Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - Based on the error message in your log file, the right angular 
bundle (rh.cab) is also failing. Looks like a similar problem with the 
right ILF, probably that tract is also affected by the blank slices in 
your volume. Nothing on the list after rh.cab gets reconstructed because 
of this error.


I'd try removing the rh.cab from the list too.

Hope this helps,
a.y

On Thu, 12 Dec 2013, David Soto wrote:


thanks Anastasia for taking the timeinto this, once again!

the logs can be found here
https://dl.dropboxusercontent.com/u/8209026/p14ab.zip
cheers
ds


On Wed, Dec 11, 2013 at 8:11 PM, Anastasia Yendiki
 wrote:

  Sorry, I can't tell what happened without looking at the log
  file. Could you send it along?

  On Wed, 11 Dec 2013, David Soto wrote:

hi Anastasia, I tried then to recontruct the
remaining tracts of this
participant for which I could not do the  right ILF
due to diffusion loss

I set the pathlist like this: set pathlist = (
lh.cst_AS rh.cst_AS \
                 lh.unc_AS rh.unc_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.ccg_PP rh.ccg_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP )

and while it generated most the lh.slfp_PP
rh.slfp_PP \
                 lh.slft_PP rh.slft_PP  are missing

is this expected given that  the issues with the
ILF?

I could not find any errors in the logs relative to
the SLFTs

cheers
ds


On Thu, Dec 5, 2013 at 2:58 PM, Anastasia Yendiki
 wrote:

      Of course, you can specify which tracts you
want to reconstruct
      in the configuration file. Both the sample
configuration file in
      $FREESURFER_HOME/dmrirc.example and the
tracula tutorial have
      the info on how to do this.

      On Thu, 5 Dec 2013, David Soto wrote:

            Hi, just a though, would it be possible
to skip
            thereconstruction of the
            right ILF, I mean to get the remaining
            tract statistics?
            that would be v/useful
            cheers
            ds


            On Wed, Dec 4, 2013 at 2:32 PM,
Anastasia Yendiki
             wrote:
                  Hi David - The screeenshots show
that several
            slices are blank
                  in the diffusion data, and these
indeed go
            through the right
                  ILF. I'd check your original
diffusion dicoms
            for this subject
                  and see if that's indeed the case.

                  a.y

                  On Wed, 4 Dec 2013, David Soto
wrote:

                  thanks Anastasia, see the link
below
           
plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip

            you will find 2 pairs of images
            pair one: there are 2 files starting by
ind2anat,
            one showing 
            the T1 and the other the FA in the same
coordinates,
            you will
            see that align
            well

            pair two: here are 2 files starting by
MNI, one
            showing the FA
            in mni space
            and the other the mni T1_1mm
template..seem fine to
            me, though
            there seem to
            be some coverage deficit in the FA map
in the bottom
            right of
            the image

            cheers
            ds


            On Mon, Dec 2, 2013 at 8:16 PM,
Anastasia Yendiki
             wrote:

                  Hi David - I am not convinced that
all the
            regisrtrations
            have
                  worked well
                  for this subject. The fact that
some of the
            coordinates of
            the
                  control
                  points, which are mapped from
template to
            individual
   

Re: [Freesurfer] trac-all inquiry

[David Soto]

thanks Anastasia for taking the time
into this, once again!

the logs can be found here
https://dl.dropboxusercontent.com/u/8209026/p14ab.zip
cheers
ds


On Wed, Dec 11, 2013 at 8:11 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Sorry, I can't tell what happened without looking at the log file. Could
> you send it along?
>
>
> On Wed, 11 Dec 2013, David Soto wrote:
>
>  hi Anastasia, I tried then to recontruct the remaining tracts of this
>> participant for which I could not do the  right ILF due to diffusion loss
>>
>> I set the pathlist like this: set pathlist = ( lh.cst_AS rh.cst_AS \
>>  lh.unc_AS rh.unc_AS \
>>  fmajor_PP fminor_PP \
>>  lh.atr_PP rh.atr_PP \
>>  lh.ccg_PP rh.ccg_PP \
>>  lh.cab_PP rh.cab_PP \
>>  lh.slfp_PP rh.slfp_PP \
>>  lh.slft_PP rh.slft_PP )
>>
>> and while it generated most the lh.slfp_PP rh.slfp_PP \
>>  lh.slft_PP rh.slft_PP  are missing
>>
>> is this expected given that  the issues with the ILF?
>>
>> I could not find any errors in the logs relative to the SLFTs
>>
>> cheers
>> ds
>>
>>
>> On Thu, Dec 5, 2013 at 2:58 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Of course, you can specify which tracts you want to reconstruct
>>   in the configuration file. Both the sample configuration file in
>>   $FREESURFER_HOME/dmrirc.example and the tracula tutorial have
>>   the info on how to do this.
>>
>>   On Thu, 5 Dec 2013, David Soto wrote:
>>
>> Hi, just a though, would it be possible to skip
>> thereconstruction of the
>> right ILF, I mean to get the remaining
>> tract statistics?
>> that would be v/useful
>> cheers
>> ds
>>
>>
>> On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki
>>  wrote:
>>   Hi David - The screeenshots show that several
>> slices are blank
>>   in the diffusion data, and these indeed go
>> through the right
>>   ILF. I'd check your original diffusion dicoms
>> for this subject
>>   and see if that's indeed the case.
>>
>>   a.y
>>
>>   On Wed, 4 Dec 2013, David Soto wrote:
>>
>>   thanks Anastasia, see the link below
>> plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip
>>
>> you will find 2 pairs of images
>> pair one: there are 2 files starting by ind2anat,
>> one showing
>> the T1 and the other the FA in the same coordinates,
>> you will
>> see that align
>> well
>>
>> pair two: here are 2 files starting by MNI, one
>> showing the FA
>> in mni space
>> and the other the mni T1_1mm template..seem fine to
>> me, though
>> there seem to
>> be some coverage deficit in the FA map in the bottom
>> right of
>> the image
>>
>> cheers
>> ds
>>
>>
>> On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi David - I am not convinced that all the
>> regisrtrations
>> have
>>   worked well
>>   for this subject. The fact that some of the
>> coordinates of
>> the
>>   control
>>   points, which are mapped from template to
>> individual
>> space, are
>>   negative
>>   in individual space (see INFO messages in log
>> file), means
>> that
>>   some part
>>   of the brain in templated space is mapped
>> outside the
>> field of
>>   view in
>>   individual DWI space. Can you send any
>> screenshots that
>> show the
>>   quality
>>   of the DWI to anatomical and DWI to MNI
>> registrations?
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 2 Dec 2013, David Soto wrote:
>>
>> > hi - thanks , not sure though...the no_dif brain
>> maskseems ok,
>> if
>> that is
>> > what you meant...
>> >
>> > I did re-run the processing and
>> > in the last run I can not see the WARN you
>> mentioned
>> > the latest preprocessing output from the
>> preprocessing can be
>> > found  here:
>>  https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>> >
>> > the dlabel/diff output got stuck with the
>> > rh.ilf_AS_avg33 which only 

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Sorry, I can't tell what happened without looking at the log file. Could 
you send it along?


On Wed, 11 Dec 2013, David Soto wrote:


hi Anastasia, I tried then to recontruct the remaining tracts of this
participant for which I could not do the  right ILF due to diffusion loss

I set the pathlist like this: set pathlist = ( lh.cst_AS rh.cst_AS \
                 lh.unc_AS rh.unc_AS \
                 fmajor_PP fminor_PP \
                 lh.atr_PP rh.atr_PP \
                 lh.ccg_PP rh.ccg_PP \
                 lh.cab_PP rh.cab_PP \
                 lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP )

and while it generated most the lh.slfp_PP rh.slfp_PP \
                 lh.slft_PP rh.slft_PP  are missing

is this expected given that  the issues with the ILF?

I could not find any errors in the logs relative to the SLFTs

cheers
ds


On Thu, Dec 5, 2013 at 2:58 PM, Anastasia Yendiki
 wrote:

  Of course, you can specify which tracts you want to reconstruct
  in the configuration file. Both the sample configuration file in
  $FREESURFER_HOME/dmrirc.example and the tracula tutorial have
  the info on how to do this.

  On Thu, 5 Dec 2013, David Soto wrote:

Hi, just a though, would it be possible to skip
thereconstruction of the
right ILF, I mean to get the remaining
tract statistics?
that would be v/useful
cheers
ds


On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki
 wrote:
      Hi David - The screeenshots show that several
slices are blank
      in the diffusion data, and these indeed go
through the right
      ILF. I'd check your original diffusion dicoms
for this subject
      and see if that's indeed the case.

      a.y

      On Wed, 4 Dec 2013, David Soto wrote:

      thanks Anastasia, see the link below
plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip

you will find 2 pairs of images
pair one: there are 2 files starting by ind2anat,
one showing 
the T1 and the other the FA in the same coordinates,
you will
see that align
well

pair two: here are 2 files starting by MNI, one
showing the FA
in mni space
and the other the mni T1_1mm template..seem fine to
me, though
there seem to
be some coverage deficit in the FA map in the bottom
right of
the image

cheers
ds


On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
 wrote:

      Hi David - I am not convinced that all the
regisrtrations
have
      worked well
      for this subject. The fact that some of the
coordinates of
the
      control
      points, which are mapped from template to
individual
space, are
      negative
      in individual space (see INFO messages in log
file), means
that
      some part
      of the brain in templated space is mapped
outside the
field of
      view in
      individual DWI space. Can you send any
screenshots that
show the
      quality
      of the DWI to anatomical and DWI to MNI
registrations?

      Thanks,
      a.y

      On Mon, 2 Dec 2013, David Soto wrote:

> hi - thanks , not sure though...the no_dif brain
maskseems ok,
if
that is
> what you meant...
>
> I did re-run the processing and
> in the last run I can not see the WARN you
mentioned
> the latest preprocessing output from the
preprocessing can be
> found  here:
 https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>
> the dlabel/diff output got stuck with the
> rh.ilf_AS_avg33 which only contains thee
 _mni_bbr_cpts_5.txt
but
nothing
> else
>
> thanks so much
>
> ds
>
>
>
> On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>  wrote:
>
>       Hi David - Sorry for the delayed response
due to
traveling.
>
>       There's a warning about the right ILF in the
log file
that may
>       offer a
>       clue:
>
   

Re: [Freesurfer] trac-all inquiry

[David Soto]

hi Anastasia, I tried then to recontruct the remaining tracts
of this participant for which I could not do the  right ILF due to
diffusion loss

I set the pathlist like this: set pathlist = ( lh.cst_AS rh.cst_AS \
 lh.unc_AS rh.unc_AS \
 fmajor_PP fminor_PP \
 lh.atr_PP rh.atr_PP \
 lh.ccg_PP rh.ccg_PP \
 lh.cab_PP rh.cab_PP \
 lh.slfp_PP rh.slfp_PP \
 lh.slft_PP rh.slft_PP )

and while it generated most the lh.slfp_PP rh.slfp_PP \
 lh.slft_PP rh.slft_PP  are missing

is this expected given that  the issues with the ILF?

