Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Thanks so much!!

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-08-03 23:15 GMT+09:00 Anastasia Yendiki :

>
> That's correct!
>
> On Wed, 3 Aug 2016, Anri WATANABE wrote:
>
> Hi Anastasia,
>> Thank you for your kind explanation. I can be understanding how TRACULA
>> tracts white matter pathways.
>> At each position (in training subjects, not in new subjects of my data)
>> probability that next goes for
>> which direction to every labels in the aparc+aseg (not with setting a
>> certain ROI) is computed with use of
>> training subjects. The prior probabilities are made from training
>> subjects (your publication in 2011) and
>> they are based on manual labeling (the manual labeling tracts are
>> referred to Wakana et al. 2007). Then
>> when white matter pathways are reconstructed in my subjects, TRACULA
>> computes anatomical priors in each
>> subjects in my data in pre-processing and probability distributions from
>> anatomical priors and by fitting
>> ball-and-stick model.
>> Is this comprehension ok?
>>
>> Best Regards,
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-07-31 22:49 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - Instead of hard-coding some ROIs in the white matter that
>> the tract is forced to go
>>   through, TRACULA uses information like "what is the probability
>> that this tract goes
>>   lateral/anterior/etc to XXX", where XXX any of the labels in the
>> aparc+aseg. TRACULA computes
>>   these prior probabilities from a set of training subjects, where
>> the tracts have been labeled
>>   manually. So it knows how likely a tract is to go through a certain
>> aparc+aseg label, or to he
>>   left, right, anterior, etc of a certain aparc+aseg label. This is
>> computed separately at each
>>   position along the tract. It's computed from the training subjects,
>> and then used when
>>   reconstructing the tract in the new subject that you run TRACULA on.
>>
>>   Hope this helps,
>>   a.y
>>
>>   On Sun, 31 Jul 2016, Anri WATANABE wrote:
>>
>> Thanks, AnastasiaI know that TRACULA use probabilistic
>> tractography but if ROIs
>> are not
>> set how determine the origin and the end of a certain tract?
>> I think that the
>> first we
>> have to determine the origin and the end of the tract, the
>> second it constructs
>> possible
>> pathway not with the deterministic way (only 1 direction / 1
>> voxel) but with the
>> probabilistic way (considering which direction should be next
>> to). Is this
>> comprehension
>> wrong?
>> Thank you.
>>
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - TRACULA does not use deterministic ROIs. It
>> uses a probabilistic
>>   model of how likely each tract is to go through or next
>> to each of the
>> labels
>>   of the freesurfer subcortical segmentation and cortical
>> parcellation, as a
>>   function of position along the trajectory of the tract.
>>
>>   Best,
>>   a.y
>>
>>   On Sun, 31 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,
>> Thank you! It seems work well!!
>> I have another question. Are ROIs for automatic
>> tractography in
>> TRACULA the same ROIs
>> presented in Wakana et al. 2007?
>>
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

That's correct!

On Wed, 3 Aug 2016, Anri WATANABE wrote:


Hi Anastasia,
Thank you for your kind explanation. I can be understanding how TRACULA tracts 
white matter pathways. 
At each position (in training subjects, not in new subjects of my data) 
probability that next goes for
which direction to every labels in the aparc+aseg (not with setting a certain 
ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects 
(your publication in 2011) and
they are based on manual labeling (the manual labeling tracts are referred to 
Wakana et al. 2007). Then
when white matter pathways are reconstructed in my subjects, TRACULA computes 
anatomical priors in each
subjects in my data in pre-processing and probability distributions from 
anatomical priors and by fitting
ball-and-stick model. 
Is this comprehension ok?

Best Regards, 
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki :

  Hi Anri - Instead of hard-coding some ROIs in the white matter that the 
tract is forced to go
  through, TRACULA uses information like "what is the probability that this 
tract goes
  lateral/anterior/etc to XXX", where XXX any of the labels in the 
aparc+aseg. TRACULA computes
  these prior probabilities from a set of training subjects, where the 
tracts have been labeled
  manually. So it knows how likely a tract is to go through a certain 
aparc+aseg label, or to he
  left, right, anterior, etc of a certain aparc+aseg label. This is 
computed separately at each
  position along the tract. It's computed from the training subjects, and 
then used when
  reconstructing the tract in the new subject that you run TRACULA on.

  Hope this helps,
  a.y

  On Sun, 31 Jul 2016, Anri WATANABE wrote:

Thanks, AnastasiaI know that TRACULA use probabilistic tractography 
but if ROIs
are not
set how determine the origin and the end of a certain tract? I 
think that the
first we
have to determine the origin and the end of the tract, the second 
it constructs
possible
pathway not with the deterministic way (only 1 direction / 1 voxel) 
but with the
probabilistic way (considering which direction should be next to). 
Is this
comprehension
wrong?
Thank you.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki 
:

      Hi Anri - TRACULA does not use deterministic ROIs. It uses a 
probabilistic
      model of how likely each tract is to go through or next to 
each of the
labels
      of the freesurfer subcortical segmentation and cortical 
parcellation, as a
      function of position along the trajectory of the tract.

