Re: [Freesurfer] TRACULA trac-all preprocessing errors

[Hao wen]

Sorry, another question, in your update package, you just offered Cnetos and 
MacOSX lion, MacOSX snow leopard, but my machine is Ubuntu14.04, So can I use 
the CentOS


Thanks in advance


Hao



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Hao wen 

Envoyé : dimanche 18 décembre 2016 21:29
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors


Ok, so I will use my own recon-alled data to follow the tutorial and at the 
same time to wait for the new version of FreeSurfer


Thanks




De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : dimanche 18 décembre 2016 14:51
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors

Hi Hao - That is strange, thank you for bringing this to our attention. The 
recons should be there. We're in the process of rerunning everything with 
version 6.0 in preparation for the release, so all this data will be updated. 
Thank you for your patience!

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Sunday, December 18, 2016 4:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA trac-all preprocessing errors


Hello, Thanks for your reply, that was what I thought, But I just download the 
tutorial data, and followed your tutorial from this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

FsTutorial/Tracula - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Back to list of all tutorials | Back to course page | Next. TRACULA tutorial. 
This tutorial will take you through the steps necessary to run TRACULA (TRActs 
...

So I think in the folder tutorial_data/diffusion_recons/elmo.2005/mri, it is 
empty, do you think before TRACULA, we have to run recon-all for these tutorial 
subjects??? i thought they are already recon-alledI defined the SUBJECT_DIR 
as

export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons

Besides, thanks for the second point:)

Hope to hear from you soon,

Thanks in advance

Hao



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : samedi 17 décembre 2016 17:26
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors

Hi Hao - It looks like it didn't find the freesurfer recons of the subjects' 
structural data. They should be under whatever you have defined as SUBJECTS_DIR.

On a separate note, it looks like you're using an old version of TRACULA. There 
is an update that you can download from the TRACULA wiki page, or you can wait 
for freesurfer 6.0, which will hopefully be out in a few days and will include 
this update.
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Saturday, December 17, 2016 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA trac-all preprocessing errors


Hello, Freesurfer experts:

I am new to Tracula, and I followed your tutorial with your tutorial data, and 
for the preprocessing pipeline, I got some errors when doing the tensor 
fitting, here is the command:

trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial


and I looked over the trac-all.log and found that the problem is from the 
command dmri_train, here is the errro log information:


'

/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train
 --outdir 
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni
 --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr 
rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr 
fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr 
rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr 
lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr 
rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr 
--slist /tmp/subj33.elmo.2005.25745.txt --trk dlabel/mni/lh.cst_AS.bbr.trk 
dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk 
dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk 
dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk 
dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk 
dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk 
dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk 
dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk 
dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk 
dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel

[Freesurfer] TRACULA to define multiple bvals

[Hao wen]

Hello, Freesurfer experts:

I want to ask you in TRACULA, we can define multiple bvecs with the variable 
'bveclist' in configuration file, so my question is if we have the same option 
for bval, or it is mandatory to have the same bvals for all the subjects??? I 
dont see any information about this...



Thanks in advance


Hao
___
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The information in this e-mail is intended only for the person to whom it is
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dispose of the e-mail.

Re: [Freesurfer] TRACULA to define multiple bvals

[Yendiki, Anastasia]

Hi Hao - This is also coming in the next version :)

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Monday, December 19, 2016 5:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA to define multiple bvals


Hello, Freesurfer experts:

I want to ask you in TRACULA, we can define multiple bvecs with the variable 
'bveclist' in configuration file, so my question is if we have the same option 
for bval, or it is mandatory to have the same bvals for all the subjects??? I 
dont see any information about this...



Thanks in advance


Hao
___
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 to define multiple bvals

[Hao wen]

Great, if you can add some choice to run these subjects in parallelized, like a 
flag '-n_threads', this will be perfect considering the time-consuming problem, 
good job!