I could not find any errors in the logs relative to the SLFTs

cheers
ds


On Thu, Dec 5, 2013 at 2:58 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Of course, you can specify which tracts you want to reconstruct in the
> configuration file. Both the sample configuration file in
> $FREESURFER_HOME/dmrirc.example and the tracula tutorial have the info on
> how to do this.
>
> On Thu, 5 Dec 2013, David Soto wrote:
>
>  Hi, just a though, would it be possible to skip thereconstruction of the
>>
>> right ILF, I mean to get the remaining
>> tract statistics?
>> that would be v/useful
>> cheers
>> ds
>>
>>
>> On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki
>>  wrote:
>>   Hi David - The screeenshots show that several slices are blank
>>   in the diffusion data, and these indeed go through the right
>>   ILF. I'd check your original diffusion dicoms for this subject
>>   and see if that's indeed the case.
>>
>>   a.y
>>
>>   On Wed, 4 Dec 2013, David Soto wrote:
>>
>>   thanks Anastasia, see the link below
>> plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip
>>
>> you will find 2 pairs of images
>> pair one: there are 2 files starting by ind2anat, one showing
>> the T1 and the other the FA in the same coordinates, you will
>> see that align
>> well
>>
>> pair two: here are 2 files starting by MNI, one showing the FA
>> in mni space
>> and the other the mni T1_1mm template..seem fine to me, though
>> there seem to
>> be some coverage deficit in the FA map in the bottom right of
>> the image
>>
>> cheers
>> ds
>>
>>
>> On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi David - I am not convinced that all the regisrtrations
>> have
>>   worked well
>>   for this subject. The fact that some of the coordinates of
>> the
>>   control
>>   points, which are mapped from template to individual
>> space, are
>>   negative
>>   in individual space (see INFO messages in log file), means
>> that
>>   some part
>>   of the brain in templated space is mapped outside the
>> field of
>>   view in
>>   individual DWI space. Can you send any screenshots that
>> show the
>>   quality
>>   of the DWI to anatomical and DWI to MNI registrations?
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 2 Dec 2013, David Soto wrote:
>>
>> > hi - thanks , not sure though...the no_dif brain maskseems ok,
>> if
>> that is
>> > what you meant...
>> >
>> > I did re-run the processing and
>> > in the last run I can not see the WARN you mentioned
>> > the latest preprocessing output from the preprocessing can be
>> > found  here:
>>  https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>> >
>> > the dlabel/diff output got stuck with the
>> > rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt
>> but
>> nothing
>> > else
>> >
>> > thanks so much
>> >
>> > ds
>> >
>> >
>> >
>> > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>> >  wrote:
>> >
>> >   Hi David - Sorry for the delayed response due to
>> traveling.
>> >
>> >   There's a warning about the right ILF in the log file
>> that may
>> >   offer a
>> >   clue:
>> >
>> >   WARN: Initial control point 37 56 -6 is not in DWI
>> volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (37 56 0)
>> >   WARN: Initial control point 38 45 -1 is not in DWI
>> volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (38 45 0)
>> >   WARN: Initial start point 37 56 0 is not in start ROI
>> >   WARN: Replacing with closest point in start ROI (31 56
>> 0)
>> >
>> >   Is the brain mask cropped on either end of the right
>> ILF? You
>> >   mentioned
>> >   that you already checked the registration of the FA map
>> to the
>> >   template
>> >   space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming
>> there's
>> >   nothing
>> >   wrong there.
>> >
>> >   a.y
>> >
>> >   On Sat, 16 Nov 2013, David Soto wrote:
>> >
>> >   > Thanks!
>> >   > for some weird unknown reason
>> >   > the log for the preprocessing file of this
>> >   > subject is unusually big (2.8 megabytes)
>> >   >  please get it from this link
>> >   >
>> https://dl.dropboxusercontent.com/u/8209026/Arch

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Sorry, trac-all requires freesurfer recons at the moment.

On Thu, 5 Dec 2013, David Soto wrote:


ok thanks I did not realise!
may I ask something else?
2 of my participants structural scan
was distorted and could not be used
by recon-all, so can not get the anatomical
priors for tracula. It may sound a stupid 
questio, but is it possible(and worthy)
to try to do some registration of the 
diffusion data into standard space and
then use a standard structural template
instead to the the anatomical priors?

cheers
ds


On Thu, Dec 5, 2013 at 2:58 PM, Anastasia Yendiki
 wrote:

  Of course, you can specify which tracts you want to reconstruct
  in the configuration file. Both the sample configuration file in
  $FREESURFER_HOME/dmrirc.example and the tracula tutorial have
  the info on how to do this.

  On Thu, 5 Dec 2013, David Soto wrote:

Hi, just a though, would it be possible to skip
thereconstruction of the
right ILF, I mean to get the remaining
tract statistics?
that would be v/useful
cheers
ds


On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki
 wrote:
      Hi David - The screeenshots show that several
slices are blank
      in the diffusion data, and these indeed go
through the right
      ILF. I'd check your original diffusion dicoms
for this subject
      and see if that's indeed the case.

      a.y

      On Wed, 4 Dec 2013, David Soto wrote:

      thanks Anastasia, see the link below
plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip

you will find 2 pairs of images
pair one: there are 2 files starting by ind2anat,
one showing 
the T1 and the other the FA in the same coordinates,
you will
see that align
well

pair two: here are 2 files starting by MNI, one
showing the FA
in mni space
and the other the mni T1_1mm template..seem fine to
me, though
there seem to
be some coverage deficit in the FA map in the bottom
right of
the image

cheers
ds


On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
 wrote:

      Hi David - I am not convinced that all the
regisrtrations
have
      worked well
      for this subject. The fact that some of the
coordinates of
the
      control
      points, which are mapped from template to
individual
space, are
      negative
      in individual space (see INFO messages in log
file), means
that
      some part
      of the brain in templated space is mapped
outside the
field of
      view in
      individual DWI space. Can you send any
screenshots that
show the
      quality
      of the DWI to anatomical and DWI to MNI
registrations?

      Thanks,
      a.y

      On Mon, 2 Dec 2013, David Soto wrote:

> hi - thanks , not sure though...the no_dif brain
maskseems ok,
if
that is
> what you meant...
>
> I did re-run the processing and
> in the last run I can not see the WARN you
mentioned
> the latest preprocessing output from the
preprocessing can be
> found  here:
 https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>
> the dlabel/diff output got stuck with the
> rh.ilf_AS_avg33 which only contains thee
 _mni_bbr_cpts_5.txt
but
nothing
> else
>
> thanks so much
>
> ds
>
>
>
> On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>  wrote:
>
>       Hi David - Sorry for the delayed response
due to
traveling.
>
>       There's a warning about the right ILF in the
log file
that may
>       offer a
>       clue:
>
>       WARN: Initial control point 37 56 -6 is not
in DWI
volume - is
>       DWI cropped?
>       WARN: Replacing with closest point in volume
(37 56 0)
>       WARN: Initial control point 38 45 -1 is not
in DWI
volume - is
>       D

Re: [Freesurfer] trac-all inquiry

[David Soto]

ok thanks I did not realise!

may I ask something else?
2 of my participants structural scan
was distorted and could not be used
by recon-all, so can not get the anatomical
priors for tracula. It may sound a stupid
questio, but is it possible(and worthy)
to try to do some registration of the
diffusion data into standard space and
then use a standard structural template
instead to the the anatomical priors?

cheers
ds


On Thu, Dec 5, 2013 at 2:58 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Of course, you can specify which tracts you want to reconstruct in the
> configuration file. Both the sample configuration file in
> $FREESURFER_HOME/dmrirc.example and the tracula tutorial have the info on
> how to do this.
>
> On Thu, 5 Dec 2013, David Soto wrote:
>
>  Hi, just a though, would it be possible to skip thereconstruction of the
>>
>> right ILF, I mean to get the remaining
>> tract statistics?
>> that would be v/useful
>> cheers
>> ds
>>
>>
>> On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki
>>  wrote:
>>   Hi David - The screeenshots show that several slices are blank
>>   in the diffusion data, and these indeed go through the right
>>   ILF. I'd check your original diffusion dicoms for this subject
>>   and see if that's indeed the case.
>>
>>   a.y
>>
>>   On Wed, 4 Dec 2013, David Soto wrote:
>>
>>   thanks Anastasia, see the link below
>> plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip
>>
>> you will find 2 pairs of images
>> pair one: there are 2 files starting by ind2anat, one showing
>> the T1 and the other the FA in the same coordinates, you will
>> see that align
>> well
>>
>> pair two: here are 2 files starting by MNI, one showing the FA
>> in mni space
>> and the other the mni T1_1mm template..seem fine to me, though
>> there seem to
>> be some coverage deficit in the FA map in the bottom right of
>> the image
>>
>> cheers
>> ds
>>
>>
>> On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi David - I am not convinced that all the regisrtrations
>> have
>>   worked well
>>   for this subject. The fact that some of the coordinates of
>> the
>>   control
>>   points, which are mapped from template to individual
>> space, are
>>   negative
>>   in individual space (see INFO messages in log file), means
>> that
>>   some part
>>   of the brain in templated space is mapped outside the
>> field of
>>   view in
>>   individual DWI space. Can you send any screenshots that
>> show the
>>   quality
>>   of the DWI to anatomical and DWI to MNI registrations?
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 2 Dec 2013, David Soto wrote:
>>
>> > hi - thanks , not sure though...the no_dif brain maskseems ok,
>> if
>> that is
>> > what you meant...
>> >
>> > I did re-run the processing and
>> > in the last run I can not see the WARN you mentioned
>> > the latest preprocessing output from the preprocessing can be
>> > found  here:
>>  https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>> >
>> > the dlabel/diff output got stuck with the
>> > rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt
>> but
>> nothing
>> > else
>> >
>> > thanks so much
>> >
>> > ds
>> >
>> >
>> >
>> > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>> >  wrote:
>> >
>> >   Hi David - Sorry for the delayed response due to
>> traveling.
>> >
>> >   There's a warning about the right ILF in the log file
>> that may
>> >   offer a
>> >   clue:
>> >
>> >   WARN: Initial control point 37 56 -6 is not in DWI
>> volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (37 56 0)
>> >   WARN: Initial control point 38 45 -1 is not in DWI
>> volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (38 45 0)
>> >   WARN: Initial start point 37 56 0 is not in start ROI
>> >   WARN: Replacing with closest point in start ROI (31 56
>> 0)
>> >
>> >   Is the brain mask cropped on either end of the right
>> ILF? You
>> >   mentioned
>> >   that you already checked the registration of the FA map
>> to the
>> >   template
>> >   space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming
>> there's
>> >   nothing
>> >   wrong there.
>> >
>> >   a.y
>> >
>> >   On Sat, 16 Nov 2013, David Soto wrote:
>> >
>> >   > Thanks!
>> >   > for some weird unknown reason
>> >   > the log for the preprocessing file of this
>> >   > subject is unusually big (2.8 megabytes)
>> >   >  please get it from this link
>> >   >
>> https://dl.dropboxusercontent.com/u/8209026/Archive.zip
>> >   > cheers
>> >   > ds
>> >   >
>> >   >
>> >   > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
>> >   >  wrote:
>> >   >
>> >   >   Hi David - This log only shows output from the
>> -path
>> >   step and
>> >   >   not from the -prep step. T

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Of course, you can specify which tracts you want to reconstruct in the 
configuration file. Both the sample configuration file in 
$FREESURFER_HOME/dmrirc.example and the tracula tutorial have the info on 
how to do this.