      Best,
      a.y

      On Sun, 31 Jul 2016, Anri WATANABE wrote:

            Hi Anastasia,
            Thank you! It seems work well!!
            I have another question. Are ROIs for automatic 
tractography in
            TRACULA the same ROIs
            presented in Wakana et al. 2007?

            Anri



            
**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
            
**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
            
**

            2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - The problem is in this line:

                               set cmd = ($cmd --ref 
$cvstempdir/$cvstemp)

    

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi Anastasia,

Thank you for your kind explanation. I can be understanding how TRACULA
tracts white matter pathways.
At each position (in training subjects, not in new subjects of my data)
probability that next goes for which direction to every labels in the
aparc+aseg (not with setting a certain ROI) is computed with use of
training subjects. The prior probabilities are made from training subjects
(your publication in 2011) and they are based on manual labeling (the
manual labeling tracts are referred to Wakana et al. 2007). Then when white
matter pathways are reconstructed in my subjects, TRACULA computes
anatomical priors in each subjects in my data in pre-processing and
probability distributions from anatomical priors and by fitting
ball-and-stick model.
Is this comprehension ok?

Best Regards,
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 22:49 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - Instead of hard-coding some ROIs in the white matter that the
> tract is forced to go through, TRACULA uses information like "what is the
> probability that this tract goes lateral/anterior/etc to XXX", where XXX
> any of the labels in the aparc+aseg. TRACULA computes these prior
> probabilities from a set of training subjects, where the tracts have been
> labeled manually. So it knows how likely a tract is to go through a certain
> aparc+aseg label, or to he left, right, anterior, etc of a certain
> aparc+aseg label. This is computed separately at each position along the
> tract. It's computed from the training subjects, and then used when
> reconstructing the tract in the new subject that you run TRACULA on.
>
> Hope this helps,
> a.y
>
> On Sun, 31 Jul 2016, Anri WATANABE wrote:
>
> Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if
>> ROIs are not
>>
>> set how determine the origin and the end of a certain tract? I think that
>> the first we
>> have to determine the origin and the end of the tract, the second it
>> constructs possible
>> pathway not with the deterministic way (only 1 direction / 1 voxel) but
>> with the
>> probabilistic way (considering which direction should be next to). Is
>> this comprehension
>> wrong?
>> Thank you.
>>
>> Anri
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-07-31 13:22 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - TRACULA does not use deterministic ROIs. It uses a
>> probabilistic
>>   model of how likely each tract is to go through or next to each of
>> the labels
>>   of the freesurfer subcortical segmentation and cortical
>> parcellation, as a
>>   function of position along the trajectory of the tract.
>>
>>   Best,
>>   a.y
>>
>>   On Sun, 31 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,
>> Thank you! It seems work well!!
>> I have another question. Are ROIs for automatic tractography
>> in
>> TRACULA the same ROIs
>> presented in Wakana et al. 2007?
>>
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - The problem is in this line:
>>
>>set cmd = ($cmd --ref $cvstempdir/$cvstemp)
>>
>>   It should be changed to this:
>>
>>set cmd = ($cmd --ref
>> $cvstempdir/$cvstemp/mri/norm.mgz)
>>
>>   For this to take effect, you need to run "which
>> trac-all"
>> and make the change in
>>   the trac-all file that the which commands shows you.
>>
>>   Hope this helps,
>>
>>   a.y
>>
>>   On Fri, 15 Jul 2016, Anri WATANABE wrote:
>>
>> Hi, AnastasiaThis is trac-all.local-copy 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - Instead of hard-coding some ROIs in the white matter that the 
tract is forced to go through, TRACULA uses information like "what is the 
probability that this tract goes lateral/anterior/etc to XXX", where XXX 
any of the labels in the aparc+aseg. TRACULA computes these prior 
probabilities from a set of training subjects, where the tracts have been 
labeled manually. So it knows how likely a tract is to go through a 
certain aparc+aseg label, or to he left, right, anterior, etc of a certain 
aparc+aseg label. This is computed separately at each position along the 
tract. It's computed from the training subjects, and then used when 
reconstructing the tract in the new subject that you run TRACULA on.


Hope this helps,
a.y

On Sun, 31 Jul 2016, Anri WATANABE wrote:


Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if ROIs 
are not
set how determine the origin and the end of a certain tract? I think that the 
first we
have to determine the origin and the end of the tract, the second it constructs 
possible
pathway not with the deterministic way (only 1 direction / 1 voxel) but with the
probabilistic way (considering which direction should be next to). Is this 
comprehension
wrong?
Thank you.

Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki :

  Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic
  model of how likely each tract is to go through or next to each of the 
labels
  of the freesurfer subcortical segmentation and cortical parcellation, as a
  function of position along the trajectory of the tract.