Good day



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : lundi 19 décembre 2016 15:10
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA to define multiple bvals

Hi Hao - This is also coming in the next version :)

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Monday, December 19, 2016 5:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA to define multiple bvals


Hello, Freesurfer experts:

I want to ask you in TRACULA, we can define multiple bvecs with the variable 
'bveclist' in configuration file, so my question is if we have the same option 
for bval, or it is mandatory to have the same bvals for all the subjects??? I 
dont see any information about this...



Thanks in advance


Hao
___
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 trac-all preprocessing errors

[Yendiki, Anastasia]

Yes, you can use centos.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Monday, December 19, 2016 3:05 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA trac-all preprocessing errors


Sorry, another question, in your update package, you just offered Cnetos and 
MacOSX lion, MacOSX snow leopard, but my machine is Ubuntu14.04, So can I use 
the CentOS


Thanks in advance


Hao



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Hao wen 

Envoyé : dimanche 18 décembre 2016 21:29
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors


Ok, so I will use my own recon-alled data to follow the tutorial and at the 
same time to wait for the new version of FreeSurfer


Thanks




De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : dimanche 18 décembre 2016 14:51
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors

Hi Hao - That is strange, thank you for bringing this to our attention. The 
recons should be there. We're in the process of rerunning everything with 
version 6.0 in preparation for the release, so all this data will be updated. 
Thank you for your patience!

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Sunday, December 18, 2016 4:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA trac-all preprocessing errors


Hello, Thanks for your reply, that was what I thought, But I just download the 
tutorial data, and followed your tutorial from this page 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula

FsTutorial/Tracula - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
Back to list of all tutorials | Back to course page | Next. TRACULA tutorial. 
This tutorial will take you through the steps necessary to run TRACULA (TRActs 
...

So I think in the folder tutorial_data/diffusion_recons/elmo.2005/mri, it is 
empty, do you think before TRACULA, we have to run recon-all for these tutorial 
subjects??? i thought they are already recon-alledI defined the SUBJECT_DIR 
as

export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons

Besides, thanks for the second point:)

Hope to hear from you soon,

Thanks in advance

Hao



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : samedi 17 décembre 2016 17:26
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA trac-all preprocessing errors

Hi Hao - It looks like it didn't find the freesurfer recons of the subjects' 
structural data. They should be under whatever you have defined as SUBJECTS_DIR.

On a separate note, it looks like you're using an old version of TRACULA. There 
is an update that you can download from the TRACULA wiki page, or you can wait 
for freesurfer 6.0, which will hopefully be out in a few days and will include 
this update.
https://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates

Best,

a.y


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Saturday, December 17, 2016 11:16 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA trac-all preprocessing errors


Hello, Freesurfer experts:

I am new to Tracula, and I followed your tutorial with your tutorial data, and 
for the preprocessing pipeline, I got some errors when doing the tensor 
fitting, here is the command:

trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial


and I looked over the trac-all.log and found that the problem is from the 
command dmri_train, here is the errro log information:


'

/aramis/Software/FreeSurfer/freesurfer-5.3.0-15052013-x86_64-centos/bin/dmri_train
 --outdir 
/aramis/dataARAMIS/users/junhao.wen/Freesurfer/Freesurfer_wiki_tutorial/Diffusion/tracula/tracula_result/elmo.2005/dlabel/mni
 --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr 
rh.ilf_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr 
fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr 
rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr 
lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr 
rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr 
--slist /tmp/subj33.elmo.2005.25745.txt --trk dlabel/mni/lh.cst_AS.bbr.trk 
dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk 
dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk 
dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk 
dlabel/mn

Re: [Freesurfer] 3d brain vessels visualisation

[Bruce Fischl]

Hi Anand

have you run recon-all yet? Ideally you would give it a non-enhanced 3D 
T1 (like an mprage). We don't segment vessels though, for that you will 
need to use some other software.

cheers
Bruce



On Mon, 19 Dec 
2016, anand iyer wrote:

> Hi
> Could you please help with this?
> 
> I am able to create a 3D model of brain with T1 volume.
> I want to superimpose the surface vessels from a T1 GAD.
> How do i go about it?
> 
> Thanks,
> 
> Anand
> Anand Iyer
> 
> 
> 
> 
>
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] TRACULA to define multiple bvals

[Yendiki, Anastasia]

There will be an option to print out command lines that can then be submitted 
to a cluster in parallel. Hope this helps.