On Thu, 5 Dec 2013, David Soto wrote:


Hi, just a though, would it be possible to skip thereconstruction of the
right ILF, I mean to get the remaining
tract statistics?
that would be v/useful
cheers
ds


On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki
 wrote:
  Hi David - The screeenshots show that several slices are blank
  in the diffusion data, and these indeed go through the right
  ILF. I'd check your original diffusion dicoms for this subject
  and see if that's indeed the case.

  a.y

  On Wed, 4 Dec 2013, David Soto wrote:

  thanks Anastasia, see the link below
plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip

you will find 2 pairs of images
pair one: there are 2 files starting by ind2anat, one showing 
the T1 and the other the FA in the same coordinates, you will
see that align
well

pair two: here are 2 files starting by MNI, one showing the FA
in mni space
and the other the mni T1_1mm template..seem fine to me, though
there seem to
be some coverage deficit in the FA map in the bottom right of
the image

cheers
ds


On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
 wrote:

      Hi David - I am not convinced that all the regisrtrations
have
      worked well
      for this subject. The fact that some of the coordinates of
the
      control
      points, which are mapped from template to individual
space, are
      negative
      in individual space (see INFO messages in log file), means
that
      some part
      of the brain in templated space is mapped outside the
field of
      view in
      individual DWI space. Can you send any screenshots that
show the
      quality
      of the DWI to anatomical and DWI to MNI registrations?

      Thanks,
      a.y

      On Mon, 2 Dec 2013, David Soto wrote:

> hi - thanks , not sure though...the no_dif brain maskseems ok,
if
that is
> what you meant...
>
> I did re-run the processing and
> in the last run I can not see the WARN you mentioned
> the latest preprocessing output from the preprocessing can be
> found  here:
 https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>
> the dlabel/diff output got stuck with the
> rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt
but
nothing
> else
>
> thanks so much
>
> ds
>
>
>
> On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>  wrote:
>
>       Hi David - Sorry for the delayed response due to
traveling.
>
>       There's a warning about the right ILF in the log file
that may
>       offer a
>       clue:
>
>       WARN: Initial control point 37 56 -6 is not in DWI
volume - is
>       DWI cropped?
>       WARN: Replacing with closest point in volume (37 56 0)
>       WARN: Initial control point 38 45 -1 is not in DWI
volume - is
>       DWI cropped?
>       WARN: Replacing with closest point in volume (38 45 0)
>       WARN: Initial start point 37 56 0 is not in start ROI
>       WARN: Replacing with closest point in start ROI (31 56
0)
>
>       Is the brain mask cropped on either end of the right
ILF? You
>       mentioned
>       that you already checked the registration of the FA map
to the
>       template
>       space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming
there's
>       nothing
>       wrong there.
>
>       a.y
>
>       On Sat, 16 Nov 2013, David Soto wrote:
>
>       > Thanks!
>       > for some weird unknown reason
>       > the log for the preprocessing file of this
>       > subject is unusually big (2.8 megabytes)
>       >  please get it from this link
>       >
https://dl.dropboxusercontent.com/u/8209026/Archive.zip
>       > cheers
>       > ds
>       >
>       >
>       > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
>       >  wrote:
>       >
>       >       Hi David - This log only shows output from the
-path
>       step and
>       >       not from the -prep step. The file that's missing
should
>       be
>       >       created during the -prep step, so there's no way
to
>       figure out
>       >       what went wrong without seeing the output from
the
>       >       pre-processing.
>       >
>       >       Please cc the freesurfer list on your reply.
>       >
>       >       Thank you,
>       >       a.y
>       >
>       >
>       >       On Sat, 16 Nov 2013, David Soto wrote:
>       >
>       >             Thanks, please see attachedI only noticed
this 
>       >            
ERROR:Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff
/rh.il
f_AS_
>       avg
>       >             33_m
>       >             ni_bbr_cpts_5_std.txt
>       >             cheers
>       >             DS
>       >
>       >
>       >             On Fri, Nov 15, 2013 at 8:55 PM, Anastasia
Yendiki
>       >              wrote:
>       >
>       >                   Hi David - Can you please s

Re: [Freesurfer] trac-all inquiry

[David Soto]

Hi, just a though, would it be possible to skip the
reconstruction of the right ILF, I mean to get the remaining
tract statistics?
that would be v/useful
cheers
ds


On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

> Hi David - The screeenshots show that several slices are blank in the
> diffusion data, and these indeed go through the right ILF. I'd check your
> original diffusion dicoms for this subject and see if that's indeed the
> case.
>
> a.y
>
>
> On Wed, 4 Dec 2013, David Soto wrote:
>
>  thanks Anastasia, see the link below
>> plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip
>>
>>
>> you will find 2 pairs of images
>> pair one: there are 2 files starting by ind2anat, one showing
>> the T1 and the other the FA in the same coordinates, you will see that
>> align
>> well
>>
>> pair two: here are 2 files starting by MNI, one showing the FA in mni
>> space
>> and the other the mni T1_1mm template..seem fine to me, though there seem
>> to
>> be some coverage deficit in the FA map in the bottom right of the image
>>
>> cheers
>> ds
>>
>>
>> On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi David - I am not convinced that all the regisrtrations have
>>   worked well
>>   for this subject. The fact that some of the coordinates of the
>>   control
>>   points, which are mapped from template to individual space, are
>>   negative
>>   in individual space (see INFO messages in log file), means that
>>   some part
>>   of the brain in templated space is mapped outside the field of
>>   view in
>>   individual DWI space. Can you send any screenshots that show the
>>   quality
>>   of the DWI to anatomical and DWI to MNI registrations?
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 2 Dec 2013, David Soto wrote:
>>
>> > hi - thanks , not sure though...the no_dif brain maskseems ok, if
>> that is
>> > what you meant...
>> >
>> > I did re-run the processing and
>> > in the last run I can not see the WARN you mentioned
>> > the latest preprocessing output from the preprocessing can be
>> > found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>> >
>> > the dlabel/diff output got stuck with the
>> > rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but
>> nothing
>> > else
>> >
>> > thanks so much
>> >
>> > ds
>> >
>> >
>> >
>> > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>> >  wrote:
>> >
>> >   Hi David - Sorry for the delayed response due to traveling.
>> >
>> >   There's a warning about the right ILF in the log file that may
>> >   offer a
>> >   clue:
>> >
>> >   WARN: Initial control point 37 56 -6 is not in DWI volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (37 56 0)
>> >   WARN: Initial control point 38 45 -1 is not in DWI volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (38 45 0)
>> >   WARN: Initial start point 37 56 0 is not in start ROI
>> >   WARN: Replacing with closest point in start ROI (31 56 0)
>> >
>> >   Is the brain mask cropped on either end of the right ILF? You
>> >   mentioned
>> >   that you already checked the registration of the FA map to the
>> >   template
>> >   space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's
>> >   nothing
>> >   wrong there.
>> >
>> >   a.y
>> >
>> >   On Sat, 16 Nov 2013, David Soto wrote:
>> >
>> >   > Thanks!
>> >   > for some weird unknown reason
>> >   > the log for the preprocessing file of this
>> >   > subject is unusually big (2.8 megabytes)
>> >   >  please get it from this link
>> >   > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
>> >   > cheers
>> >   > ds
>> >   >
>> >   >
>> >   > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
>> >   >  wrote:
>> >   >
>> >   >   Hi David - This log only shows output from the -path
>> >   step and
>> >   >   not from the -prep step. The file that's missing
>> should
>> >   be
>> >   >   created during the -prep step, so there's no way to
>> >   figure out
>> >   >   what went wrong without seeing the output from the
>> >   >   pre-processing.
>> >   >
>> >   >   Please cc the freesurfer list on your reply.
>> >   >
>> >   >   Thank you,
>> >   >   a.y
>> >   >
>> >   >
>> >   >   On Sat, 16 Nov 2013, David Soto wrote:
>> >   >
>> >   > Thanks, please see attachedI only noticed this
>> >   > ERROR:Couldnotopen/home/dsoto/
>> Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.il
>> f_AS_
>> >   avg
>> >   > 33_m
>> >   > ni_bbr_cpts_5_std.txt
>> >   > cheers
>> >   > DS
>> >   >
>> >   >
>> >   > On Fri, No

Re: [Freesurfer] trac-all inquiry

[David Soto]

thanks for that, it is not so clear the missing slices from the  FA scan
in subject space but guess that is the issue!
cheers
ds


On Wed, Dec 4, 2013 at 2:32 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

> Hi David - The screeenshots show that several slices are blank in the
> diffusion data, and these indeed go through the right ILF. I'd check your
> original diffusion dicoms for this subject and see if that's indeed the
> case.
>
> a.y
>
>
> On Wed, 4 Dec 2013, David Soto wrote:
>
>  thanks Anastasia, see the link below
>> plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip
>>
>>
>> you will find 2 pairs of images
>> pair one: there are 2 files starting by ind2anat, one showing
>> the T1 and the other the FA in the same coordinates, you will see that
>> align
>> well
>>
>> pair two: here are 2 files starting by MNI, one showing the FA in mni
>> space
>> and the other the mni T1_1mm template..seem fine to me, though there seem
>> to
>> be some coverage deficit in the FA map in the bottom right of the image
>>
>> cheers
>> ds
>>
>>
>> On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi David - I am not convinced that all the regisrtrations have
>>   worked well
>>   for this subject. The fact that some of the coordinates of the
>>   control
>>   points, which are mapped from template to individual space, are
>>   negative
>>   in individual space (see INFO messages in log file), means that
>>   some part
>>   of the brain in templated space is mapped outside the field of
>>   view in
>>   individual DWI space. Can you send any screenshots that show the
>>   quality
>>   of the DWI to anatomical and DWI to MNI registrations?
>>
>>   Thanks,
>>   a.y
>>
>>   On Mon, 2 Dec 2013, David Soto wrote:
>>
>> > hi - thanks , not sure though...the no_dif brain maskseems ok, if
>> that is
>> > what you meant...
>> >
>> > I did re-run the processing and
>> > in the last run I can not see the WARN you mentioned
>> > the latest preprocessing output from the preprocessing can be
>> > found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>> >
>> > the dlabel/diff output got stuck with the
>> > rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but
>> nothing
>> > else
>> >
>> > thanks so much
>> >
>> > ds
>> >
>> >
>> >
>> > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>> >  wrote:
>> >
>> >   Hi David - Sorry for the delayed response due to traveling.
>> >
>> >   There's a warning about the right ILF in the log file that may
>> >   offer a
>> >   clue:
>> >
>> >   WARN: Initial control point 37 56 -6 is not in DWI volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (37 56 0)
>> >   WARN: Initial control point 38 45 -1 is not in DWI volume - is
>> >   DWI cropped?
>> >   WARN: Replacing with closest point in volume (38 45 0)
>> >   WARN: Initial start point 37 56 0 is not in start ROI
>> >   WARN: Replacing with closest point in start ROI (31 56 0)
>> >
>> >   Is the brain mask cropped on either end of the right ILF? You
>> >   mentioned
>> >   that you already checked the registration of the FA map to the
>> >   template
>> >   space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's
>> >   nothing
>> >   wrong there.
>> >
>> >   a.y
>> >
>> >   On Sat, 16 Nov 2013, David Soto wrote:
>> >
>> >   > Thanks!
>> >   > for some weird unknown reason
>> >   > the log for the preprocessing file of this
>> >   > subject is unusually big (2.8 megabytes)
>> >   >  please get it from this link
>> >   > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
>> >   > cheers
>> >   > ds
>> >   >
>> >   >
>> >   > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
>> >   >  wrote:
>> >   >
>> >   >   Hi David - This log only shows output from the -path
>> >   step and
>> >   >   not from the -prep step. The file that's missing
>> should
>> >   be
>> >   >   created during the -prep step, so there's no way to
>> >   figure out
>> >   >   what went wrong without seeing the output from the
>> >   >   pre-processing.
>> >   >
>> >   >   Please cc the freesurfer list on your reply.
>> >   >
>> >   >   Thank you,
>> >   >   a.y
>> >   >
>> >   >
>> >   >   On Sat, 16 Nov 2013, David Soto wrote:
>> >   >
>> >   > Thanks, please see attachedI only noticed this
>> >   > ERROR:Couldnotopen/home/dsoto/
>> Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.il
>> f_AS_
>> >   avg
>> >   > 33_m
>> >   > ni_bbr_cpts_5_std.txt
>> >   > cheers
>> >   > DS
>> >   >
>> >   >
>> >   > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia
>>

