Re: [Freesurfer] Tracula skip steps

2016-05-31 Thread Jacobs H (NP) 
Aha, Ok, I will try to get my hands on that data and give it a go.
Thanks for the help!
Heidi

On 6/1/16, 4:01 AM, "Anastasia Yendiki" 
wrote:

>
>The input needs to be the diffusion-weighted images, not the FA, MD, etc.
>There should be as many volumes in this input nifti as there are b-values
>in bval file and gradient vectors in the bvec file. The image
>registration, tractography, etc etc is performed on the
>diffusion-weighted
>images, not on the FA, MD, etc. The FA, MD, etc are used only in the very
>end, to extract FA, MD, etc for each tract. But to get the tracts in the
>first place, you need the images.
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Yes, each nifti contains one volume. I have different nifti’s for the
>> different metrics (FA, MD,..)
>> Is there a way I can use the trac-all on these files?
>>
>> On 5/31/16, 9:26 PM, "Anastasia Yendiki" 
>> wrote:
>>
>>>
>>> Some of the errors make me suspect that your input DWI files contain
>>>only
>>> one volume. Could this be the case?
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Hmm, weird, as I put a #  in front of it. Putting the eddy current to
0
 gives the same error. Enclosed is the config file.
 Thank you so much
 Heidi

 On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
 of
 Anastasia Yendiki"  wrote:

>
> Hi Heidi - It knows where to find the freesurfer recons of the T1's
> from
> SUBJECTS_DIR (see example config file). Based on your log file, it
> looks
> like you haven't turned off the eddy current compensation, because
>it's
> trying to run it. If you attach your config file, I'll take a look.
>
> Best,
> a.y
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Thanks! I tried to adapt the configuration file and it got a bit
>> further,
>> but then crashes again. Not sure why? I have added the log file, so
>> that
>> maybe you could have a look at what is happening?
>> Also, how does the trac-all command knows where to find the T1 data?
>> Thanks
>> Heidi
>>
>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
>>behalf
>> of
>> Anastasia Yendiki" > of
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> No, it should be pointed to the DWI data, which can be corrected
>>> niftis
>>> instead of the original dicoms. I would recommend turning off all
>>>the
>>> corrections in the configuration file, and then running everything
>>> without
>>> skipping steps. This will create all the files that are expected to
>>> be
>>> there for the registration.
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear Anastasia,

 Thanks for the feedback. So, does this mean that the dcm root
should
 be
 pointed towards the T1¹s? I have the FreeSurfer recon-all output
in
 a
 different folder.
 Enclosed is the log file (of one subject) and the configuration
 file.
 You
 will see that I tried the inter and intra option, because I
thought
 that
 for the inter it would not need anything else than the MNI
template
 and
 the DTI images.

 Thanks

 Best
 Heidi

 On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
 behalf
 of
 Anastasia Yendiki"  wrote:

>
> Hi Heidi - The intra-subject registration step that you're trying
> to
> run
> registers your subject's DWI and T1 images. It expects to find
> those
> images. It doesn't use the FA, MD, etc in any way.
>
> Did the log file get created in scripts/trac-all.log? If so, can
> you
> please send that file and your configuration file? Thanks!
>
> a.y
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear FreeSurfers,
>>
>> The data I have is preprocessed, so I have the all the metrics
>> (FA,
>> MD,
>> L1, L2, L3,..) in nifti format.
>> On this data I would like to start tracula starting from step
>>1.3.
>>
>> I have organized the data as mentioned on the wiki:
>> For example:
>> / dtifit_FA.nii.gz
>>
>> I have also filled in the configuration file, canceling out the
>> things
>> I don¹t need and then I tried to run:
>> Trac-all ­intra ­c

Re: [Freesurfer] Tracula skip steps

2016-05-31 Thread Anastasia Yendiki 


The input needs to be the diffusion-weighted images, not the FA, MD, etc. 
There should be as many volumes in this input nifti as there are b-values 
in bval file and gradient vectors in the bvec file. The image 
registration, tractography, etc etc is performed on the diffusion-weighted 
images, not on the FA, MD, etc. The FA, MD, etc are used only in the very 
end, to extract FA, MD, etc for each tract. But to get the tracts in the 
first place, you need the images.