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Monday, December 19, 2016 9:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] TRACULA to define multiple bvals


Great, if you can add some choice to run these subjects in parallelized, like a 
flag '-n_threads', this will be perfect considering the time-consuming problem, 
good job!

Good day



De : freesurfer-boun...@nmr.mgh.harvard.edu 
 de la part de Yendiki, Anastasia 

Envoyé : lundi 19 décembre 2016 15:10
À : Freesurfer support list
Objet : Re: [Freesurfer] TRACULA to define multiple bvals

Hi Hao - This is also coming in the next version :)

a.y

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Hao wen 
[hao.freesur...@hotmail.com]
Sent: Monday, December 19, 2016 5:43 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] TRACULA to define multiple bvals


Hello, Freesurfer experts:

I want to ask you in TRACULA, we can define multiple bvecs with the variable 
'bveclist' in configuration file, so my question is if we have the same option 
for bval, or it is mandatory to have the same bvals for all the subjects??? I 
dont see any information about this...



Thanks in advance


Hao
___
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] Ynt: Neighborhood of a vertex

[Onur Uğurlu]

Hi Bruce,


Thank you so much for the answer.


I have used "read_surf.m" function and got the list of vertex locations and a 
list of faces. However, the list contains 107106 vertices whereas the 
lh.thickness.asc file contains 118603 vertices. How can I match the thickness 
values which are inlh.thickness.asc file with the vertices which were obtained 
from "read_surf.m" function?


Sincerely yours,

Onur



Gönderen: Bruce Fischl  adına 
freesurfer-boun...@nmr.mgh.harvard.edu 
Gönderildi: 18 Aralık 2016 Pazar 17:54
Kime: Freesurfer support list
Konu: Re: [Freesurfer] Neighborhood of a vertex

Hi Onur

for that you need a surface file. If you are using matlab you can load a
surface file in with read_surf.m. The  will then be an index
into the surface (although note that you will need to add 1 to it since
matlab is 1-based when you index into the vertex list). It will return a
list of vertex locations and also a list of faces. The faces contain the
(0-based) indices of the vertices in each triangle, which can be used to
compile a list of neighbors.

cheers
Bruce



On Sun, 18 Dec 2016, Onur Uğurlu wrote:

>
> Hi all,
>
>
> I have a 'lh.thickness.asc' file which contains thickness values of each
> vertex.
>
> The format of the file is following;
>
> 
>
> However, x,y,z are not integer. What is the unit of the x,y,z values in the
> file? I am trying to find all the neighborhood of any given vertex as x,y,z
> -> x+1,y,z etc, can you suggest a method for this problem.
>
>
> Sincerely yours,
>
> Onur
>
>
>
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Ynt: Neighborhood of a vertex

[Bruce Fischl]

that shouldn't be the case. Run mris_info or mris_euler_number on your 
input surface. Can you load the thickness as a surface overlay? It may be 
that you regenerated surface  and not the htickness, or visa-versa. Which 
surface are you using?


On Mon, 19 Dec 2016, Onur Uğurlu wrote:



Hi Bruce,


Thank you so much for the answer.


I have used "read_surf.m" function and got the list of vertex locations and
a list of faces. However, the list contains 107106 vertices whereas the
lh.thickness.asc file contains 118603 vertices. How can I match the
thickness values which are inlh.thickness.asc file with the vertices which
were obtained from "read_surf.m" function?