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - The screeenshots show that several slices are blank in the 
diffusion data, and these indeed go through the right ILF. I'd check your 
original diffusion dicoms for this subject and see if that's indeed the 
case.


a.y

On Wed, 4 Dec 2013, David Soto wrote:


thanks Anastasia, see the link below
plshttps://dl.dropboxusercontent.com/u/8209026/regs.zip

you will find 2 pairs of images
pair one: there are 2 files starting by ind2anat, one showing 
the T1 and the other the FA in the same coordinates, you will see that align
well

pair two: here are 2 files starting by MNI, one showing the FA in mni space
and the other the mni T1_1mm template..seem fine to me, though there seem to
be some coverage deficit in the FA map in the bottom right of the image

cheers
ds


On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki
 wrote:

  Hi David - I am not convinced that all the regisrtrations have
  worked well
  for this subject. The fact that some of the coordinates of the
  control
  points, which are mapped from template to individual space, are
  negative
  in individual space (see INFO messages in log file), means that
  some part
  of the brain in templated space is mapped outside the field of
  view in
  individual DWI space. Can you send any screenshots that show the
  quality
  of the DWI to anatomical and DWI to MNI registrations?

  Thanks,
  a.y

  On Mon, 2 Dec 2013, David Soto wrote:

> hi - thanks , not sure though...the no_dif brain maskseems ok, if
that is
> what you meant...
>
> I did re-run the processing and
> in the last run I can not see the WARN you mentioned
> the latest preprocessing output from the preprocessing can be
> found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt
>
> the dlabel/diff output got stuck with the
> rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but
nothing
> else
>
> thanks so much
>
> ds
>
>
>
> On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
>  wrote:
>
>       Hi David - Sorry for the delayed response due to traveling.
>
>       There's a warning about the right ILF in the log file that may
>       offer a
>       clue:
>
>       WARN: Initial control point 37 56 -6 is not in DWI volume - is
>       DWI cropped?
>       WARN: Replacing with closest point in volume (37 56 0)
>       WARN: Initial control point 38 45 -1 is not in DWI volume - is
>       DWI cropped?
>       WARN: Replacing with closest point in volume (38 45 0)
>       WARN: Initial start point 37 56 0 is not in start ROI
>       WARN: Replacing with closest point in start ROI (31 56 0)
>
>       Is the brain mask cropped on either end of the right ILF? You
>       mentioned
>       that you already checked the registration of the FA map to the
>       template
>       space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's
>       nothing
>       wrong there.
>
>       a.y
>
>       On Sat, 16 Nov 2013, David Soto wrote:
>
>       > Thanks!
>       > for some weird unknown reason
>       > the log for the preprocessing file of this
>       > subject is unusually big (2.8 megabytes)
>       >  please get it from this link
>       > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
>       > cheers
>       > ds
>       >
>       >
>       > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
>       >  wrote:
>       >
>       >       Hi David - This log only shows output from the -path
>       step and
>       >       not from the -prep step. The file that's missing
should
>       be
>       >       created during the -prep step, so there's no way to
>       figure out
>       >       what went wrong without seeing the output from the
>       >       pre-processing.
>       >
>       >       Please cc the freesurfer list on your reply.
>       >
>       >       Thank you,
>       >       a.y
>       >
>       >
>       >       On Sat, 16 Nov 2013, David Soto wrote:
>       >
>       >             Thanks, please see attachedI only noticed this 
>       >             
ERROR:Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.il
f_AS_
>       avg
>       >             33_m
>       >             ni_bbr_cpts_5_std.txt
>       >             cheers
>       >             DS
>       >
>       >
>       >             On Fri, Nov 15, 2013 at 8:55 PM, Anastasia
Yendiki
>       >              wrote:
>       >
>       >                   Hi David - Can you please send us the
>       >             trac-all.log file for this
>       >                   subject?
>       >                   Without seeing where it stopped and what
>       error
>       >             messages there
>       >                   are it's
>       >                   hard to guess what's going on.
>       >
>       >                   Thanks,
>       >                   a.y
>       >
>       >                   On Fri, 15 Nov 2013, David Soto wrote:
>       >
>       >                   >  Hi -  
>       > 

Re: [Freesurfer] trac-all inquiry

[David Soto]

thanks Anastasia, see the link below pls
https://dl.dropboxusercontent.com/u/8209026/regs.zip

you will find 2 pairs of images
pair one: there are 2 files starting by ind2anat, one showing
the T1 and the other the FA in the same coordinates, you will see that align
well

pair two: here are 2 files starting by MNI, one showing the FA in mni space
and the other the mni T1_1mm template..seem fine to me, though there seem
to be some coverage deficit in the FA map in the bottom right of the image

cheers
ds


On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi David - I am not convinced that all the regisrtrations have worked well
> for this subject. The fact that some of the coordinates of the control
> points, which are mapped from template to individual space, are negative
> in individual space (see INFO messages in log file), means that some part
> of the brain in templated space is mapped outside the field of view in
> individual DWI space. Can you send any screenshots that show the quality
> of the DWI to anatomical and DWI to MNI registrations?
>
> Thanks,
> a.y
>
> On Mon, 2 Dec 2013, David Soto wrote:
>
> > hi - thanks , not sure though...the no_dif brain maskseems ok, if that is
> > what you meant...
> >
> > I did re-run the processing and
> > in the last run I can not see the WARN you mentioned
> > the latest preprocessing output from the preprocessing can be
> > found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt
> >
> > the dlabel/diff output got stuck with the
> > rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but nothing
> > else
> >
> > thanks so much
> >
> > ds
> >
> >
> >
> > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
> >  wrote:
> >
> >   Hi David - Sorry for the delayed response due to traveling.
> >
> >   There's a warning about the right ILF in the log file that may
> >   offer a
> >   clue:
> >
> >   WARN: Initial control point 37 56 -6 is not in DWI volume - is
> >   DWI cropped?
> >   WARN: Replacing with closest point in volume (37 56 0)
> >   WARN: Initial control point 38 45 -1 is not in DWI volume - is
> >   DWI cropped?
> >   WARN: Replacing with closest point in volume (38 45 0)
> >   WARN: Initial start point 37 56 0 is not in start ROI
> >   WARN: Replacing with closest point in start ROI (31 56 0)
> >
> >   Is the brain mask cropped on either end of the right ILF? You
> >   mentioned
> >   that you already checked the registration of the FA map to the
> >   template
> >   space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's
> >   nothing
> >   wrong there.
> >
> >   a.y
> >
> >   On Sat, 16 Nov 2013, David Soto wrote:
> >
> >   > Thanks!
> >   > for some weird unknown reason
> >   > the log for the preprocessing file of this
> >   > subject is unusually big (2.8 megabytes)
> >   >  please get it from this link
> >   > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
> >   > cheers
> >   > ds
> >   >
> >   >
> >   > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
> >   >  wrote:
> >   >
> >   >   Hi David - This log only shows output from the -path
> >   step and
> >   >   not from the -prep step. The file that's missing should
> >   be
> >   >   created during the -prep step, so there's no way to
> >   figure out
> >   >   what went wrong without seeing the output from the
> >   >   pre-processing.
> >   >
> >   >   Please cc the freesurfer list on your reply.
> >   >
> >   >   Thank you,
> >   >   a.y
> >   >
> >   >
> >   >   On Sat, 16 Nov 2013, David Soto wrote:
> >   >
> >   > Thanks, please see attachedI only noticed this
> >   > ERROR:
> Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_
> >   avg
> >   > 33_m
> >   > ni_bbr_cpts_5_std.txt
> >   > cheers
> >   > DS
> >   >
> >   >
> >   > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
> >   >  wrote:
> >   >
> >   >   Hi David - Can you please send us the
> >   > trac-all.log file for this
> >   >   subject?
> >   >   Without seeing where it stopped and what
> >   error
> >   > messages there
> >   >   are it's
> >   >   hard to guess what's going on.
> >   >
> >   >   Thanks,
> >   >   a.y
> >   >
> >   >   On Fri, 15 Nov 2013, David Soto wrote:
> >   >
> >   >   >  Hi -
> >   >   > trac-all completed in all my Ps except one
> >   >   > and I n

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - I am not convinced that all the regisrtrations have worked well 
for this subject. The fact that some of the coordinates of the control 
points, which are mapped from template to individual space, are negative 
in individual space (see INFO messages in log file), means that some part 
of the brain in templated space is mapped outside the field of view in 
individual DWI space. Can you send any screenshots that show the quality 
of the DWI to anatomical and DWI to MNI registrations?


Thanks,
a.y

On Mon, 2 Dec 2013, David Soto wrote:


hi - thanks , not sure though...the no_dif brain maskseems ok, if that is
what you meant...

I did re-run the processing and
in the last run I can not see the WARN you mentioned
the latest preprocessing output from the preprocessing can be
found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt

the dlabel/diff output got stuck with the
rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but nothing
else

thanks so much

ds



On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki
 wrote:

  Hi David - Sorry for the delayed response due to traveling.

  There's a warning about the right ILF in the log file that may
  offer a
  clue:

  WARN: Initial control point 37 56 -6 is not in DWI volume - is
  DWI cropped?
  WARN: Replacing with closest point in volume (37 56 0)
  WARN: Initial control point 38 45 -1 is not in DWI volume - is
  DWI cropped?
  WARN: Replacing with closest point in volume (38 45 0)
  WARN: Initial start point 37 56 0 is not in start ROI
  WARN: Replacing with closest point in start ROI (31 56 0)

  Is the brain mask cropped on either end of the right ILF? You
  mentioned
  that you already checked the registration of the FA map to the
  template
  space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's
  nothing
  wrong there.

  a.y

  On Sat, 16 Nov 2013, David Soto wrote:

  > Thanks!
  > for some weird unknown reason
  > the log for the preprocessing file of this
  > subject is unusually big (2.8 megabytes)
  >  please get it from this link
  > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
  > cheers
  > ds
  >
  >
  > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
  >  wrote:
  >
  >       Hi David - This log only shows output from the -path
  step and
  >       not from the -prep step. The file that's missing should
  be
  >       created during the -prep step, so there's no way to
  figure out
  >       what went wrong without seeing the output from the
  >       pre-processing.
  >
  >       Please cc the freesurfer list on your reply.
  >
  >       Thank you,
  >       a.y
  >
  >
  >       On Sat, 16 Nov 2013, David Soto wrote:
  >
  >             Thanks, please see attachedI only noticed this 
  >             ERROR: 
Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_
  avg
  >             33_m
  >             ni_bbr_cpts_5_std.txt
  >             cheers
  >             DS
  >
  >
  >             On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
  >              wrote:
  >
  >                   Hi David - Can you please send us the
  >             trac-all.log file for this
  >                   subject?
  >                   Without seeing where it stopped and what
  error
  >             messages there
  >                   are it's
  >                   hard to guess what's going on.
  >
  >                   Thanks,
  >                   a.y
  >
  >                   On Fri, 15 Nov 2013, David Soto wrote:
  >
  >                   >  Hi -  
  >                   > trac-all completed in all my Ps except one
  >                   > and I noticed that the  dlabel/diff output
  >             does not contain
  >                   all the files
  >                   >
  >                   > I assessed whether it could be do to poor
  >             registration, by
  >                   checking
  >                   > the  aparc+aseg
  >                   > file and looks allright
  >                   >
  >                   > I also checked the registration of FA maps
  >             to standard space
  >                   by 
  >                   > freeview -v
  >             $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
  >                   > dtifit_FA.bbr.nii.gz 
  >                   > and seems fine
  >                   >
  >                   > also
  >                   >
  >                   > freeview -v brain_anat_orig.nii.gz
  >             lowb_brain.nii.gz 
  >                   >
  >                   > which also seems fine
  >   

Re: [Freesurfer] trac-all inquiry

[David Soto]

hi - thanks , not sure though...the no_dif brain mask
seems ok, if that is what you meant...