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?

On 5/31/16, 9:26 PM, "Anastasia Yendiki" 
wrote:



Some of the errors make me suspect that your input DWI files contain only
one volume. Could this be the case?

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - It knows where to find the freesurfer recons of the T1's
from
SUBJECTS_DIR (see example config file). Based on your log file, it
looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.

Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit
further,
but then crashes again. Not sure why? I have added the log file, so
that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



No, it should be pointed to the DWI data, which can be corrected
niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to
be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should
be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in
a
different folder.
Enclosed is the log file (of one subject) and the configuration
file.
You
will see that I tried the inter and intra option, because I thought
that
for the inter it would not need anything else than the MNI template
and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying
to
run
registers your subject's DWI and T1 images. It expects to find
those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can
you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics
(FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the
things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out
of
range

I do not have the original filesŠ is there a way that I can get
the
script working?

Many thanks.
Heidi










___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


___
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] Tracula skip steps

2016-05-31 Thread Jacobs H (NP) 
Yes, each nifti contains one volume. I have different nifti’s for the
different metrics (FA, MD,..)
Is there a way I can use the trac-all on these files?

On 5/31/16, 9:26 PM, "Anastasia Yendiki" 
wrote:

>
>Some of the errors make me suspect that your input DWI files contain only
>one volume. Could this be the case?
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
>> gives the same error. Enclosed is the config file.
>> Thank you so much
>> Heidi
>>
>> On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" > ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - It knows where to find the freesurfer recons of the T1's
>>>from
>>> SUBJECTS_DIR (see example config file). Based on your log file, it
>>>looks
>>> like you haven't turned off the eddy current compensation, because it's
>>> trying to run it. If you attach your config file, I'll take a look.
>>>
>>> Best,
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Thanks! I tried to adapt the configuration file and it got a bit
 further,
 but then crashes again. Not sure why? I have added the log file, so
that
 maybe you could have a look at what is happening?
 Also, how does the trac-all command knows where to find the T1 data?
 Thanks
 Heidi

 On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
 of
 Anastasia Yendiki"  wrote:

>
> No, it should be pointed to the DWI data, which can be corrected
>niftis
> instead of the original dicoms. I would recommend turning off all the
> corrections in the configuration file, and then running everything
> without
> skipping steps. This will create all the files that are expected to
>be
> there for the registration.
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear Anastasia,
>>
>> Thanks for the feedback. So, does this mean that the dcm root should
>> be
>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in
>>a
>> different folder.
>> Enclosed is the log file (of one subject) and the configuration
>>file.
>> You
>> will see that I tried the inter and intra option, because I thought
>> that
>> for the inter it would not need anything else than the MNI template
>> and
>> the DTI images.
>>
>> Thanks
>>
>> Best
>> Heidi
>>
>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on
>>behalf
>> of
>> Anastasia Yendiki" > of
>> ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - The intra-subject registration step that you're trying
>>>to
>>> run
>>> registers your subject's DWI and T1 images. It expects to find
>>>those
>>> images. It doesn't use the FA, MD, etc in any way.
>>>
>>> Did the log file get created in scripts/trac-all.log? If so, can
>>>you
>>> please send that file and your configuration file? Thanks!
>>>
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear FreeSurfers,

 The data I have is preprocessed, so I have the all the metrics
(FA,
 MD,
 L1, L2, L3,..) in nifti format.
 On this data I would like to start tracula starting from step 1.3.