Sincerely yours,

Onur



Gönderen: Bruce Fischl  adına
freesurfer-boun...@nmr.mgh.harvard.edu

Gönderildi: 18 Aralık 2016 Pazar 17:54
Kime: Freesurfer support list
Konu: Re: [Freesurfer] Neighborhood of a vertex  
Hi Onur

for that you need a surface file. If you are using matlab you can load a
surface file in with read_surf.m. The  will then be an index
into the surface (although note that you will need to add 1 to it since
matlab is 1-based when you index into the vertex list). It will return a
list of vertex locations and also a list of faces. The faces contain the
(0-based) indices of the vertices in each triangle, which can be used to
compile a list of neighbors.

cheers
Bruce



On Sun, 18 Dec 2016, Onur Uğurlu wrote:

>
> Hi all,
>
>
> I have a 'lh.thickness.asc' file which contains thickness values of each
> vertex.
>
> The format of the file is following;
>
> 
>
> However, x,y,z are not integer. What is the unit of the x,y,z values in
the
> file? I am trying to find all the neighborhood of any given vertex as
x,y,z
> -> x+1,y,z etc, can you suggest a method for this problem.
>
>
> Sincerely yours,
>
> Onur
>
>
>

___
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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Tracula Set: No Match

[Katherine Damme]

This is being generated by an earlier step in the trac-all -prep right?

On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> It doesn't recognize the format of your field map. It assumes that the
> field map has either 2 frames (2 phase maps) or 1 frame (a phase difference
> map).
>
> --
> *From:* Katherine Damme [katherine.da...@gmail.com]
> *Sent:* Friday, December 16, 2016 5:18 PM
> *To:* Freesurfer support list; Anastasia Yendiki
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> When I run this on the command line it seems to be completing the fslroi
> step fine:
>
> "fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/b0pha.nii.gz
> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>
> trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016
>
> [ksd770@katelinux Temple_Tracula]# fslroi /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_
> Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
> [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"
>
> What is the next step in the code where it is failing?
>
> On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <
> katherine.da...@gmail.com> wrote:
>
>> I am now getting this error. I am not sure if this is a new issue or
>> related.
>>
>> fslorient -forceradiological /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/b0pha.nii.gz
>>
>> mri_probedicom --i //media/Data/Temple/Temple_Tra
>> cula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
>> > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
>>
>> TE: Subscript out of range.
>>
>> fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>
>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/b0pha.nii.gz
>>
>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
>> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> I check all of these images and I can open them.
>>
>> On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia <
>> ayend...@mgh.harvard.edu> wrote:
>>
>>> Hi Katherine - Can you please use the attached version and tell me if it
>>> works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the
>>> version of xfmrot that you have now. If it works, we'll include it in the
>>> next version. Thanks!
>>>
>>> a.y
>>>
>>> --
>>> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
>>> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
>>> katherine.da...@gmail.com]
>>> *Sent:* Tuesday, December 13, 2016 9:38 AM
>>>
>>> *To:* Freesurfer support list
>>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>>
>>>
>>>
>>> On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
 Ok, if you also send me the first file, /media/Data/Temple/Temple_Trac
 ula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the
 error.

 --
 *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
 katherine.da...@gmail.com]
 *Sent:* Tuesday, December 13, 2016 9:21 AM

 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] Tracula Set: No Match

 Yes. I immediately tried to enter the command in manually, checked the
 paths, and looked at the command manual for any format errors.

 [ksd770@katelinux Temple_Tracula]$ xfmrot
 /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
 /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
 /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs

 set: No match.

 On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <
 ayend...@mgh.harvard.edu> wrote:

> Thanks. This looks fine. When you run that xfmrot command directly on
> the linux command line, do you get the same error?
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
> katherine.da...@gmail.com]
> *Sent:* Wednesday, December 07, 2016 12:41 PM
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
>
>
> On Mon, Dec 5, 2016 at 12:00 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> Hi Katherine - The error occurs when processing this file:
>> /media/Data/Te

Re: [Freesurfer] Tracula Set: No Match

[Yendiki, Anastasia]

No, it's a separate scan that you provide.