I did re-run the processing and
in the last run I can not see the WARN you mentioned
the latest preprocessing output from the preprocessing can be
found  here:  https://dl.dropboxusercontent.com/u/8209026/prepro.txt

the dlabel/diff output got stuck with the
rh.ilf_AS_avg33 which only contains thee  _mni_bbr_cpts_5.txt but nothing
else

thanks so much

ds



On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi David - Sorry for the delayed response due to traveling.
>
> There's a warning about the right ILF in the log file that may offer a
> clue:
>
> WARN: Initial control point 37 56 -6 is not in DWI volume - is DWI cropped?
> WARN: Replacing with closest point in volume (37 56 0)
> WARN: Initial control point 38 45 -1 is not in DWI volume - is DWI cropped?
> WARN: Replacing with closest point in volume (38 45 0)
> WARN: Initial start point 37 56 0 is not in start ROI
> WARN: Replacing with closest point in start ROI (31 56 0)
>
> Is the brain mask cropped on either end of the right ILF? You mentioned
> that you already checked the registration of the FA map to the template
> space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's nothing
> wrong there.
>
> a.y
>
> On Sat, 16 Nov 2013, David Soto wrote:
>
> > Thanks!
> > for some weird unknown reason
> > the log for the preprocessing file of this
> > subject is unusually big (2.8 megabytes)
> >  please get it from this link
> > https://dl.dropboxusercontent.com/u/8209026/Archive.zip
> > cheers
> > ds
> >
> >
> > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
> >  wrote:
> >
> >   Hi David - This log only shows output from the -path step and
> >   not from the -prep step. The file that's missing should be
> >   created during the -prep step, so there's no way to figure out
> >   what went wrong without seeing the output from the
> >   pre-processing.
> >
> >   Please cc the freesurfer list on your reply.
> >
> >   Thank you,
> >   a.y
> >
> >
> >   On Sat, 16 Nov 2013, David Soto wrote:
> >
> > Thanks, please see attachedI only noticed this
> > ERROR: Could
> notopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg
> > 33_m
> > ni_bbr_cpts_5_std.txt
> > cheers
> > DS
> >
> >
> > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
> >  wrote:
> >
> >   Hi David - Can you please send us the
> > trac-all.log file for this
> >   subject?
> >   Without seeing where it stopped and what error
> > messages there
> >   are it's
> >   hard to guess what's going on.
> >
> >   Thanks,
> >   a.y
> >
> >   On Fri, 15 Nov 2013, David Soto wrote:
> >
> >   >  Hi -
> >   > trac-all completed in all my Ps except one
> >   > and I noticed that the  dlabel/diff output
> > does not contain
> >   all the files
> >   >
> >   > I assessed whether it could be do to poor
> > registration, by
> >   checking
> >   > the  aparc+aseg
> >   > file and looks allright
> >   >
> >   > I also checked the registration of FA maps
> > to standard space
> >   by
> >   > freeview -v
> > $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
> >   > dtifit_FA.bbr.nii.gz
> >   > and seems fine
> >   >
> >   > also
> >   >
> >   > freeview -v brain_anat_orig.nii.gz
> > lowb_brain.nii.gz
> >   >
> >   > which also seems fine
> >   >
> >   > any ideas pls?
> >   >
> >   > thanks!
> >   >
> >   > ds
> >   >
> >   >
> >   >
> >   > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia
> > Yendiki
> >   >  wrote:
> >   >
> >   >   I suspect the current problem is
> > caused by poor
> >   registration.
> >   >   Have you checked the aparc+aseg and/or
> > the registration
> >   from
> >   >   diffusion to anatomical and from
> > anatomical to MNI?
> >   >
> >   >   On Fri, 16 Aug 2013, David Soto
> > wrote:
> >   >
> >   >
> >   >
> >   > --
> >   

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - Sorry for the delayed response due to traveling.

There's a warning about the right ILF in the log file that may offer a 
clue:


WARN: Initial control point 37 56 -6 is not in DWI volume - is DWI cropped?
WARN: Replacing with closest point in volume (37 56 0)
WARN: Initial control point 38 45 -1 is not in DWI volume - is DWI cropped?
WARN: Replacing with closest point in volume (38 45 0)
WARN: Initial start point 37 56 0 is not in start ROI
WARN: Replacing with closest point in start ROI (31 56 0)

Is the brain mask cropped on either end of the right ILF? You mentioned 
that you already checked the registration of the FA map to the template 
space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's nothing 
wrong there.


a.y

On Sat, 16 Nov 2013, David Soto wrote:


Thanks!
for some weird unknown reason
the log for the preprocessing file of this
subject is unusually big (2.8 megabytes)
 please get it from this link
https://dl.dropboxusercontent.com/u/8209026/Archive.zip
cheers
ds


On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki
 wrote:

  Hi David - This log only shows output from the -path step and
  not from the -prep step. The file that's missing should be
  created during the -prep step, so there's no way to figure out
  what went wrong without seeing the output from the
  pre-processing.

  Please cc the freesurfer list on your reply.

  Thank you,
  a.y


  On Sat, 16 Nov 2013, David Soto wrote:

Thanks, please see attachedI only noticed this 
ERROR: Could 
notopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg
33_m
ni_bbr_cpts_5_std.txt
cheers
DS


On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
 wrote:

      Hi David - Can you please send us the
trac-all.log file for this
      subject?
      Without seeing where it stopped and what error
messages there
      are it's
      hard to guess what's going on.

      Thanks,
      a.y

      On Fri, 15 Nov 2013, David Soto wrote:

      >  Hi -  
      > trac-all completed in all my Ps except one
      > and I noticed that the  dlabel/diff output
does not contain
      all the files
      >
      > I assessed whether it could be do to poor
registration, by
      checking
      > the  aparc+aseg
      > file and looks allright
      >
      > I also checked the registration of FA maps
to standard space
      by 
      > freeview -v
$FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
      > dtifit_FA.bbr.nii.gz 
      > and seems fine
      >
      > also
      >
      > freeview -v brain_anat_orig.nii.gz
lowb_brain.nii.gz 
      >
      > which also seems fine
      >
      > any ideas pls?
      >
      > thanks!
      >
      > ds
      >
      >
      >
      > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia
Yendiki
      >  wrote:
      >        
      >       I suspect the current problem is
caused by poor
      registration.
      >       Have you checked the aparc+aseg and/or
the registration
      from
      >       diffusion to anatomical and from
anatomical to MNI?
      >
      >       On Fri, 16 Aug 2013, David Soto
wrote: 
      >
      >
      >
      > --
      >
http://www1.imperial.ac.uk/medicine/people/d.soto/
      >
      >
      >  
      >
      >


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___

Re: [Freesurfer] trac-all inquiry

[David Soto]

hi , I have run this subject again, checking all the processing
stages, and still get the same issues. I have placed the
new output from the preprocessing stage (this is only
1.4 megabytes as the previous one had 2 preprocessing jobs
appended)
you can find it here:
https://dl.dropboxusercontent.com/u/8209026/prepro.txt

as I reminder, one issue I spotted is that the dlabel/diff output does not
contain
all the files

just these
anat_brain_mask.bbr.nii.gz
anat_brain_mask-vent.bbr.nii.gz
aparc+aseg+2mm.bbr.nii.gz
aparc+aseg.bbr.nii.gz
aparc+aseg_mask.bbr.nii.gz
cortex+2mm.bbr.nii.gz
cortex+2mm+bs.bbr.nii.gz
cortex.bbr.nii.gz
lowb_brain_mask.nii.gz
notventricles.bbr.nii.gz
White-Matter.bbr.nii.gz
White-Matter++.bbr.nii.g

WHILE FOR THE TRACT RELATED ONES
it contains all the relevant file extensions to
lh.cst_AS_avg33
lh.ilf_AS_avg33
rh.cst_AS_avg33

but for this one
rh.ilf_AS_avg33 (only does he  _mni_bbr_cpts_5.txt but does not generate
the .nii)


any help much appreciated

cheers

DS


On Sat, Nov 16, 2013 at 3:41 PM, David Soto  wrote:

> Thanks!
> for some weird unknown reason
> the log for the preprocessing file of this
> subject is unusually big (2.8 megabytes)
>  please get it from this link
> https://dl.dropboxusercontent.com/u/8209026/Archive.zip
> cheers
> ds
>
>
> On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki <
> ayend...@nmr.mgh.harvard.edu> wrote:
>
>>
>> Hi David - This log only shows output from the -path step and not from
>> the -prep step. The file that's missing should be created during the -prep
>> step, so there's no way to figure out what went wrong without seeing the
>> output from the pre-processing.
>>
>> Please cc the freesurfer list on your reply.
>>
>> Thank you,
>> a.y
>>
>>
>> On Sat, 16 Nov 2013, David Soto wrote:
>>
>>  Thanks, please see attachedI only noticed this
>>>
>>> ERROR: Could not open/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/
>>> dlabel/diff/rh.ilf_AS_avg33_m
>>> ni_bbr_cpts_5_std.txt
>>> cheers
>>> DS
>>>
>>>
>>> On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
>>>  wrote:
>>>
>>>   Hi David - Can you please send us the trac-all.log file for this
>>>   subject?
>>>   Without seeing where it stopped and what error messages there
>>>   are it's
>>>   hard to guess what's going on.
>>>
>>>   Thanks,
>>>   a.y
>>>
>>>   On Fri, 15 Nov 2013, David Soto wrote:
>>>
>>>   >  Hi -
>>>   > trac-all completed in all my Ps except one
>>>   > and I noticed that the  dlabel/diff output does not contain
>>>   all the files
>>>   >
>>>   > I assessed whether it could be do to poor registration, by
>>>   checking
>>>   > the  aparc+aseg
>>>   > file and looks allright
>>>   >
>>>   > I also checked the registration of FA maps to standard space
>>>   by
>>>   > freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
>>>   > dtifit_FA.bbr.nii.gz
>>>   > and seems fine
>>>   >
>>>   > also
>>>   >
>>>   > freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz
>>>   >
>>>   > which also seems fine
>>>   >
>>>   > any ideas pls?
>>>   >
>>>   > thanks!
>>>   >
>>>   > ds
>>>   >
>>>   >
>>>   >
>>>   > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki
>>>   >  wrote:
>>>   >
>>>   >   I suspect the current problem is caused by poor
>>>   registration.
>>>   >   Have you checked the aparc+aseg and/or the registration
>>>   from
>>>   >   diffusion to anatomical and from anatomical to MNI?
>>>   >
>>>   >   On Fri, 16 Aug 2013, David Soto wrote:
>>>   >
>>>   >
>>>   >
>>>   > --
>>>   > http://www1.imperial.ac.uk/medicine/people/d.soto/
>>>   >
>>>   >
>>>   >
>>>   >
>>>   >
>>>
>>>
>>> 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.
>>>
>>>
>>>
>>>
>>> --
>>> http://www1.imperial.ac.uk/medicine/people/d.soto/
>>>
>>> --
>>> 
>>> 
>>> http://www1.imperial.ac.uk/medicine/people/d.soto/
>>>
>>> --
>>> http://www1.imperial.ac.uk/medicine/people/d.soto/
>>>
>>>
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Re: [Freesurfer] trac-all inquiry

