares in each monitor.
Best,
Fernando
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Tuesday, October 30, 2012 1:24 PM
To: Fernando Ventrice
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small
See screenshot now :)
On Tue, 30 Oct 2012, Anastasia Yendiki wrote:
Hi Fernando - Thanks for uploading your data. Looking at the primary
directions from tensor fit on the data that you sent me (see screenshot),
they seem to be off by a 90 degree angle from what you'd expect them. This
means that your gradient table is probably off as well.
Hope this helps,
a.y
On Thu, 18 Oct 2012, Fernando Ventrice wrote:
Dear Freesurfer/Tracula users,
Finally I could successfully test Tracula and I think it is amazing what
it can do automatically. These are the commands I used:
export FREESURFER_HOME=${HOME}/Programs/freesurfer_510 && source
$FREESURFER_HOME/SetUpFreeSurfer.sh
source /etc/fsl/fsl.sh
export FSLPARALLEL=condor
trac-all -prep -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
trac-all -bedp -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
# "trac-all -bedp" gave some errors so I used bedpostx directly:
bedpostx
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri
trac-all -path -c
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/dmrirc_Fernando_Ventrice
freeview -tv
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dpath/merged_avg33_mni_flt.mgz
-v
/home/labneuroimg/STATION_FLENI/Tensores/Fernando_Ventrice/20120112_VENTRICE_FERNANDO/dmri/dtifit_FA.nii.gz
&
All finished without errors, but there seems to be a problem with CC
Forceps Mayor volume, which gave very small values. Is this OK or I made
some mistake? First I tested with some patient and other fiber tracks also
gave very small volumes. I attached some pictures and the dmrirc and
trac-all log files.
Best,
Fernando Ventrice
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está
dirigido, pudiendo contener información legalmente protegida. Queda
prohibida la revisión, divulgación, publicación, modificación, copia,
distribución o acción en relación con esta información, por personas o
entidades distintas al destinatario. Si usted, por alguna razón, lo ha
recibido por error, por favor tenga la amabilidad de eliminarlo de su
sistema. Las opiniones contenidas, son exclusivas de su autor, y no
representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
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.
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
El contenido del presente mensaje y el de sus adjuntos, es confidencial,
privado y de uso exclusivo de los destinatarios a los cuales está dirigido,
pudiendo contener información legalmente protegida. Queda prohibida la
revisión, divulgación, publicación, modificación, copia, distribución o acción
en relación con esta información, por personas o entidades distintas al
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son
exclusivas de su autor, y no representa necesariament