From: Katherine Damme [katherine.da...@gmail.com]
Sent: Monday, December 19, 2016 1:43 PM
To: Freesurfer support list; Anastasia Yendiki
Subject: Re: [Freesurfer] Tracula Set: No Match

This is being generated by an earlier step in the trac-all -prep right?

On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
It doesn't recognize the format of your field map. It assumes that the field 
map has either 2 frames (2 phase maps) or 1 frame (a phase difference map).


From: Katherine Damme 
[katherine.da...@gmail.com]
Sent: Friday, December 16, 2016 5:18 PM
To: Freesurfer support list; Anastasia Yendiki
Subject: Re: [Freesurfer] Tracula Set: No Match

When I run this on the command line it seems to be completing the fslroi step 
fine:

"fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
ERROR: Unrecognized format of phase map 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz
Linux katelinux.psych.northwestern.edu 
2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016

[ksd770@katelinux Temple_Tracula]# fslroi 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
[ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"

What is the next step in the code where it is failing?

On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme 
mailto:katherine.da...@gmail.com>> wrote:
I am now getting this error. I am not sure if this is a new issue or related.


fslorient -forceradiological 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz

mri_probedicom --i 
//media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
 > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat

TE: Subscript out of range.

fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1

ERROR: Unrecognized format of phase map 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz

Linux katelinux.psych.northwestern.edu 
2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 
x86_64 GNU/Linux

I check all of these images and I can open them.

On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Katherine - Can you please use the attached version and tell me if it works? 
You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the version of 
xfmrot that you have now. If it works, we'll include it in the next version. 
Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Katherine Damme 
[katherine.da...@gmail.com]
Sent: Tuesday, December 13, 2016 9:38 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Set: No Match



On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Ok, if you also send me the first file, 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog,
 I'll see if I can replicate the error.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Katherine Damme 
[katherine.da...@gmail.com]
Sent: Tuesday, December 13, 2016 9:21 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Set: No Match

Yes. I immediately tried to enter the command in manually, checked the paths, 
and looked at the command manual for any format errors.


[ksd770@katelinux Temple_Tracula]$ xfmrot 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs

set: No match.

On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Thanks. This looks fine. When you run that xfmrot command directly on the linux 
command line, do you get the same error?


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu<

[Freesurfer] Poorly Designed Matrix Two Stage Longitudinal Model

[Timothy Hendrickson]

FreeSurfer experts,

I am attempting to use the two stage model for longitudinal analysis,
however I keep receiving an error message that my design matrix is poorly
scaled.
I'm curious, I've used the same format of design matrix on cross
sectional without problem.

Anyway here is the command line input:

 mri_glmfit --glmdir
rh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir \
--X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \
--y rh.testretest.thickness-spc.stack.fwhm10.mgh \
--C 
DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_pairedAnalysis.DOSSDS.mtx
\
--label rh.testretest.fsaverage.cortex.label \
--surf fsaverage rh

The error message is attached within file
error_designMtx_12_19_16.txt

Additionally I've included my analysis script, all timepoint qdec file,
temporal average qdec file, fsgd file, and design matrix.
Any help would be extremely beneficial.

-Tim

Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
Design matrix --
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  -1.878;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  -2.325;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  -1.967;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  -0.552   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000  -0.121   0.000   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000  -0.588   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   1.101   0.000;
 0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  -2.205;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.775   0.000   0.000   0.000;
 1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   1.316   0.000   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  -0.590   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000  -1.093   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000  -1.880   0.000   0.000;
 0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000  -2.131   0.000   0.000;
 0.000   0.000   1.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.632   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.908   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   1.447   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000  -1.635   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000  -0.859   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000  -0.588   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   1.000   0.000   0.000   0.000  -0.858   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000  -0.051;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   1.000   0.000   0.000   0.000  -1.641   0.000   0.000   0.000;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 0.000   0.000   0.000   0.000   0.000   1.000   0.000   0.000   0.000   0.217;
 0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000  
 

[Freesurfer] Talairach error in monkey brain

[Qi Ting]

Dear Freesurfer experts,


I'm using freesurfer to process my monkey brain data. It reported errors during 
Talairach registration step. So I added no-tal-check tag to run recon-all 
autorecon1 and used tkregister2 to manually edit registration. However, I 
couldn't let them perfectly fitted, especially deformation in sagittal view. 
But when I checked the final parcellation, I found it worked well. So I was 
wondering whether the Talairach registration step matters a lot for the final 
results? And whether I did correctly?