  Best,
  a.y

  On Sun, 31 Jul 2016, Anri WATANABE wrote:

Hi Anastasia,
Thank you! It seems work well!!
I have another question. Are ROIs for automatic tractography in
TRACULA the same ROIs
presented in Wakana et al. 2007?

Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - The problem is in this line:

                   set cmd = ($cmd --ref $cvstempdir/$cvstemp)

      It should be changed to this:

                   set cmd = ($cmd --ref
$cvstempdir/$cvstemp/mri/norm.mgz)

      For this to take effect, you need to run "which trac-all"
and make the change in
      the trac-all file that the which commands shows you.

      Hope this helps,

      a.y

      On Fri, 15 Jul 2016, Anri WATANABE wrote:

            Hi, AnastasiaThis is trac-all.local-copy from 1
subject. Thank you!

            Anri

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of
Medicine
           

**

            2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - This may be a bug that was fixed at
some point. Can
                  you send me the scripts/trac-all.local-copy from
one of your
                  subjects? Thanks!

                  a.y

                  On Mon, 11 Jul 2016, Anri WATANABE wrote:

                        Hi Anastasia,There is an error in .log
files of left
                        corticospinal tract in cvs template and I
attached
                        one
                        of file. In addition 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Thanks, Anastasia
I know that TRACULA use probabilistic tractography but if ROIs are not set
how determine the origin and the end of a certain tract? I think that the
first we have to determine the origin and the end of the tract, the second
it constructs possible pathway not with the deterministic way (only 1
direction / 1 voxel) but with the probabilistic way (considering which
direction should be next to). Is this comprehension wrong?
Thank you.

Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic
> model of how likely each tract is to go through or next to each of the
> labels of the freesurfer subcortical segmentation and cortical
> parcellation, as a function of position along the trajectory of the tract.
>
> Best,
> a.y
>
>
> On Sun, 31 Jul 2016, Anri WATANABE wrote:
>
> Hi Anastasia,
>> Thank you! It seems work well!!
>> I have another question. Are ROIs for automatic tractography in TRACULA
>> the same ROIs
>> presented in Wakana et al. 2007?
>>
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-07-27 13:17 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - The problem is in this line:
>>
>>set cmd = ($cmd --ref $cvstempdir/$cvstemp)
>>
>>   It should be changed to this:
>>
>>set cmd = ($cmd --ref
>> $cvstempdir/$cvstemp/mri/norm.mgz)
>>
>>   For this to take effect, you need to run "which trac-all" and make
>> the change in
>>   the trac-all file that the which commands shows you.
>>
>>   Hope this helps,
>>
>>   a.y
>>
>>   On Fri, 15 Jul 2016, Anri WATANABE wrote:
>>
>> Hi, AnastasiaThis is trac-all.local-copy from 1 subject.
>> Thank you!
>>
>> Anri
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - This may be a bug that was fixed at some
>> point. Can
>>   you send me the scripts/trac-all.local-copy from one of
>> your
>>   subjects? Thanks!
>>
>>   a.y
>>
>>   On Mon, 11 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,There is an error in .log files of
>> left
>> corticospinal tract in cvs template and I attached
>> one
>> of file. In addition .log files of right
>> corticospinal tract in cvs template doesn't
>> exist.
>> Thanks in advance.
>>
>> Anri
>>
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University
>> of
>> Medicine
>>
>>
>> **
>>
>> 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - Is there an error in the
>> stats/*.log
>> files for the different tracts?
>>
>>   a.y
>>
>>   On Tue, 5 Jul 2016, Anri WATANABE wrote:
>>
>> Dear Anastasia,
>>
>> I use TRACULA to obtain diffusion
>> measures at each voxel in a certain 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic 
model of how likely each tract is to go through or next to each of the 
labels of the freesurfer subcortical segmentation and cortical 
parcellation, as a function of position along the trajectory of the tract.


Best,
a.y

On Sun, 31 Jul 2016, Anri WATANABE wrote:


Hi Anastasia,
Thank you! It seems work well!!
I have another question. Are ROIs for automatic tractography in TRACULA the 
same ROIs
presented in Wakana et al. 2007?

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-27 13:17 GMT+09:00 Anastasia Yendiki :

  Hi Anri - The problem is in this line:

               set cmd = ($cmd --ref $cvstempdir/$cvstemp)

  It should be changed to this:

               set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)

  For this to take effect, you need to run "which trac-all" and make the 
change in
  the trac-all file that the which commands shows you.

  Hope this helps,

  a.y

  On Fri, 15 Jul 2016, Anri WATANABE wrote:

Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you!

Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - This may be a bug that was fixed at some point. Can
      you send me the scripts/trac-all.local-copy from one of your
      subjects? Thanks!

      a.y

      On Mon, 11 Jul 2016, Anri WATANABE wrote:

            Hi Anastasia,There is an error in .log files of left
            corticospinal tract in cvs template and I attached
            one
            of file. In addition .log files of right
            corticospinal tract in cvs template doesn't exist. 
            Thanks in advance.