 I have organized the data as mentioned on the wiki:
 For example:
 / dtifit_FA.nii.gz

 I have also filled in the configuration file, canceling out the
 things
 I don¹t need and then I tried to run:
 Trac-all ­intra ­c 

 Unfortunately, it does not work, it says: dcmlist: subscript out
of
 range

 I do not have the original filesŠ is there a way that I can get
the
 script working?

 Many thanks.
 Heidi

>>

>>


___
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] Tracula skip steps

2016-05-31 Thread Anastasia Yendiki 


Some of the errors make me suspect that your input DWI files contain only 
one volume. Could this be the case?


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:



Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks
like you haven't turned off the eddy current compensation, because it's
trying to run it. If you attach your config file, I'll take a look.

Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit
further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should
be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file.
You
will see that I tried the inter and intra option, because I thought
that
for the inter it would not need anything else than the MNI template
and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying to
run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the
things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi







___
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] Tracula skip steps

2016-05-31 Thread Jacobs H (NP) 
Hmm, weird, as I put a #  in front of it. Putting the eddy current to 0
gives the same error. Enclosed is the config file.
Thank you so much
Heidi

On 5/31/16, 8:13 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:

>
>Hi Heidi - It knows where to find the freesurfer recons of the T1's from
>SUBJECTS_DIR (see example config file). Based on your log file, it looks
>like you haven't turned off the eddy current compensation, because it's
>trying to run it. If you attach your config file, I'll take a look.
>
>Best,
>a.y
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Thanks! I tried to adapt the configuration file and it got a bit
>>further,
>> but then crashes again. Not sure why? I have added the log file, so that
>> maybe you could have a look at what is happening?
>> Also, how does the trac-all command knows where to find the T1 data?
>> Thanks
>> Heidi
>>
>> On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" > ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> No, it should be pointed to the DWI data, which can be corrected niftis
>>> instead of the original dicoms. I would recommend turning off all the
>>> corrections in the configuration file, and then running everything
>>> without
>>> skipping steps. This will create all the files that are expected to be
>>> there for the registration.
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear Anastasia,

 Thanks for the feedback. So, does this mean that the dcm root should
be
 pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
 different folder.
 Enclosed is the log file (of one subject) and the configuration file.
 You
 will see that I tried the inter and intra option, because I thought
that
 for the inter it would not need anything else than the MNI template
and
 the DTI images.

 Thanks

 Best
 Heidi

 On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
 of
 Anastasia Yendiki"  wrote:

>
> Hi Heidi - The intra-subject registration step that you're trying to
> run
> registers your subject's DWI and T1 images. It expects to find those
> images. It doesn't use the FA, MD, etc in any way.
>
> Did the log file get created in scripts/trac-all.log? If so, can you
> please send that file and your configuration file? Thanks!
>
> a.y
>
> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear FreeSurfers,
>>
>> The data I have is preprocessed, so I have the all the metrics (FA,
>> MD,
>> L1, L2, L3,..) in nifti format.
>> On this data I would like to start tracula starting from step 1.3.
>>
>> I have organized the data as mentioned on the wiki:
>> For example:
>> / dtifit_FA.nii.gz
>>
>> I have also filled in the configuration file, canceling out the
>>things
>> I don¹t need and then I tried to run:
>> Trac-all ­intra ­c 
>>
>> Unfortunately, it does not work, it says: dcmlist: subscript out of
>> range
>>
>> I do not have the original filesŠ is there a way that I can get the
>> script working?
>>
>> Many thanks.
>> Heidi
>>

>>

#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: ayendiki $
#$Date: 2013/12/05 23:08:54 $
#$Revision: 1.12 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
#setenv SUBJECTS_DIR /path/to/recons/of/ducks
#
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/dtifit/

# Subject IDs

set subjlist = ` echo S_11XDXA S_1GQ9QV S_1OR6QC S_22ZHN3 S_2AL8RA S_2BB4H2 
S_2C71QF S_2N88VA S_38ZNK5 S_3RSPPP S_3VZEQN S_46JBNZ S_4MPQCY S_4WJ2CR 
S_556CFT S_591HTP S_5KA3RS S_65UK1S S_693X4P S_6D51EY

Re: [Freesurfer] Tracula skip steps

2016-05-31 Thread Anastasia Yendiki 


Hi Heidi - It knows where to find the freesurfer recons of the T1's from
SUBJECTS_DIR (see example config file). Based on your log file, it looks 
like you haven't turned off the eddy current compensation, because it's 
trying to run it. If you attach your config file, I'll take a look.