[David Soto]

Thanks!
for some weird unknown reason
the log for the preprocessing file of this
subject is unusually big (2.8 megabytes)
 please get it from this link
https://dl.dropboxusercontent.com/u/8209026/Archive.zip
cheers
ds


On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Hi David - This log only shows output from the -path step and not from the
> -prep step. The file that's missing should be created during the -prep
> step, so there's no way to figure out what went wrong without seeing the
> output from the pre-processing.
>
> Please cc the freesurfer list on your reply.
>
> Thank you,
> a.y
>
>
> On Sat, 16 Nov 2013, David Soto wrote:
>
>  Thanks, please see attachedI only noticed this
>>
>> ERROR: Could not open/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/
>> dlabel/diff/rh.ilf_AS_avg33_m
>> ni_bbr_cpts_5_std.txt
>> cheers
>> DS
>>
>>
>> On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
>>  wrote:
>>
>>   Hi David - Can you please send us the trac-all.log file for this
>>   subject?
>>   Without seeing where it stopped and what error messages there
>>   are it's
>>   hard to guess what's going on.
>>
>>   Thanks,
>>   a.y
>>
>>   On Fri, 15 Nov 2013, David Soto wrote:
>>
>>   >  Hi -
>>   > trac-all completed in all my Ps except one
>>   > and I noticed that the  dlabel/diff output does not contain
>>   all the files
>>   >
>>   > I assessed whether it could be do to poor registration, by
>>   checking
>>   > the  aparc+aseg
>>   > file and looks allright
>>   >
>>   > I also checked the registration of FA maps to standard space
>>   by
>>   > freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
>>   > dtifit_FA.bbr.nii.gz
>>   > and seems fine
>>   >
>>   > also
>>   >
>>   > freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz
>>   >
>>   > which also seems fine
>>   >
>>   > any ideas pls?
>>   >
>>   > thanks!
>>   >
>>   > ds
>>   >
>>   >
>>   >
>>   > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki
>>   >  wrote:
>>   >
>>   >   I suspect the current problem is caused by poor
>>   registration.
>>   >   Have you checked the aparc+aseg and/or the registration
>>   from
>>   >   diffusion to anatomical and from anatomical to MNI?
>>   >
>>   >   On Fri, 16 Aug 2013, David Soto wrote:
>>   >
>>   >
>>   >
>>   > --
>>   > http://www1.imperial.ac.uk/medicine/people/d.soto/
>>   >
>>   >
>>   >
>>   >
>>   >
>>
>>
>> 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.
>>
>>
>>
>>
>> --
>> http://www1.imperial.ac.uk/medicine/people/d.soto/
>>
>> --
>> http://www1.imperial.ac.uk/medicine/people/d.soto/
>>
>>
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Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - This log only shows output from the -path step and not from the 
-prep step. The file that's missing should be created during the -prep 
step, so there's no way to figure out what went wrong without seeing the 
output from the pre-processing.


Please cc the freesurfer list on your reply.

Thank you,
a.y


On Sat, 16 Nov 2013, David Soto wrote:


Thanks, please see attachedI only noticed this 
ERROR: Could not 
open/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg33_m
ni_bbr_cpts_5_std.txt
cheers
DS


On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki
 wrote:

  Hi David - Can you please send us the trac-all.log file for this
  subject?
  Without seeing where it stopped and what error messages there
  are it's
  hard to guess what's going on.

  Thanks,
  a.y

  On Fri, 15 Nov 2013, David Soto wrote:

  >  Hi -  
  > trac-all completed in all my Ps except one
  > and I noticed that the  dlabel/diff output does not contain
  all the files
  >
  > I assessed whether it could be do to poor registration, by
  checking
  > the  aparc+aseg
  > file and looks allright
  >
  > I also checked the registration of FA maps to standard space
  by 
  > freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
  > dtifit_FA.bbr.nii.gz 
  > and seems fine
  >
  > also
  >
  > freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz 
  >
  > which also seems fine
  >
  > any ideas pls?
  >
  > thanks!
  >
  > ds
  >
  >
  >
  > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki
  >  wrote:
  >        
  >       I suspect the current problem is caused by poor
  registration.
  >       Have you checked the aparc+aseg and/or the registration
  from
  >       diffusion to anatomical and from anatomical to MNI?
  >
  >       On Fri, 16 Aug 2013, David Soto wrote: 
  >
  >
  >
  > --
  > http://www1.imperial.ac.uk/medicine/people/d.soto/
  >
  >
  >  
  >
  >


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Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Hi David - Can you please send us the trac-all.log file for this subject? 
Without seeing where it stopped and what error messages there are it's 
hard to guess what's going on.


Thanks,
a.y

On Fri, 15 Nov 2013, David Soto wrote:


 Hi -  
trac-all completed in all my Ps except one
and I noticed that the  dlabel/diff output does not contain all the files

I assessed whether it could be do to poor registration, by checking
the  aparc+aseg
file and looks allright

I also checked the registration of FA maps to standard space by 
freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
dtifit_FA.bbr.nii.gz 
and seems fine

also

freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz 

which also seems fine

any ideas pls?

thanks!

ds



On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki
 wrote:
   
  I suspect the current problem is caused by poor registration.
  Have you checked the aparc+aseg and/or the registration from
  diffusion to anatomical and from anatomical to MNI?

  On Fri, 16 Aug 2013, David Soto wrote: 



--
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[Freesurfer] trac-all inquiry

[David Soto]

 Hi -
trac-all completed in all my Ps except one
and I noticed that the  dlabel/diff output does not contain all the files

I assessed whether it could be do to poor registration, by checking
the  aparc+aseg
file and looks allright

I also checked the registration of FA maps to standard space by
freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz
dtifit_FA.bbr.nii.gz
and seems fine

also

freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz

which also seems fine

any ideas pls?

thanks!

ds



On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> I suspect the current problem is caused by poor registration. Have you
> checked the aparc+aseg and/or the registration from diffusion to anatomical
> and from anatomical to MNI?
>
>
> On Fri, 16 Aug 2013, David Soto wrote:
>


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Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Great to hear. Thanks, Alan!

On Mon, 19 Aug 2013, Alan Francis wrote:


Hi Anastasia:
I wish to echo David's sentiments. Thanks for this great software. I was able 
to process and extract data for all
brains without losing any of the brains. Thanks so much. 

best,

Alan


On Fri, Aug 16, 2013 at 12:14 PM, Anastasia Yendiki 
 wrote:

  Ok, actually the error about the data and bvals/bvecs not having the same
  size occured the first time you ran trac-all, but it seems to have been
  fixed the second time you ran it, based on the log file.

  I suspect the current problem is caused by poor registration. Have you
  checked the aparc+aseg and/or the registration from diffusion to
  anatomical and from anatomical to MNI?

  On Fri, 16 Aug 2013, David Soto wrote:

> hi - yes it as 65 -output pasted below, cheers
>
> dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info
> dwi.nii.gz Volume information for dwi.nii.gz
>          type: nii
>    dimensions: 96 x 96 x 46 x 65
>   voxel sizes: 2., 2., 2.2999
>          type: FLOAT (3)
>           fov: 224.000
>           dof: 0
>        xstart: -112.0, xend: 112.0
>        ystart: -112.0, yend: 112.0
>        zstart: -52.9, zend: 52.9
>            TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00
> degrees
>       nframes: 65
>       PhEncDir: UNKNOWN
> ras xform present
>    xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
> 0.
>              : x_a =   0., y_a =   0.9774, z_a =  -0.2112, c_a =
> 2.1015
>              : x_s =   0., y_s =   0.2112, z_s =   0.9774, c_s =
> 19.9194
> Orientation   : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>               -2.   0.   0.   112.
>                0.   2.2807  -0.4858   -96.1994
>                0.   0.4928   2.2480   -55.4405
>                0.   0.   0.     1.
>
> voxel-to-ras determinant -12.5217
>
> ras to voxel transform:
>               -0.4286   0.   0.    48.
>               -0.   0.4189   0.0905    45.3166
>               -0.  -0.0918   0.4250    14.7274
>                0.   0.   0.     1.
>
> http://www1.imperial.ac.uk/medicine/people/d.soto/
> On 16/08/13 16:13, Anastasia Yendiki wrote:
>> mri_info dmri/dwi.nii.gz
>
>
>
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Re: [Freesurfer] trac-all inquiry

[Alan Francis]

Hi Anastasia:

I wish to echo David's sentiments. Thanks for this great software. I was
able to process and extract data for all brains without losing any of the
brains. Thanks so much.

best,

Alan


On Fri, Aug 16, 2013 at 12:14 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:

>
> Ok, actually the error about the data and bvals/bvecs not having the same
> size occured the first time you ran trac-all, but it seems to have been
> fixed the second time you ran it, based on the log file.
>
> I suspect the current problem is caused by poor registration. Have you
> checked the aparc+aseg and/or the registration from diffusion to
> anatomical and from anatomical to MNI?
>
> On Fri, 16 Aug 2013, David Soto wrote:
>
> > hi - yes it as 65 -output pasted below, cheers
> >
> > dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info
> > dwi.nii.gz Volume information for dwi.nii.gz
> >  type: nii
> >dimensions: 96 x 96 x 46 x 65
> >   voxel sizes: 2., 2., 2.2999
> >  type: FLOAT (3)
> >   fov: 224.000
> >   dof: 0
> >xstart: -112.0, xend: 112.0
> >ystart: -112.0, yend: 112.0
> >zstart: -52.9, zend: 52.9
> >TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
> 0.00
> > degrees
> >   nframes: 65
> >   PhEncDir: UNKNOWN
> > ras xform present
> >xform info: x_r =  -1., y_r =   0., z_r =   0., c_r =
> > 0.
> >  : x_a =   0., y_a =   0.9774, z_a =  -0.2112, c_a =
> > 2.1015
> >  : x_s =   0., y_s =   0.2112, z_s =   0.9774, c_s =
> > 19.9194
> > Orientation   : LAS
> > Primary Slice Direction: axial
> >
> > voxel to ras transform:
> >   -2.   0.   0.   112.
> >0.   2.2807  -0.4858   -96.1994
> >0.   0.4928   2.2480   -55.4405
> >0.   0.   0. 1.
> >
> > voxel-to-ras determinant -12.5217
> >
> > ras to voxel transform:
> >   -0.4286   0.   0.48.
> >   -0.   0.4189   0.090545.3166
> >   -0.  -0.0918   0.425014.7274
> >0.   0.   0. 1.
> >
> > http://www1.imperial.ac.uk/medicine/people/d.soto/
> > On 16/08/13 16:13, Anastasia Yendiki wrote:
> >> mri_info dmri/dwi.nii.gz
> >
> >
> >
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Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

Ok, actually the error about the data and bvals/bvecs not having the same 
size occured the first time you ran trac-all, but it seems to have been 
fixed the second time you ran it, based on the log file.