            Anri



           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of
            Medicine
           

**

            2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - Is there an error in the stats/*.log
            files for the different tracts?

                  a.y

                  On Tue, 5 Jul 2016, Anri WATANABE wrote:

                        Dear Anastasia, 

                        I use TRACULA to obtain diffusion
            measures at each voxel in a certain pathway for
                        group analysis, but
                        there aren't stats/*.path.mean.txt
            files. I found .log files
                        (_PP.avg33_mni_bbr.log) which
            exist
                        1 file per 1 tract, except corticospinal
            tract which has 2 .log files.

                        Command: trac-all –stat –c
            $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

                        Error log: Loading output reference
            volume from
                       
            /Applications/freesurfer/subjects/cvs_avg35

                        corRead(): can't open file
            /Applications/freesurfer/subjects/cvs_avg35/COR-.info

                        ERROR: Could not read
            /Applications/freesurfer/subjects/cvs_avg35


                        I 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi Anastasia,

Thank you! It seems work well!!
I have another question. Are ROIs for automatic tractography in TRACULA the
same ROIs presented in Wakana et al. 2007?

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-27 13:17 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - The problem is in this line:
>
>  set cmd = ($cmd --ref $cvstempdir/$cvstemp)
>
> It should be changed to this:
>
>  set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)
>
> For this to take effect, you need to run "which trac-all" and make the
> change in the trac-all file that the which commands shows you.
>
> Hope this helps,
>
> a.y
>
> On Fri, 15 Jul 2016, Anri WATANABE wrote:
>
> Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you!
>>
>>
>> Anri
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-07-13 6:16 GMT+09:00 Anastasia Yendiki > >:
>>
>>   Hi Anri - This may be a bug that was fixed at some point. Can
>>   you send me the scripts/trac-all.local-copy from one of your
>>   subjects? Thanks!
>>
>>   a.y
>>
>>   On Mon, 11 Jul 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,There is an error in .log files of left
>> corticospinal tract in cvs template and I attached
>> one
>> of file. In addition .log files of right
>> corticospinal tract in cvs template doesn't exist.
>> Thanks in advance.
>>
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of
>> Medicine
>>
>> **
>>
>> 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - Is there an error in the stats/*.log
>> files for the different tracts?
>>
>>   a.y
>>
>>   On Tue, 5 Jul 2016, Anri WATANABE wrote:
>>
>> Dear Anastasia,
>>
>> I use TRACULA to obtain diffusion
>> measures at each voxel in a certain pathway for
>> group analysis, but
>> there aren't stats/*.path.mean.txt
>> files. I found .log files
>> (_PP.avg33_mni_bbr.log) which
>> exist
>> 1 file per 1 tract, except corticospinal
>> tract which has 2 .log files.
>>
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference
>> volume from
>>
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> I attached dmrirc.example (configuration
>> file) and /scripts/trac-all.log.
>>
>>
>> Thanks in advance,
>> Anri
>>
>>
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural
>> University of Medicine
>>
>>
>> **
>>
>> 2016-06-03 9:51 GMT+09:00 Anri WATANABE
>> :
>>   Hi, Anastasia.
>> There aren't any .log files but text
>> 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - The problem is in this line:

 set cmd = ($cmd --ref $cvstempdir/$cvstemp)

It should be changed to this:

 set cmd = ($cmd --ref $cvstempdir/$cvstemp/mri/norm.mgz)

For this to take effect, you need to run "which trac-all" and make the 
change in the trac-all file that the which commands shows you.


Hope this helps,

a.y

On Fri, 15 Jul 2016, Anri WATANABE wrote:


Hi, AnastasiaThis is trac-all.local-copy from 1 subject. Thank you!

Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-13 6:16 GMT+09:00 Anastasia Yendiki :

  Hi Anri - This may be a bug that was fixed at some point. Can
  you send me the scripts/trac-all.local-copy from one of your
  subjects? Thanks!

  a.y

  On Mon, 11 Jul 2016, Anri WATANABE wrote:

Hi Anastasia,There is an error in .log files of left
corticospinal tract in cvs template and I attached
one
of file. In addition .log files of right
corticospinal tract in cvs template doesn't exist. 
Thanks in advance.

Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of
Medicine

**

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - Is there an error in the stats/*.log
files for the different tracts?

      a.y

      On Tue, 5 Jul 2016, Anri WATANABE wrote:

            Dear Anastasia, 

            I use TRACULA to obtain diffusion
measures at each voxel in a certain pathway for
            group analysis, but
            there aren't stats/*.path.mean.txt
files. I found .log files
            (_PP.avg33_mni_bbr.log) which
exist
            1 file per 1 tract, except corticospinal
tract which has 2 .log files.

            Command: trac-all –stat –c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

            Error log: Loading output reference
volume from
           
/Applications/freesurfer/subjects/cvs_avg35

            corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

            ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35


            I attached dmrirc.example (configuration
file) and /scripts/trac-all.log.


            Thanks in advance,
            Anri




           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural
University of Medicine
           

**

            2016-06-03 9:51 GMT+09:00 Anri WATANABE
:
                  Hi, Anastasia.
            There aren't any .log files but text
files like lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
            I guess text
            files complete all pathways and
measures.