Best,
a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Thanks! I tried to adapt the configuration file and it got a bit further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:



No, it should be pointed to the DWI data, which can be corrected niftis
instead of the original dicoms. I would recommend turning off all the
corrections in the configuration file, and then running everything
without
skipping steps. This will create all the files that are expected to be
there for the registration.

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file.
You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying to
run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA,
MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi





___
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] Tracula skip steps

2016-05-31 Thread Jacobs H (NP) 
Thanks! I tried to adapt the configuration file and it got a bit further,
but then crashes again. Not sure why? I have added the log file, so that
maybe you could have a look at what is happening?
Also, how does the trac-all command knows where to find the T1 data?
Thanks
Heidi

On 5/31/16, 5:07 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:

>
>No, it should be pointed to the DWI data, which can be corrected niftis
>instead of the original dicoms. I would recommend turning off all the
>corrections in the configuration file, and then running everything
>without 
>skipping steps. This will create all the files that are expected to be
>there for the registration.
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear Anastasia,
>>
>> Thanks for the feedback. So, does this mean that the dcm root should be
>> pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
>> different folder.
>> Enclosed is the log file (of one subject) and the configuration file.
>>You
>> will see that I tried the inter and intra option, because I thought that
>> for the inter it would not need anything else than the MNI template and
>> the DTI images.
>>
>> Thanks
>>
>> Best
>> Heidi
>>
>> On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>of
>> Anastasia Yendiki" > ayend...@nmr.mgh.harvard.edu> wrote:
>>
>>>
>>> Hi Heidi - The intra-subject registration step that you're trying to
>>>run
>>> registers your subject's DWI and T1 images. It expects to find those
>>> images. It doesn't use the FA, MD, etc in any way.
>>>
>>> Did the log file get created in scripts/trac-all.log? If so, can you
>>> please send that file and your configuration file? Thanks!
>>>
>>> a.y
>>>
>>> On Tue, 31 May 2016, Jacobs H (NP) wrote:
>>>
 Dear FreeSurfers,

 The data I have is preprocessed, so I have the all the metrics (FA,
MD,
 L1, L2, L3,..) in nifti format.
 On this data I would like to start tracula starting from step 1.3.

 I have organized the data as mentioned on the wiki:
 For example:
 / dtifit_FA.nii.gz

 I have also filled in the configuration file, canceling out the things
 I don¹t need and then I tried to run:
 Trac-all ­intra ­c 

 Unfortunately, it does not work, it says: dcmlist: subscript out of
 range

 I do not have the original filesŠ is there a way that I can get the
 script working?

 Many thanks.
 Heidi

>>



dwi.ecclog
Description: dwi.ecclog


trac-all.log
Description: trac-all.log
___
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] Tracula skip steps

2016-05-31 Thread Anastasia Yendiki 


No, it should be pointed to the DWI data, which can be corrected niftis 
instead of the original dicoms. I would recommend turning off all the 
corrections in the configuration file, and then running everything without 
skipping steps. This will create all the files that are expected to be 
there for the registration.


On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file. You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:



Hi Heidi - The intra-subject registration step that you're trying to run
registers your subject's DWI and T1 images. It expects to find those
images. It doesn't use the FA, MD, etc in any way.

