[Freesurfer] about issues with "recon-all"

[Abel Lei]

Hi FreeSurfers,

I’m a very beginner to both the Linux OS and the FreeSurfer program. 
After finally setting up the FreeSurfer, I was trying to do recon-all 
for my trial subject. But when I ran the “recon-all” command, it 
returned with a long error message indicating many commands not found. 
The message is copied and pasted below. I also attached the 
recon-all.log and recon-all.error in this email, which (probably) 
contains two failed attempts of the same command. Please let me know if 
you need any other info from me. I appreciate your help and time 
greatly! Thank you so much!



Chia-Ming (Abel) Lei

PhD Student/Graduate Student Researcher

Language and Brain Lab (LABlab) & Adult Language Lab

Department of Communication Sciences and Disorders

School of Health and Rehabilitation Science

University of Pittsburgh


-below is the long~ error message--
chiaming-PORTEGE-R835:~> recon-all -all -s mike_dickeySubject Stamp: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is 
/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot

Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer
-rw-rw-r-- 1 chia-ming chia-ming 2119 Sep  6 01:34 
/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log
Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 
01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

mri_motion_correct.fsl: Command not found.
talairach_avi: Command not found.
tkregister2_cmdl: Command not found.
nu_correct: Command not found.
mri_make_uchar: Command not found.
mri_normalize: Command not found.
mri_watershed: Command not found.
mri_gcut: Command not found.
mri_segment: Command not found.
mri_label2label: Command not found.
mri_em_register: Command not found.
mri_ca_normalize: Command not found.
mri_ca_register: Command not found.
mri_ca_label: Command not found.
mri_pretess: Command not found.
mri_fill: Command not found.
mri_tessellate: Command not found.
mri_concatenate_lta: Command not found.
mri_normalize_tp2: Command not found.
mris_smooth: Command not found.
mris_inflate: Command not found.
mris_curvature: Command not found.
mris_sphere: Command not found.
mris_fix_topology: Command not found.
mris_topo_fixer: Command not found.
mris_ca_label: Command not found.
mris_euler_number: Command not found.
mris_make_surfaces: Command not found.
mris_register: Command not found.
mris_volmask: Command not found.
mris_anatomical_stats: Command not found.
mrisp_paint: Command not found.
mris_curvature_stats: Command not found.
mris_calc: Command not found.
mri_robust_register: Command not found.
mri_robust_template: Command not found.
mri_and: Command not found.
mri_or: Command not found.
mri_fuse_segmentations: Command not found.
mri_segstats: Command not found.
cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or 
directory

#
#@# MotionCor Sat Sep  6 01:40:13 EDT 2014
ERROR: no run data found in 
/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri. Make 
sure to
have a volume called 001.mgz in 
/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri/orig.

If you have a second run of data call it 002.mgz, etc.
See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion
Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 
01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s mike_dickey exited with ERRORS at Sat Sep  6 01:40:13 EDT 2014

For more details, see the log file 
/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log
To report a problem, see 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


Sat Sep  6 01:34:42 EDT 2014
/home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey
Desktop/freesurfer/bin/recon-all
-all -i Desktop/freesurfer/subjects/Dickey-Pilot/003/003-0001-1-0.dcm -s mike_dickey
subjid mike_dickey
setenv SUBJECTS_DIR /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot
FREESURFER_HOME Desktop/freesurfer
Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer
Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
cputime  unlimited
filesize unlimited
datasize unlimited
stacksize8192 kbytes
coredumpsize 0 kbytes
memoryuseunlimited
vmemoryuse   unlimited
descriptors  1024 
memorylocked 64 kbytes
maxproc  62935 
maxlocks unlimited
maxsignal62935 
maxmessage   819200 
maxnice  0 
maxrtprio0 
maxrttimeunlimited

 total   used   free sharedbuffers cached
Mem:   807733220317206045612 224048 1572441008468
-/+ buffers/cache: 8660087211324
Swap:  8288252  08288252


program versions used
$Id: recon-all,v 1.379

Re: [Freesurfer] tracula: bvec-error

[Barbara Kreilkamp]

Hi Robby,

Thanks for sharing this and making me aware of the update (great that 
this one will give you the motion parameters as well!).

So also for me it works now!
Have fun with your tracts of many subjects then :)!
Barbara


On 05/09/2014 09:22, Robby De Pauw wrote:

Hi Anastasia and Barbara

I updated Tracula and now everything is running fine.