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural
University of Medicine
           

**

  

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi, Anastasia
This is trac-all.local-copy from 1 subject. Thank you!

Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-13 6:16 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - This may be a bug that was fixed at some point. Can you send me
> the scripts/trac-all.local-copy from one of your subjects? Thanks!
>
> a.y
>
> On Mon, 11 Jul 2016, Anri WATANABE wrote:
>
> Hi Anastasia,There is an error in .log files of left corticospinal tract
>> in cvs template and I attached one
>>
>> of file. In addition .log files of right corticospinal tract in cvs
>> template doesn't exist.
>> Thanks in advance.
>>
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-07-07 20:12 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - Is there an error in the stats/*.log files for the
>> different tracts?
>>
>>   a.y
>>
>>   On Tue, 5 Jul 2016, Anri WATANABE wrote:
>>
>> Dear Anastasia,
>>
>> I use TRACULA to obtain diffusion measures at each voxel in a
>> certain pathway for
>> group analysis, but
>> there aren't stats/*.path.mean.txt files. I found .log files
>> (_PP.avg33_mni_bbr.log) which exist
>> 1 file per 1 tract, except corticospinal tract which has 2
>> .log files.
>>
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference volume from
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> I attached dmrirc.example (configuration file) and
>> /scripts/trac-all.log.
>>
>>
>> Thanks in advance,
>> Anri
>>
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-06-03 9:51 GMT+09:00 Anri WATANABE <
>> z2aa...@koto.kpu-m.ac.jp>:
>>   Hi, Anastasia.
>> There aren't any .log files but text files like
>> lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
>> I guess text
>> files complete all pathways and measures.
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-06-02 3:03 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Thanks, Anri. So the previous steps seem to have run
>> fine. Are there any .log
>> files
>>   created in the stats/ folder, which is created by
>> trac-all -stat?
>>
>>   On Wed, 1 Jun 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia, This is a
>> /scripts/trac-all.log of one subject of
>> the group.
>>
>> Thanks,
>> Anri
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University
>> of Medicine
>>
>> **
>>
>> 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
>>

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - This may be a bug that was fixed at some point. Can you send me 
the scripts/trac-all.local-copy from one of your subjects? Thanks!


a.y

On Mon, 11 Jul 2016, Anri WATANABE wrote:


Hi Anastasia,There is an error in .log files of left corticospinal tract in cvs 
template and I attached one
of file. In addition .log files of right corticospinal tract in cvs template 
doesn't exist. 
Thanks in advance.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki :

  Hi Anri - Is there an error in the stats/*.log files for the different 
tracts?

  a.y

  On Tue, 5 Jul 2016, Anri WATANABE wrote:

Dear Anastasia, 

I use TRACULA to obtain diffusion measures at each voxel in a 
certain pathway for
group analysis, but
there aren't stats/*.path.mean.txt files. I found .log files
(_PP.avg33_mni_bbr.log) which exist
1 file per 1 tract, except corticospinal tract which has 2 .log 
files.

Command: trac-all –stat –c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file 
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


I attached dmrirc.example (configuration file) and 
/scripts/trac-all.log.


Thanks in advance,
Anri





**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-06-03 9:51 GMT+09:00 Anri WATANABE :
      Hi, Anastasia.
There aren't any .log files but text files like 
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt.
I guess text
files complete all pathways and measures.


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-06-02 3:03 GMT+09:00 Anastasia Yendiki 
:

      Thanks, Anri. So the previous steps seem to have run fine. 
Are there any .log
files
      created in the stats/ folder, which is created by trac-all 
-stat?

      On Wed, 1 Jun 2016, Anri WATANABE wrote:

            Hi Anastasia, This is a /scripts/trac-all.log 
of one subject of
            the group.

            Thanks,
            Anri

            
**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
            
**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
            
**

            2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - Can you also send your log file 
(scripts/trac-all.log)?
            I'll need to see what
                  exactly was running when the error occurred. 
Thanks!

                  a.y

                  On Sat, 28 May 2016, Anri WATANABE wrote:

                        Hello Anastasia,sorry for few information 
and let me tell
you
            command and
                        error log.
                        Command: trac-all –stat –c
            $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi Anastasia,
There is an error in .log files of left corticospinal tract in cvs template
and I attached one of file. In addition .log files of right corticospinal
tract in cvs template doesn't exist.
Thanks in advance.

Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-07 20:12 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - Is there an error in the stats/*.log files for the different
> tracts?
>
> a.y
>
>
> On Tue, 5 Jul 2016, Anri WATANABE wrote:
>
> Dear Anastasia,
>>
>> I use TRACULA to obtain diffusion measures at each voxel in a certain
>> pathway for group analysis, but
>> there aren't stats/*.path.mean.txt files. I found .log files
>> (_PP.avg33_mni_bbr.log) which exist
>> 1 file per 1 tract, except corticospinal tract which has 2 .log files.
>>
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference volume from
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> I attached dmrirc.example (configuration file) and
>> /scripts/trac-all.log.
>>
>>
>> Thanks in advance,
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-06-03 9:51 GMT+09:00 Anri WATANABE :
>>   Hi, Anastasia.
>> There aren't any .log files but text files like
>> lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text
>> files complete all pathways and measures.
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-06-02 3:03 GMT+09:00 Anastasia Yendiki > >:
>>
>>   Thanks, Anri. So the previous steps seem to have run fine. Are
>> there any .log files
>>   created in the stats/ folder, which is created by trac-all -stat?
>>
>>   On Wed, 1 Jun 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia, This is a /scripts/trac-all.log of one
>> subject of
>> the group.
>>
>> Thanks,
>> Anri
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - Can you also send your log file
>> (scripts/trac-all.log)?
>> I'll need to see what
>>   exactly was running when the error occurred. Thanks!
>>
>>   a.y
>>
>>   On Sat, 28 May 2016, Anri WATANABE wrote:
>>
>> Hello Anastasia,sorry for few information and let
>> me tell you
>> command and
>> error log.
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference volume from
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>>
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> dmrirc.example (configuration file) is attached
>> to this
>> e-mail.
>>
>> Thanks in advance,
>> Anri
>>
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>>
>> 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - Is there an error in the stats/*.log files for the different 
tracts?


a.y

On Tue, 5 Jul 2016, Anri WATANABE wrote:


Dear Anastasia, 

I use TRACULA to obtain diffusion measures at each voxel in a certain pathway 
for group analysis, but
there aren't stats/*.path.mean.txt files. I found .log files 
(_PP.avg33_mni_bbr.log) which exist
1 file per 1 tract, except corticospinal tract which has 2 .log files.

Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from 
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file /Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


I attached dmrirc.example (configuration file) and /scripts/trac-all.log.


Thanks in advance,
Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-06-03 9:51 GMT+09:00 Anri WATANABE :
  Hi, Anastasia.
There aren't any .log files but text files like 
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text
files complete all pathways and measures.

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-06-02 3:03 GMT+09:00 Anastasia Yendiki :

  Thanks, Anri. So the previous steps seem to have run fine. Are there any 
.log files
  created in the stats/ folder, which is created by trac-all -stat?

  On Wed, 1 Jun 2016, Anri WATANABE wrote:

Hi Anastasia, This is a /scripts/trac-all.log of one 
subject of
the group.

Thanks,
Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-05-31 22:55 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - Can you also send your log file 
(scripts/trac-all.log)?
I'll need to see what
      exactly was running when the error occurred. Thanks!

      a.y

      On Sat, 28 May 2016, Anri WATANABE wrote:

            Hello Anastasia,sorry for few information and let me 
tell you
command and
            error log.
            Command: trac-all –stat –c
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

            Error log: Loading output reference volume from
            /Applications/freesurfer/subjects/cvs_avg35

            corRead(): can't open file
            /Applications/freesurfer/subjects/cvs_avg35/COR-.info

            ERROR: Could not read
/Applications/freesurfer/subjects/cvs_avg35


            dmrirc.example (configuration file) is attached to this
e-mail.

            Thanks in advance,
            Anri



           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
           

**

            2016-05-27 22:57 GMT+09:00 Anastasia Yendiki
:

                  Hi Anri - I do not know what command line you ran 
and
what your
            configuration file looks like, so it is very
                  hard for me to suggest solutions.

                  Best,
                  a.y

                  On Fri, 27 May 2016, Anri WATANABE wrote:

                        Hi 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi, Anastasia.
There aren't any .log files but text files like
lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt. I guess text files complete all
pathways and measures.

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-06-02 3:03 GMT+09:00 Anastasia Yendiki :