Did the log file get created in scripts/trac-all.log? If so, can you
please send that file and your configuration file? Thanks!

a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD,
L1, L2, L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things
I don¹t need and then I tried to run:
Trac-all ­intra ­c 

Unfortunately, it does not work, it says: dcmlist: subscript out of
range

I do not have the original filesŠ is there a way that I can get the
script working?

Many thanks.
Heidi



___
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] Tracula skip steps

2016-05-31 Thread Jacobs H (NP) 
Dear Anastasia,

Thanks for the feedback. So, does this mean that the dcm root should be
pointed towards the T1¹s? I have the FreeSurfer recon-all output in a
different folder.
Enclosed is the log file (of one subject) and the configuration file. You
will see that I tried the inter and intra option, because I thought that
for the inter it would not need anything else than the MNI template and
the DTI images.

Thanks

Best
Heidi

On 5/31/16, 4:01 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Anastasia Yendiki"  wrote:

>
>Hi Heidi - The intra-subject registration step that you're trying to run
>registers your subject's DWI and T1 images. It expects to find those
>images. It doesn't use the FA, MD, etc in any way.
>
>Did the log file get created in scripts/trac-all.log? If so, can you
>please send that file and your configuration file? Thanks!
>
>a.y
>
>On Tue, 31 May 2016, Jacobs H (NP) wrote:
>
>> Dear FreeSurfers,
>> 
>> The data I have is preprocessed, so I have the all the metrics (FA, MD,
>>L1, L2, L3,..) in nifti format.
>> On this data I would like to start tracula starting from step 1.3.
>> 
>> I have organized the data as mentioned on the wiki:
>> For example:
>> / dtifit_FA.nii.gz
>> 
>> I have also filled in the configuration file, canceling out the things
>>I don¹t need and then I tried to run:
>> Trac-all ­intra ­c 
>> 
>> Unfortunately, it does not work, it says: dcmlist: subscript out of
>>range
>> 
>> I do not have the original filesŠ is there a way that I can get the
>>script working?
>> 
>> Many thanks.
>> Heidi
>> 

#
# dmrirc.example
#
# This file contains commands that will be run by trac-all before an analysis.
# It is used to set all parameters needed for the analysis.
#
# Remove a parameter from your dmrirc file if you want use the default value.
# Parameters that don't have default values must be specified.
#
# Any other commands that you might want to run before an analysis can be added
# to this file.
#
# Original Author: Anastasia Yendiki
# CVS Revision Info:
#$Author: ayendiki $
#$Date: 2013/12/05 23:08:54 $
#$Revision: 1.12 $
#
# Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
# https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#

# FreeSurfer SUBJECTS_DIR
# T1 images and FreeSurfer segmentations are expected to be found here
# 
#setenv SUBJECTS_DIR /path/to/recons/of/ducks
#
# Output directory where trac-all results will be saved
# Default: Same as SUBJECTS_DIR
#
set dtroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/dtifit/