Thx,

Robby

Robby De Pauw, drs.
*Ghent University*
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be 






On 04 Sep 2014, at 22:01, Anastasia Yendiki 
mailto:ayend...@nmr.mgh.harvard.edu>> 
wrote:




Hi Robby - The option to specify a different gradient table for each 
scan (with bveclist) was introduced more recently. See:

http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates

The version that you're using doesn't recognize bveclist.

Hope this helps,
a.y

On Tue, 26 Aug 2014, Robby De Pauw wrote:


Hi Anastasia,

I'm using this version of tracula.

trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp

I've attached the log-file you requested.

Robby De Pauw, dra.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be






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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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Re: [Freesurfer] Tracula

[Anastasia Yendiki]

If your label is in diffusion space, then replace the MNI brain with any 
volume that's in diffusion space.

On Fri, 5 Sep 2014, Emily Louise Belleau wrote:

> Hi Anastasia,
>
> This would be in diffusion space though. Since I converted all of my seeds to 
> diffusion space.
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: Friday, September 05, 2014 11:32 AM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula
>
> To view your label over the MNI average brain:
>
> fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz 
> your_label_in_MNI_space.nii.gz -l Red
>
> There are no settings, other than choosing a different color for the
> label.
>
> On Fri, 5 Sep 2014, Emily Louise Belleau wrote:
>
>> Hi Anastasia,
>>
>> I am still having a bit of trouble understanding how to properly view my 
>> tract through fsl view.
>>
>> What is the appropriate underlay to use/settings?
>>
>> Thanks again for your continued help!
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Anastasia Yendiki 
>> 
>> Sent: Thursday, September 04, 2014 4:54 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Tracula
>>
>> Certainly you can, and it's a good idea for troubleshooting this. In FSL
>> you can do it with:
>>
>> flirt -in your_label_in_MNI_space.nii.gz -out 
>> your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init 
>> dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour
>>
>> Then you can overlay the transformed label on some of the other inputs
>> that you're giving probtrackx (e.g. a volume from the bedpostx directory)
>> to make sure they look right in fslview.
>>
>>
>> On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
>>
>>> Hi Anastasia,
>>>
>>> Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat 
>>> file in the dmri folder and placed it into FSL's probtractx, I developed a 
>>> track that was in the wrong area of the brain, so I am thinking there is 
>>> something wrong happening with the transformation to diffusion space.
>>>
>>> Can I transform the amygdala mask into diffusion space prior to putting it 
>>> into FSL's probtrackx viz bb register. If so, how might I go about doing 
>>> that?
>>>
>>> Thanks so much for your help,
>>>
>>> Emily
>>> 
>>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>>  on behalf of Anastasia Yendiki 
>>> 
>>> Sent: Thursday, September 04, 2014 4:26 PM
>>> To: Freesurfer support list
>>> Subject: Re: [Freesurfer] Tracula
>>>
>>> Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the
>>> seed-to-diffusion transformation would be the MNI-to-diffusion
>>> transformation.
>>>
>>> a.y
>>>
>>> On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
>>>
 Hello,

 I did all of my DTI preprocessing through tracula.  I now am using FSL 
 probtractx (which utilizes the bedpost stage output) to explore pathways 
 from the amygdala to the ventromedial prefontal cortex.

 When I used FSL's probtractx, when I viewed the tract. The tract was in 
 the wrong area of the brain.

 So, I think this may have something to do with the transfromation matrices 
 I gave it via tracula.

 *FSL asks for the seed to diffusion transformation matrix so that it can 
 convert your seed masks from MNI space to diffusion space. I gave the 
 transformation matrix  in the dmri folder under xfms, titled 
 mni2diff.bbr.mat. I have a feeling this may be the issue.

 * I then tried to use the FLIRT registration tool through FSL to get the 
 appropriate transformation matrices.  It asks for the bedpost directory. I 
 got an error saying it could not read my no_dif_brain_mask.nii.

 I am not sure what transformation matrix to give and was wondering if you 
 could give me some guidance.

 Thanks,

 Emily


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>>> ___
>>> Freesurfer mailing list
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>>> 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.
>>>
>>>
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>>> Freesurfer@nmr.mgh

Re: [Freesurfer] Tracula

[Emily Louise Belleau]

Hi Anastasia,

This would be in diffusion space though. Since I converted all of my seeds to 
diffusion space.

Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Anastasia Yendiki 

Sent: Friday, September 05, 2014 11:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula

To view your label over the MNI average brain:

fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz 
your_label_in_MNI_space.nii.gz -l Red

There are no settings, other than choosing a different color for the
label.