>
> Thanks, Anri. So the previous steps seem to have run fine. Are there any
> .log files created in the stats/ folder, which is created by trac-all -stat?
>
>
> On Wed, 1 Jun 2016, Anri WATANABE wrote:
>
> Hi Anastasia, This is a /scripts/trac-all.log of one subject of
>> the group.
>>
>> Thanks,
>> Anri
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-05-31 22:55 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - Can you also send your log file (scripts/trac-all.log)?
>> I'll need to see what
>>   exactly was running when the error occurred. Thanks!
>>
>>   a.y
>>
>>   On Sat, 28 May 2016, Anri WATANABE wrote:
>>
>> Hello Anastasia,sorry for few information and let me tell you
>> command and
>> error log.
>> Command: trac-all –stat –c
>> $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example
>>
>> Error log: Loading output reference volume from
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>> corRead(): can't open file
>> /Applications/freesurfer/subjects/cvs_avg35/COR-.info
>>
>> ERROR: Could not read
>> /Applications/freesurfer/subjects/cvs_avg35
>>
>>
>> dmrirc.example (configuration file) is attached to this
>> e-mail.
>>
>> Thanks in advance,
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>> 2016-05-27 22:57 GMT+09:00 Anastasia Yendiki <
>> ayend...@nmr.mgh.harvard.edu>:
>>
>>   Hi Anri - I do not know what command line you ran and
>> what your
>> configuration file looks like, so it is very
>>   hard for me to suggest solutions.
>>
>>   Best,
>>   a.y
>>
>>   On Fri, 27 May 2016, Anri WATANABE wrote:
>>
>> Hi Anastasia,
>> Thank you for your answer.
>> There aren't stats/*.path.mean.txt files and
>> terminal says 'Could
>> not read
>> /Applications/freesurfer/subjects/cvs_avg35.' I
>> checked
>> /Application/freesurfer/subjects/cvs_avg35 folder and
>> couldn't find COR-.info file.
>> Could you tell me any resolutions, please?
>>
>> Thanks,
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University
>> of Medicine
>>
>>
>> **
>>
>> 2016-05-21 6:48 GMT+09:00 Anastasia Yendiki
>> :
>>
>>   Hi Anri - The FA values are extracted in
>> the native space
>> of each subject, which is why
>> those are the only
>>   coordinates that you see. If you want to
>> display the
>> results of your analysis on an average
>> path, after
>>   running trac-all -stat, you can use the
>> stats/*.path.mean.txt files (see also the last part
>> of the TRACULA
>>   tutorial).

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Thanks, Anri. So the previous steps seem to have run fine. Are there any 
.log files created in the stats/ folder, which is created by trac-all 
-stat?


On Wed, 1 Jun 2016, Anri WATANABE wrote:


Hi Anastasia, This is a /scripts/trac-all.log of one subject of the 
group.

Thanks,
Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-31 22:55 GMT+09:00 Anastasia Yendiki :

  Hi Anri - Can you also send your log file (scripts/trac-all.log)? I'll 
need to see what
  exactly was running when the error occurred. Thanks!

  a.y

  On Sat, 28 May 2016, Anri WATANABE wrote:

Hello Anastasia,sorry for few information and let me tell you 
command and
error log.
Command: trac-all –stat –c 
$TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


dmrirc.example (configuration file) is attached to this e-mail.

Thanks in advance,
Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-05-27 22:57 GMT+09:00 Anastasia Yendiki 
:

      Hi Anri - I do not know what command line you ran and what 
your
configuration file looks like, so it is very
      hard for me to suggest solutions.

      Best,
      a.y

      On Fri, 27 May 2016, Anri WATANABE wrote:

            Hi Anastasia, 
            Thank you for your answer.
            There aren't stats/*.path.mean.txt files and terminal 
says 'Could
not read
            /Applications/freesurfer/subjects/cvs_avg35.' I
            checked /Application/freesurfer/subjects/cvs_avg35 
folder and
couldn't find COR-.info file.
            Could you tell me any resolutions, please?

            Thanks, 
            Anri

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of 
Medicine
           

**

            2016-05-21 6:48 GMT+09:00 Anastasia Yendiki
:

                  Hi Anri - The FA values are extracted in the 
native space
of each subject, which is why
            those are the only
                  coordinates that you see. If you want to display 
the
results of your analysis on an average
            path, after
                  running trac-all -stat, you can use the
stats/*.path.mean.txt files (see also the last part
            of the TRACULA
                  tutorial).

                  Best,
                  a.y

                  On Wed, 18 May 2016, Anri WATANABE wrote:

                        Dear experts, 
                        I use TRACULA to examine a measure (FA) at 
each voxel
in one pathway.
                        pathstats.byvoxel.txt files show 
coordinates in
native space and after converting
            those the new
                        files don't show any coordinates which are 
in MNI
space.
                        Could you tell me how can I know MNI 
coordinate
values?

                        Thank you!


             

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hello Anastasia,
sorry for few information and let me tell you command and error log.

Command: trac-all –stat –c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.example

Error log: Loading output reference volume from
/Applications/freesurfer/subjects/cvs_avg35

corRead(): can't open file
/Applications/freesurfer/subjects/cvs_avg35/COR-.info

ERROR: Could not read /Applications/freesurfer/subjects/cvs_avg35


dmrirc.example (configuration file) is attached to this e-mail.