I suspect the current problem is caused by poor registration. Have you 
checked the aparc+aseg and/or the registration from diffusion to 
anatomical and from anatomical to MNI?

On Fri, 16 Aug 2013, David Soto wrote:

> hi - yes it as 65 -output pasted below, cheers
>
> dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info 
> dwi.nii.gz Volume information for dwi.nii.gz
>  type: nii
>dimensions: 96 x 96 x 46 x 65
>   voxel sizes: 2., 2., 2.2999
>  type: FLOAT (3)
>   fov: 224.000
>   dof: 0
>xstart: -112.0, xend: 112.0
>ystart: -112.0, yend: 112.0
>zstart: -52.9, zend: 52.9
>TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 
> degrees
>   nframes: 65
>   PhEncDir: UNKNOWN
> ras xform present
>xform info: x_r =  -1., y_r =   0., z_r =   0., c_r = 
> 0.
>  : x_a =   0., y_a =   0.9774, z_a =  -0.2112, c_a = 
> 2.1015
>  : x_s =   0., y_s =   0.2112, z_s =   0.9774, c_s = 
> 19.9194
> Orientation   : LAS
> Primary Slice Direction: axial
>
> voxel to ras transform:
>   -2.   0.   0.   112.
>0.   2.2807  -0.4858   -96.1994
>0.   0.4928   2.2480   -55.4405
>0.   0.   0. 1.
>
> voxel-to-ras determinant -12.5217
>
> ras to voxel transform:
>   -0.4286   0.   0.48.
>   -0.   0.4189   0.090545.3166
>   -0.  -0.0918   0.425014.7274
>0.   0.   0. 1.
>
> http://www1.imperial.ac.uk/medicine/people/d.soto/
> On 16/08/13 16:13, Anastasia Yendiki wrote:
>> mri_info dmri/dwi.nii.gz
>
>
>
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Re: [Freesurfer] trac-all inquiry

[David Soto]

hi - yes it as 65 -output pasted below, cheers

dsoto@wmen-dsoto3:~/Documents/fmri/rsdtianawmgui/14AB/dmri$ mri_info 
dwi.nii.gz Volume information for dwi.nii.gz
   type: nii
 dimensions: 96 x 96 x 46 x 65
voxel sizes: 2., 2., 2.2999
   type: FLOAT (3)
fov: 224.000
dof: 0
 xstart: -112.0, xend: 112.0
 ystart: -112.0, yend: 112.0
 zstart: -52.9, zend: 52.9
 TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 
0.00 degrees
nframes: 65
PhEncDir: UNKNOWN
ras xform present
 xform info: x_r =  -1., y_r =   0., z_r =   0., c_r 
= 0.
   : x_a =   0., y_a =   0.9774, z_a =  -0.2112, c_a 
= 2.1015
   : x_s =   0., y_s =   0.2112, z_s =   0.9774, c_s 
=19.9194
Orientation   : LAS
Primary Slice Direction: axial

voxel to ras transform:
-2.   0.   0.   112.
 0.   2.2807  -0.4858   -96.1994
 0.   0.4928   2.2480   -55.4405
 0.   0.   0. 1.

voxel-to-ras determinant -12.5217

ras to voxel transform:
-0.4286   0.   0.48.
-0.   0.4189   0.090545.3166
-0.  -0.0918   0.425014.7274
 0.   0.   0. 1.

http://www1.imperial.ac.uk/medicine/people/d.soto/
On 16/08/13 16:13, Anastasia Yendiki wrote:
> mri_info dmri/dwi.nii.gz

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Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

I didn't mean run mri_convert on the nifti output of another program. I 
meant run mri_convert directly on the original dicom to convert it to 
nifti:

mri_convert yourimage.dcm yourimage.nii.gz

On Fri, 9 Aug 2013, Soto, David wrote:


I see - as said the diffusion output.nii from MRIConverter
http://lcni.uoregon.edu/~jolinda/MRIConvert/ [to not confound it with 
mri_converter)
is not read by Freeview and mri_converter does not like it either
---
MD00071523-2:RSDTI_WMGUI/ACH_AMO/diff] dsoto% mri_convert output.nii data.mgz
mri_convert output.nii data.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from output.nii...
nifti1Read(): unsupported slice timing pattern 5 in 
/Users/dsoto/Documents/fMRI/RSDTI_WMGUI/ACH_AMO/diff/output.nii
No such file or directory
---

NOW, I find that if I use FSL and run bet with a fractional intensity threshold 
of 0,
I get an output file which is read by Freeview- which should allow me to proceed
with all the necessary preprocessing steps in trac-all

would this be fine? I dont think the bet I run will affect the image

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 23:15
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

When you apply a rotation to the DWIs (as eddy_correct does), you need to
apply the same rotation to the corresponding gradient vectors. See for
example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated
when correcting for subject motion in DTI data. Magn Reson Med 61 (6),
1336–49.

If you don't want to pass the dicoms to trac-all directly, you can use
mri_convert to convert from dicom to nifti.

On Fri, 9 Aug 2013, Soto, David wrote:


hi - am afraid not because I am feeding to trac-all
already eddycorrected images then in the config file
I have

# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
set doeddy = 0
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)

is this critical??

unfortunately, this is the only way I manage to get it to work
as said my diffusion outputs from mriconverter
are not read by FS, only through mediation
of some FSL operation on the files, then FS
likes those.

I could start from scratch using dicoms but would prefer
not to  as the data is already well organised

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 22:44
To: Soto, David
Subject: Re: [Freesurfer]  trac-all inquiry

Are you rotating the gradient vectors accordingly? This is done in
trac-all after running eddy_correct.

On Fri, 9 Aug 2013, Soto, David wrote:


Hi Anastasia, stuff is running smoothly at last one quick question, is there
any 'disadvantage' in
using FSL to do the eddy correct and then feed
those images to trace-all ?
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/

On 9 Aug 2013, at 15:33, David Soto 
 wrote:

  hi, for some reason FS does not like the
  nii file from Mriconverter, ( I saw
  a post about this
  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html
  ) but does like
  the nii.gz outputs from FSL...

  I'll try to debug the bepostx error

  thanks!

  ds

  http://www1.imperial.ac.uk/medicine/people/d.soto/
On 09/08/13 14:26, Anastasia Yendiki wrote:

  There is no reason to conevrt to .mnc. You should use your
  original .nii, if that shows up correctly in freeview.

  As for the bedpostx error, this is an Ubuntu issue that
  has come to my attention very recently. In Ubuntu /bin/sh
  is not a bash shell any more. To get around this, you'll
  have to edit the first line of the scripts
  $FREESURFER_HOME/bin/bedpostx_mgh and
  $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace
  "/bin/sh" with "/bin/bash" on the first line of those two
  scripts.

  On Fri, 9 Aug 2013, David Soto wrote:

hi- I tried to convert from nii to mnc becos
that is what i did when
I did recon-all

but I also tried with nii at the beggining and
got the same issues.
In fact in my last post (pasted below
again)the input was a nii file
could you please check the stuff below?
thanks! ds


Hi, further to my prior email
I made some progress. I noted that nii2mnc
does not seem to work on the diffusion
output.nii that I got from Mri

Re: [Freesurfer] trac-all inquiry

[Soto, David]

I see - as said the diffusion output.nii from MRIConverter
http://lcni.uoregon.edu/~jolinda/MRIConvert/ [to not confound it with 
mri_converter)
is not read by Freeview and mri_converter does not like it either
---
MD00071523-2:RSDTI_WMGUI/ACH_AMO/diff] dsoto% mri_convert output.nii data.mgz
mri_convert output.nii data.mgz 
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from output.nii...
nifti1Read(): unsupported slice timing pattern 5 in 
/Users/dsoto/Documents/fMRI/RSDTI_WMGUI/ACH_AMO/diff/output.nii
No such file or directory
---

NOW, I find that if I use FSL and run bet with a fractional intensity threshold 
of 0,
I get an output file which is read by Freeview- which should allow me to proceed
with all the necessary preprocessing steps in trac-all

would this be fine? I dont think the bet I run will affect the image

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 23:15
To: Soto, David
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

When you apply a rotation to the DWIs (as eddy_correct does), you need to
apply the same rotation to the corresponding gradient vectors. See for
example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated
when correcting for subject motion in DTI data. Magn Reson Med 61 (6),
1336–49.

If you don't want to pass the dicoms to trac-all directly, you can use
mri_convert to convert from dicom to nifti.

On Fri, 9 Aug 2013, Soto, David wrote:

> hi - am afraid not because I am feeding to trac-all
> already eddycorrected images then in the config file
> I have
>
> # Perform registration-based eddy-current compensation?
> # Default: 1 (yes)
> set doeddy = 0
> # Rotate diffusion gradient vectors to match eddy-current compensation?
> # Only used if doeddy = 1
> # Default: 1 (yes)
>
> is this critical??
>
> unfortunately, this is the only way I manage to get it to work
> as said my diffusion outputs from mriconverter
> are not read by FS, only through mediation
> of some FSL operation on the files, then FS
> likes those.
>
> I could start from scratch using dicoms but would prefer
> not to  as the data is already well organised
>
> cheers
> ds
> http://www1.imperial.ac.uk/medicine/people/d.soto/
>
> 
> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
> Sent: 09 August 2013 22:44
> To: Soto, David
> Subject: Re: [Freesurfer]  trac-all inquiry
>
> Are you rotating the gradient vectors accordingly? This is done in
> trac-all after running eddy_correct.
>
> On Fri, 9 Aug 2013, Soto, David wrote:
>
>> Hi Anastasia, stuff is running smoothly at last one quick question, is there
>> any 'disadvantage' in
>> using FSL to do the eddy correct and then feed
>> those images to trace-all ?
>> cheers
>> ds
>> http://www1.imperial.ac.uk/medicine/people/d.soto/
>>
>> On 9 Aug 2013, at 15:33, David Soto 
>>  wrote:
>>
>>   hi, for some reason FS does not like the
>>   nii file from Mriconverter, ( I saw
>>   a post about this
>>   
>> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html
>>   ) but does like
>>   the nii.gz outputs from FSL...
>>
>>   I'll try to debug the bepostx error
>>
>>   thanks!
>>
>>   ds
>>
>>   http://www1.imperial.ac.uk/medicine/people/d.soto/
>> On 09/08/13 14:26, Anastasia Yendiki wrote:
>>
>>   There is no reason to conevrt to .mnc. You should use your
>>   original .nii, if that shows up correctly in freeview.
>>
>>   As for the bedpostx error, this is an Ubuntu issue that
>>   has come to my attention very recently. In Ubuntu /bin/sh
>>   is not a bash shell any more. To get around this, you'll
>>   have to edit the first line of the scripts
>>   $FREESURFER_HOME/bin/bedpostx_mgh and
>>   $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace
>>   "/bin/sh" with "/bin/bash" on the first line of those two
>>   scripts.
>>
>>   On Fri, 9 Aug 2013, David Soto wrote:
>>
>> hi- I tried to convert from nii to mnc becos
>> that is what i did when
>> I did recon-all
>>
>> but I also tried with nii at the beggining and
>> got the same issues.
>>

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

When you apply a rotation to the DWIs (as eddy_correct does), you need to 
apply the same rotation to the corresponding gradient vectors. See for 
example: Leemans, A., Jones, D. K., Jun 2009. The B-matrix must be rotated 
when correcting for subject motion in DTI data. Magn Reson Med 61 (6), 
1336–49.