Thanks in advance!


with best regards,

Ting Qi

___
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 Set: No Match

[Katherine Damme]

Is this meant to be calculated from the B0 dicoms?

On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia <
ayend...@mgh.harvard.edu> wrote:

> No, it's a separate scan that you provide.
>
> --
> *From:* Katherine Damme [katherine.da...@gmail.com]
> *Sent:* Monday, December 19, 2016 1:43 PM
>
> *To:* Freesurfer support list; Anastasia Yendiki
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> This is being generated by an earlier step in the trac-all -prep right?
>
> On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> It doesn't recognize the format of your field map. It assumes that the
>> field map has either 2 frames (2 phase maps) or 1 frame (a phase difference
>> map).
>>
>> --
>> *From:* Katherine Damme [katherine.da...@gmail.com]
>> *Sent:* Friday, December 16, 2016 5:18 PM
>> *To:* Freesurfer support list; Anastasia Yendiki
>> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>>
>> When I run this on the command line it seems to be completing the fslroi
>> step fine:
>>
>> "fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/b0pha.nii.gz
>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
>> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>
>> trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016
>>
>> [ksd770@katelinux Temple_Tracula]# fslroi /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/dwi_eddy.nii.gz /media/Data/Temple/Temple_Trac
>> ula/31313422_10128/dmri/lowb.nii.gz 0 1
>> [ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"
>>
>> What is the next step in the code where it is failing?
>>
>> On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme <
>> katherine.da...@gmail.com> wrote:
>>
>>> I am now getting this error. I am not sure if this is a new issue or
>>> related.
>>>
>>> fslorient -forceradiological /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>
>>> mri_probedicom --i //media/Data/Temple/Temple_Tra
>>> cula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
>>> > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat
>>>
>>> TE: Subscript out of range.
>>>
>>> fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz
>>> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
>>>
>>> ERROR: Unrecognized format of phase map /media/Data/Temple/Temple_Trac
>>> ula/31313422_10128/dmri/b0pha.nii.gz
>>>
>>> Linux katelinux.psych.northwestern.edu 2.6.32-642.6.2.el6.x86_64 #1 SMP
>>> Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> I check all of these images and I can open them.
>>>
>>> On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia <
>>> ayend...@mgh.harvard.edu> wrote:
>>>
 Hi Katherine - Can you please use the attached version and tell me if
 it works? You'll have to copy it into $FREESURFER_HOME/bin, to overwrite
 the version of xfmrot that you have now. If it works, we'll include it in
 the next version. Thanks!

 a.y

 --
 *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
 freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
 katherine.da...@gmail.com]
 *Sent:* Tuesday, December 13, 2016 9:38 AM

 *To:* Freesurfer support list
 *Subject:* Re: [Freesurfer] Tracula Set: No Match



 On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia <
 ayend...@mgh.harvard.edu> wrote:

> Ok, if you also send me the first file, /media/Data/Temple/Temple_Trac
> ula/31313422_10128/dmri/dwi.ecclog, I'll see if I can replicate the
> error.
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu [
> freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme [
> katherine.da...@gmail.com]
> *Sent:* Tuesday, December 13, 2016 9:21 AM
>
> *To:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Tracula Set: No Match
>
> Yes. I immediately tried to enter the command in manually, checked the
> paths, and looked at the command manual for any format errors.
>
> [ksd770@katelinux Temple_Tracula]$ xfmrot
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs.norot
> /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/bvecs
>
> set: No match.
>
> On Wed, Dec 7, 2016 at 2:41 PM, Yendiki, Anastasia <
> ayend...@mgh.harvard.edu> wrote:
>
>> Thanks. This looks fine. When you run that xfmrot command directly on
>> the linux command line, do you get the same error?
>>
>> ---

Re: [Freesurfer] Tracula Set: No Match

[Yendiki, Anastasia]

No - there is no relation between B0 field inhomogeneities (measured by a field 
map) and b=0 volumes. The capital B refers to the magnetic field in the 
scanner, the small b is the b-value (diffusion weighting).