Thanks in advance,
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-27 22:57 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - I do not know what command line you ran and what your
> configuration file looks like, so it is very hard for me to suggest
> solutions.
>
> Best,
> a.y
>
>
> On Fri, 27 May 2016, Anri WATANABE wrote:
>
> Hi Anastasia,
>> Thank you for your answer.
>> There aren't stats/*.path.mean.txt files and terminal says 'Could not
>> read /Applications/freesurfer/subjects/cvs_avg35.' I
>> checked /Application/freesurfer/subjects/cvs_avg35 folder and couldn't
>> find COR-.info file.
>> Could you tell me any resolutions, please?
>>
>> Thanks,
>> Anri
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>> 2016-05-21 6:48 GMT+09:00 Anastasia Yendiki > >:
>>
>>   Hi Anri - The FA values are extracted in the native space of each
>> subject, which is why those are the only
>>   coordinates that you see. If you want to display the results of
>> your analysis on an average path, after
>>   running trac-all -stat, you can use the stats/*.path.mean.txt files
>> (see also the last part of the TRACULA
>>   tutorial).
>>
>>   Best,
>>   a.y
>>
>>   On Wed, 18 May 2016, Anri WATANABE wrote:
>>
>> Dear experts,
>> I use TRACULA to examine a measure (FA) at each voxel in one
>> pathway.
>> pathstats.byvoxel.txt files show coordinates in native space
>> and after converting those the new
>> files don't show any coordinates which are in MNI space.
>> Could you tell me how can I know MNI coordinate values?
>>
>> Thank you!
>>
>>
>> Regards,
>> Anri
>>
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>>
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>>
>> **
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
>>
>>
>>
> ___
> Freesurfer 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.
>
>


dmrirc.example
Description: Binary data
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addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient 

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - I do not know what command line you ran and what your 
configuration file looks like, so it is very hard for me to suggest 
solutions.


Best,
a.y

On Fri, 27 May 2016, Anri WATANABE wrote:


Hi Anastasia, 
Thank you for your answer.
There aren't stats/*.path.mean.txt files and terminal says 'Could not read 
/Applications/freesurfer/subjects/cvs_avg35.' I
checked /Application/freesurfer/subjects/cvs_avg35 folder and couldn't find 
COR-.info file.
Could you tell me any resolutions, please?

Thanks, 
Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-21 6:48 GMT+09:00 Anastasia Yendiki :

  Hi Anri - The FA values are extracted in the native space of each 
subject, which is why those are the only
  coordinates that you see. If you want to display the results of your 
analysis on an average path, after
  running trac-all -stat, you can use the stats/*.path.mean.txt files (see 
also the last part of the TRACULA
  tutorial).

  Best,
  a.y

  On Wed, 18 May 2016, Anri WATANABE wrote:

Dear experts, 
I use TRACULA to examine a measure (FA) at each voxel in one 
pathway.
pathstats.byvoxel.txt files show coordinates in native space and 
after converting those the new
files don't show any coordinates which are in MNI space.
Could you tell me how can I know MNI coordinate values?

Thank you!


Regards, 
Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**


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The information in this e-mail is intended only for the person to whom it is
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The information in this e-mail is intended only for the person to whom it is
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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Hi Anastasia,

Thank you for your answer.
There aren't stats/*.path.mean.txt files and terminal says 'Could not read
/Applications/freesurfer/subjects/cvs_avg35.' I checked
/Application/freesurfer/subjects/cvs_avg35 folder and couldn't find
COR-.info file.
Could you tell me any resolutions, please?

Thanks,
Anri

**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-05-21 6:48 GMT+09:00 Anastasia Yendiki :

>
> Hi Anri - The FA values are extracted in the native space of each subject,
> which is why those are the only coordinates that you see. If you want to
> display the results of your analysis on an average path, after running
> trac-all -stat, you can use the stats/*.path.mean.txt files (see also the
> last part of the TRACULA tutorial).
>
> Best,
> a.y
>
>
> On Wed, 18 May 2016, Anri WATANABE wrote:
>
> Dear experts,
>> I use TRACULA to examine a measure (FA) at each voxel in one pathway.
>> pathstats.byvoxel.txt files show coordinates in native space and after
>> converting those the new files don't show any coordinates which are in MNI
>> space.
>> Could you tell me how can I know MNI coordinate values?
>>
>> Thank you!
>>
>>
>> Regards,
>> Anri
>>
>>
>>
>> **
>> 京都府立医科大学附属病院
>> 精神科・心療内科
>> 渡辺 杏里
>> **
>> Anri WATANABE, M.D.
>> Department of Psychiatry,
>> University Hospital, Kyoto Prefectural University of Medicine
>> **
>>
>>
> ___
> Freesurfer mailing list
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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.
>
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - The FA values are extracted in the native space of each subject, 
which is why those are the only coordinates that you see. If you want to 
display the results of your analysis on an average path, after running 
trac-all -stat, you can use the stats/*.path.mean.txt files (see also the 
last part of the TRACULA tutorial).


Best,
a.y

On Wed, 18 May 2016, Anri WATANABE wrote:


Dear experts, 
I use TRACULA to examine a measure (FA) at each voxel in one pathway.
pathstats.byvoxel.txt files show coordinates in native space and after 
converting those the new files don't show any coordinates which are in MNI 
space.
Could you tell me how can I know MNI coordinate values?

Thank you!


Regards, 
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

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dispose of the e-mail.

[Freesurfer] Coordinates in TRACULA group analysis

[Anri WATANABE]

Dear experts,

I use TRACULA to examine a measure (FA) at each voxel in one pathway.
pathstats.byvoxel.txt files show coordinates in native space and after
converting those the new files don't show any coordinates which are in MNI
space.
Could you tell me how can I know MNI coordinate values?

Thank you!


Regards,
Anri



**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**
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