If you don't want to pass the dicoms to trac-all directly, you can use 
mri_convert to convert from dicom to nifti.


On Fri, 9 Aug 2013, Soto, David wrote:


hi - am afraid not because I am feeding to trac-all
already eddycorrected images then in the config file
I have

# Perform registration-based eddy-current compensation?
# Default: 1 (yes)
set doeddy = 0
# Rotate diffusion gradient vectors to match eddy-current compensation?
# Only used if doeddy = 1
# Default: 1 (yes)

is this critical??

unfortunately, this is the only way I manage to get it to work
as said my diffusion outputs from mriconverter
are not read by FS, only through mediation
of some FSL operation on the files, then FS
likes those.

I could start from scratch using dicoms but would prefer
not to  as the data is already well organised 

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: 09 August 2013 22:44
To: Soto, David
Subject: Re: [Freesurfer]  trac-all inquiry

Are you rotating the gradient vectors accordingly? This is done in
trac-all after running eddy_correct.

On Fri, 9 Aug 2013, Soto, David wrote:


Hi Anastasia, stuff is running smoothly at last one quick question, is there
any 'disadvantage' in
using FSL to do the eddy correct and then feed
those images to trace-all ?
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/

On 9 Aug 2013, at 15:33, David Soto 
 wrote:

  hi, for some reason FS does not like the
  nii file from Mriconverter, ( I saw
  a post about this
  http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19526.html
  ) but does like
  the nii.gz outputs from FSL...

  I'll try to debug the bepostx error

  thanks!

  ds

  http://www1.imperial.ac.uk/medicine/people/d.soto/
On 09/08/13 14:26, Anastasia Yendiki wrote:

  There is no reason to conevrt to .mnc. You should use your
  original .nii, if that shows up correctly in freeview.

  As for the bedpostx error, this is an Ubuntu issue that
  has come to my attention very recently. In Ubuntu /bin/sh
  is not a bash shell any more. To get around this, you'll
  have to edit the first line of the scripts
  $FREESURFER_HOME/bin/bedpostx_mgh and
  $FREESURFER_HOME/bin/fsl_sub_mgh. You'll have to replace
  "/bin/sh" with "/bin/bash" on the first line of those two
  scripts.

  On Fri, 9 Aug 2013, David Soto wrote:

hi- I tried to convert from nii to mnc becos
that is what i did when
I did recon-all

but I also tried with nii at the beggining and
got the same issues.
In fact in my last post (pasted below
again)the input was a nii file
could you please check the stuff below?
thanks! ds


Hi, further to my prior email
I made some progress. I noted that nii2mnc
does not seem to work on the diffusion
output.nii that I got from Mriconverter as the
output.mnc brain has parts chopped in
Freeview.

(I think there may be something funny about
this, as the recon-all does like the T1 output
form Mriconverter)

HENCE I tried use the output of eddycorrect
from FSL (which I already run for other thing)
Then I created a new folder where i placed the
output of FSL eddycorrect and in the
configuration file I did
(i)  set dcmlist =
(fsleddycorrectoutput.nii.gz)
(ii) turned 'set doeddy = 0'

then run it
trac-all -c traculatest.txt -prep -log
trac_from_fsleddy


it seemed to complete without errors (log
attached)n and I checked the preprocessing
outputs in Freeview (FA, masks and
aparc+asegs) and all seemed
fine.

However when I attempt the next stage in
trac-all
i.e. trac-all -c traculatest.txt -bedp -log
trac_from_fsleddy_bedp
it fails saying the following
/usr/local/freesurfer/bin/bedpostx_mgh: 131:
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax
error: "(" unexpected


the log is also attached.

any advise appreciated!

cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
http://www1.imperial.ac.uk/medicine/people/d.soto/

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

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.

Re: [Freesurfer] trac-all inquiry

[Soto, David]

Hi - further to my prior email
find attached please a clean
version of the log file - without the append of 
previous attempts
as you can see there are no errors in the log
although as i said the last line in the Terminal
said
Segmentation fault (core dumped)
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/


From: Soto, David
Sent: 07 August 2013 23:47
To: Anastasia Yendiki
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer]  trac-all inquiry

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.
>
>
>
>
/usr/local/freesurfer/bin/trac-preproc 
mri_convert /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/diffree/diffdata.mnc 
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi_orig.nii

Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

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


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Re: [Freesurfer] trac-all inquiry

[Anastasia Yendiki]

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
___
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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] trac-all inquiry

[Anastasia Yendiki]

Hi David - You need to run each of the steps (-prep, -bedp, -path) 
separately. You can't run them all at the same time. See tutorial:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/RunningTracula

Hope this helps,
a.y

On Fri, 2 Aug 2013, David Soto wrote:

> Hi,
>
> I have successfully run recon-all in my dataset
> and now am attempting to use trac-all on my diffusion data
> obtained on a Siemens scanner.
>
> Diffusion dicoms were transformed to .nii using MRIConverter
> and then to .mnc using
>
> nii2mnc output.nii output_t.mnc.
>
> I am trying to run trac-all on a single subject and for this I
> have created the configuration file attached (tracula02ST)
>
> As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
> and within each subject the T1 serving as input for recon-all are in
> mri/orig
>
> while the diffusion images are in a folder call diffdata (named output_t.mnc)
> which also contains the bvecs and bvals files, which were transposed and 
> organised
> according to the tutorial (named as bvecs_t.txt and bvals_t.txt)
>
> When I run:
> trac-all -c tracula02ST.txt
>
> I get:
> ERROR: no analysis step (-{prep,bedp,path}) has been selected
>
> THEN I run:
> trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so
> and then gives the long output text below with an error message.
>
> Segmentation fault (core dumped)
> foreach: No match.
>
> The trac-all.log is attached also.
>
> Could you please help?
>
> Cheers
>
> David
>
>
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] trac-all inquiry

[David Soto]

hi - I note though I changed the shell to tcsh
before running the code and performed all the relevant setenv
Also a single subject but not multiple subjs, is being entered
cheers
ds
http://www1.imperial.ac.uk/medicine/people/d.soto/
On 02/08/13 10:19, Watson, Christopher wrote:
> I've found that when using the Bash shell, putting multiple subjects in the 
> config file doesn't work. Maybe that's the issue here? Although, I simply 
> never bothered to look into it any more.
>
> Chris
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Soto 
> [d.s...@imperial.ac.uk]
> Sent: Friday, August 02, 2013 5:09 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] trac-all inquiry
>
> Hi,
>
> I have successfully run recon-all in my dataset
> and now am attempting to use trac-all on my diffusion data
> obtained on a Siemens scanner.
>
> Diffusion dicoms were transformed to .nii using MRIConverter
> and then to .mnc using
>
> nii2mnc output.nii output_t.mnc.
>
> I am trying to run trac-all on a single subject and for this I
> have created the configuration file attached (tracula02ST)
>
> As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
> and within each subject the T1 serving as input for recon-all are in
> mri/orig
>
> while the diffusion images are in a folder call diffdata (named
> output_t.mnc)
> which also contains the bvecs and bvals files, which were transposed and
> organised
> according to the tutorial (named as bvecs_t.txt and bvals_t.txt)
>
> When I run:
> trac-all -c tracula02ST.txt
>
> I get:
> ERROR: no analysis step (-{prep,bedp,path}) has been selected
>
> THEN I run:
> trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so
> and then gives the long output text below with an error message.
>
> Segmentation fault (core dumped)
> foreach: No match.
>
> The trac-all.log is attached also.
>
> Could you please help?
>
> Cheers
>
> David
>
>
> --
> http://www1.imperial.ac.uk/medicine/people/d.soto/
>
>
>
>
>
>
> wmen-dsoto3:~/Documents/fmri/rsdtianawmgui> trac-all -prep -bedp -path
> -c tracula02ST.txt
> INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
> INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui
> Actual FREESURFER_HOME /usr/local/freesurfer
> trac-paths -c
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/dmrirc.local -log
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.log -cmd
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.cmd
> #-
> /usr/local/freesurfer/bin/trac-paths
> #-
> #@# Path reconstruction Fri Aug  2 09:44:20 BST 2013
> /usr/local/freesurfer/bin/dmri_paths --outdir
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cst_AS_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cst_AS_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ilf_AS_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ilf_AS_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.unc_AS_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.unc_AS_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fmajor_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fminor_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.atr_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.atr_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ccg_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ccg_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cab_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cab_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slfp_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slfp_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slft_PP_avg33_mni_bbr
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slft_PP_avg33_mni_bbr
> --dwi /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz
> --grad /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs --bval
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals --mask
> /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz
> --bpdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri.bedpostX
> --ntr 2 --fmin 0.05 --roi1
> /home/dsoto/Do

Re: [Freesurfer] trac-all inquiry

[Watson, Christopher]

I've found that when using the Bash shell, putting multiple subjects in the 
config file doesn't work. Maybe that's the issue here? Although, I simply never 
bothered to look into it any more.

Chris


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of David Soto 
[d.s...@imperial.ac.uk]
Sent: Friday, August 02, 2013 5:09 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] trac-all inquiry

Hi,

I have successfully run recon-all in my dataset
and now am attempting to use trac-all on my diffusion data
obtained on a Siemens scanner.

Diffusion dicoms were transformed to .nii using MRIConverter
and then to .mnc using

nii2mnc output.nii output_t.mnc.

I am trying to run trac-all on a single subject and for this I
have created the configuration file attached (tracula02ST)

As you can see the SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
and within each subject the T1 serving as input for recon-all are in
mri/orig

while the diffusion images are in a folder call diffdata (named
output_t.mnc)
which also contains the bvecs and bvals files, which were transposed and
organised
according to the tutorial (named as bvecs_t.txt and bvals_t.txt)

When I run:
trac-all -c tracula02ST.txt

I get:
ERROR: no analysis step (-{prep,bedp,path}) has been selected

THEN I run:
trac-all -prep -bedp -path -c tracula02ST.txt which runs for 5 seconds or so
and then gives the long output text below with an error message.

Segmentation fault (core dumped)
foreach: No match.

The trac-all.log is attached also.

Could you please help?

Cheers

David


--
http://www1.imperial.ac.uk/medicine/people/d.soto/






wmen-dsoto3:~/Documents/fmri/rsdtianawmgui> trac-all -prep -bedp -path
-c tracula02ST.txt
INFO: SUBJECTS_DIR is /home/dsoto/Documents/fmri/rsdtianawmgui
INFO: Diffusion root is /home/dsoto/Documents/fmri/rsdtianawmgui
Actual FREESURFER_HOME /usr/local/freesurfer
trac-paths -c
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/dmrirc.local -log
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.log -cmd
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/scripts/trac-all.cmd
#-
/usr/local/freesurfer/bin/trac-paths
#-
#@# Path reconstruction Fri Aug  2 09:44:20 BST 2013
/usr/local/freesurfer/bin/dmri_paths --outdir
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cst_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cst_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ilf_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ilf_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.unc_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.unc_AS_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fmajor_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/fminor_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.atr_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.atr_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.ccg_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.ccg_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.cab_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.cab_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slfp_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slfp_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/lh.slft_PP_avg33_mni_bbr
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dpath/rh.slft_PP_avg33_mni_bbr
--dwi /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/dwi.nii.gz
--grad /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvecs --bval
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri/bvals --mask
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/diff/lowb_brain_mask.nii.gz
--bpdir /home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dmri.bedpostX
--ntr 2 --fmin 0.05 --roi1
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtianawmgui/02ST/dlabel/mni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz
/home/dsoto/Documents/fmri/rsdtian