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Katherine Damme 
[katherine.da...@gmail.com]
Sent: Monday, December 19, 2016 11:01 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Set: No Match

Is this meant to be calculated from the B0 dicoms?

On Mon, Dec 19, 2016 at 12:44 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
No, it's a separate scan that you provide.


From: Katherine Damme 
[katherine.da...@gmail.com]
Sent: Monday, December 19, 2016 1:43 PM

To: Freesurfer support list; Anastasia Yendiki
Subject: Re: [Freesurfer] Tracula Set: No Match

This is being generated by an earlier step in the trac-all -prep right?

On Fri, Dec 16, 2016 at 4:23 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
It doesn't recognize the format of your field map. It assumes that the field 
map has either 2 frames (2 phase maps) or 1 frame (a phase difference map).


From: Katherine Damme 
[katherine.da...@gmail.com]
Sent: Friday, December 16, 2016 5:18 PM
To: Freesurfer support list; Anastasia Yendiki
Subject: Re: [Freesurfer] Tracula Set: No Match

When I run this on the command line it seems to be completing the fslroi step 
fine:

"fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
ERROR: Unrecognized format of phase map 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz
Linux katelinux.psych.northwestern.edu 
2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec 16 15:38:48 CST 2016

[ksd770@katelinux Temple_Tracula]# fslroi 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1
[ksd770@katelinux Temple_Tracula]# trac-all -prep -c dmrirc_10128.txt"

What is the next step in the code where it is failing?

On Wed, Dec 14, 2016 at 9:19 PM, Katherine Damme 
mailto:katherine.da...@gmail.com>> wrote:
I am now getting this error. I am not sure if this is a new issue or related.


fslorient -forceradiological 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz

mri_probedicom --i 
//media/Data/Temple/Temple_Tracula/31313422_10128/dti_dicom/31313422_10128.MR.Temple.9.1.20140806.182244.xfrp16.dcm
 > /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0info.dat

TE: Subscript out of range.

fslroi /media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi_eddy.nii.gz 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/lowb.nii.gz 0 1

ERROR: Unrecognized format of phase map 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/b0pha.nii.gz

Linux katelinux.psych.northwestern.edu 
2.6.32-642.6.2.el6.x86_64 #1 SMP Mon Oct 24 10:22:33 EDT 2016 x86_64 x86_64 
x86_64 GNU/Linux

I check all of these images and I can open them.

On Tue, Dec 13, 2016 at 7:59 PM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Hi Katherine - Can you please use the attached version and tell me if it works? 
You'll have to copy it into $FREESURFER_HOME/bin, to overwrite the version of 
xfmrot that you have now. If it works, we'll include it in the next version. 
Thanks!

a.y


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Katherine Damme 
[katherine.da...@gmail.com]
Sent: Tuesday, December 13, 2016 9:38 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Set: No Match



On Tue, Dec 13, 2016 at 8:34 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:
Ok, if you also send me the first file, 
/media/Data/Temple/Temple_Tracula/31313422_10128/dmri/dwi.ecclog,
 I'll see if I can replicate the error.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
[freesurfer-boun...@nmr.mgh.harvard.edu]
 on behalf of Katherine Damme 
[katherine.da...@gmail.com]
Sent: Tuesday, December 13, 2016 9:21 AM

To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula Set: No Match

Yes. I immediately tried to enter the command in manually, checked the paths, 
and looked at the