# Subject IDs
#
set subjlist = ` echo S_11XDXA S_1GQ9QV S_1OR6QC S_22ZHN3 S_2AL8RA S_2BB4H2 
S_2C71QF S_2N88VA S_38ZNK5 S_3RSPPP S_3VZEQN S_46JBNZ S_4MPQCY S_4WJ2CR 
S_556CFT S_591HTP S_5KA3RS S_65UK1S S_693X4P S_6D51EY S_6FWKZD S_6FZL4U 
S_6SB9KZ S_6YRT6A S_71GPF7 S_7HSOBN S_7KFHPW S_7NOX7M S_7WP6BG S_82FZ4L 
S_8BWFJ6 S_9737MM S_9EUNFD S_9K8SLX S_9N8KQW S_9P3JR7 S_9ZVDZV S_A1F2CM 
S_ALV5CB S_AUL7R4 S_BZ4FBH S_CCCMW3 S_CMM2WL S_CTY2ER S_CU4FZA S_CURLLB 
S_DL4N2Q S_DNQ9KU S_DQ1ZSG S_DTW7J6 S_DWA2LP S_DXM9JK S_EHDWX1 S_ENG47C 
S_F4PH5M S_F8P42D S_FCBAMR S_FDJ6UU S_FMSJER S_FQHJWH S_FSK1HD S_FWFNC5 
S_G7KP27 S_H7YAA1 S_HCFNSF S_HW7R19 S_HWGXLJ S_J9HY8A S_JY5M58 S_K1K5LS 
S_K8ZC3B S_KBGJQU S_KCT9S6 S_KL5Q3P S_KMUW5L S_L33YSL S_LABYUQ S_LJ1GWN 
S_LLPPCW S_MEEDAH S_MFUFDS S_MX83QU S_NE58SM S_NIQUVD S_P4K6DM S_PE9J6U 
S_Q9A2UG S_QS6SFY S_R3BPAK S_RANV43 S_RFDRD6 S_RHXWND S_SO63PR S_SVAQUY 
S_T1LVDV S_T8CBM1 S_TJIU8X S_TMNXYB S_TNS7IM S_U2V5FD S_U98RJE S_U9U9QL 
S_UHC6WM S_V36DLL S_VTMXMZ S_WA1CLD S_WDVBAY S_X69RWA S_XFNM9K S_XRZQKV 
S_XTDEMR S_XXMGFN S_XY62WP S_Y97L76 S_YANQMX S_YEFGQ2 S_ZASXXZ S_ZNUP4E 
S_ZPBHLL TAU_001 TAU_024 TAU_029 TAU_064 TAU_074 TAU_122 TAU_151 TAU_154 
TAU_156 TAU_157 TAU_160 TAU_161 TAU_169 TAU_175 TAU_178 TAU_180`

# In case you want to analyze only Huey and Louie
# Default: Run analysis on all subjects
#
#set runlist = (1 3)
#
# Input diffusion DICOMs (file names relative to dcmroot)
# If original DICOMs don't exist, these can be in other image format
# but then the gradient table and b-value table must be specified (see below)
#
#set dcmroot = /Volumes/MACPRO1/EXPLORE_DTI_analyses/prep/
#set dcmlist = (huey/day1/XXX-1.dcm dewey/day1/XXX-1.dcm louie/day2/XXX-1.dcm)

# Diffusion gradient tables (if there is a different one for each scan)
# Must be specified if inputs are not MGH DICOMs
# The tables must have either three columns, where each row is a gradient vector
# or three rows, where each column is a gradient vector
# There must be as many gradient vectors as volumes in the diffusion data set
# Default: Read from DICOM header
#

Re: [Freesurfer] Tracula skip steps

2016-05-31 Thread Anastasia Yendiki 


Hi Heidi - The intra-subject registration step that you're trying to run 
registers your subject's DWI and T1 images. It expects to find those 
images. It doesn't use the FA, MD, etc in any way.


Did the log file get created in scripts/trac-all.log? If so, can you 
please send that file and your configuration file? Thanks!


a.y

On Tue, 31 May 2016, Jacobs H (NP) wrote:


Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, 
L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3. 

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things I don’t 
need and then I tried to run:
Trac-all –intra –c 

Unfortunately, it does not work, it says: dcmlist: subscript out of range

I do not have the original files… is there a way that I can get the script 
working?

Many thanks.
Heidi

___
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] Tracula skip steps

2016-05-30 Thread Jacobs H (NP) 
Dear FreeSurfers,

The data I have is preprocessed, so I have the all the metrics (FA, MD, L1, L2, 
L3,..) in nifti format.
On this data I would like to start tracula starting from step 1.3.

I have organized the data as mentioned on the wiki:
For example:
/ dtifit_FA.nii.gz

I have also filled in the configuration file, canceling out the things I don't 
need and then I tried to run:
Trac-all -intra -c 

Unfortunately, it does not work, it says: dcmlist: subscript out of range

I do not have the original files... is there a way that I can get the script 
working?

Many thanks.
Heidi
___
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.