On Fri, 5 Sep 2014, Emily Louise Belleau wrote:

> Hi Anastasia,
>
> I am still having a bit of trouble understanding how to properly view my 
> tract through fsl view.
>
> What is the appropriate underlay to use/settings?
>
> Thanks again for your continued help!
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: Thursday, September 04, 2014 4:54 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula
>
> Certainly you can, and it's a good idea for troubleshooting this. In FSL
> you can do it with:
>
> flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz 
> -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp 
> nearestneighbour
>
> Then you can overlay the transformed label on some of the other inputs
> that you're giving probtrackx (e.g. a volume from the bedpostx directory)
> to make sure they look right in fslview.
>
>
> On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
>
>> Hi Anastasia,
>>
>> Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat 
>> file in the dmri folder and placed it into FSL's probtractx, I developed a 
>> track that was in the wrong area of the brain, so I am thinking there is 
>> something wrong happening with the transformation to diffusion space.
>>
>> Can I transform the amygdala mask into diffusion space prior to putting it 
>> into FSL's probtrackx viz bb register. If so, how might I go about doing 
>> that?
>>
>> Thanks so much for your help,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Anastasia Yendiki 
>> 
>> Sent: Thursday, September 04, 2014 4:26 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Tracula
>>
>> Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the
>> seed-to-diffusion transformation would be the MNI-to-diffusion
>> transformation.
>>
>> a.y
>>
>> On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
>>
>>> Hello,
>>>
>>> I did all of my DTI preprocessing through tracula.  I now am using FSL 
>>> probtractx (which utilizes the bedpost stage output) to explore pathways 
>>> from the amygdala to the ventromedial prefontal cortex.
>>>
>>> When I used FSL's probtractx, when I viewed the tract. The tract was in the 
>>> wrong area of the brain.
>>>
>>> So, I think this may have something to do with the transfromation matrices 
>>> I gave it via tracula.
>>>
>>> *FSL asks for the seed to diffusion transformation matrix so that it can 
>>> convert your seed masks from MNI space to diffusion space. I gave the 
>>> transformation matrix  in the dmri folder under xfms, titled 
>>> mni2diff.bbr.mat. I have a feeling this may be the issue.
>>>
>>> * I then tried to use the FLIRT registration tool through FSL to get the 
>>> appropriate transformation matrices.  It asks for the bedpost directory. I 
>>> got an error saying it could not read my no_dif_brain_mask.nii.
>>>
>>> I am not sure what transformation matrix to give and was wondering if you 
>>> could give me some guidance.
>>>
>>> Thanks,
>>>
>>> Emily
>>>
>>>
>>> ___
>>> 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.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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Re: [Freesurfer] Tracula

[Anastasia Yendiki]

To view your label over the MNI average brain:

fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz 
your_label_in_MNI_space.nii.gz -l Red

There are no settings, other than choosing a different color for the 
label.

On Fri, 5 Sep 2014, Emily Louise Belleau wrote:

> Hi Anastasia,
>
> I am still having a bit of trouble understanding how to properly view my 
> tract through fsl view.
>
> What is the appropriate underlay to use/settings?
>
> Thanks again for your continued help!
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: Thursday, September 04, 2014 4:54 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula
>
> Certainly you can, and it's a good idea for troubleshooting this. In FSL
> you can do it with:
>
> flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz 
> -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp 
> nearestneighbour
>
> Then you can overlay the transformed label on some of the other inputs
> that you're giving probtrackx (e.g. a volume from the bedpostx directory)
> to make sure they look right in fslview.
>
>
> On Thu, 4 Sep 2014, Emily Louise Belleau wrote:
>
>> Hi Anastasia,
>>
>> Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat 
>> file in the dmri folder and placed it into FSL's probtractx, I developed a 
>> track that was in the wrong area of the brain, so I am thinking there is 
>> something wrong happening with the transformation to diffusion space.
>>
>> Can I transform the amygdala mask into diffusion space prior to putting it 
>> into FSL's probtrackx viz bb register. If so, how might I go about doing 
>> that?
>>
>> Thanks so much for your help,
>>
>> Emily
>> 
>> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Anastasia Yendiki 
>> 
>> Sent: Thursday, September 04, 2014 4:26 PM
>> To: Freesurfer support list
>> Subject: Re: [Freesurfer] Tracula
>>
>> Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the
>> seed-to-diffusion transformation would be the MNI-to-diffusion
>> transformation.
>>
>> a.y
>>
>> On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
>>
>>> Hello,
>>>
>>> I did all of my DTI preprocessing through tracula.  I now am using FSL 
>>> probtractx (which utilizes the bedpost stage output) to explore pathways 
>>> from the amygdala to the ventromedial prefontal cortex.
>>>
>>> When I used FSL's probtractx, when I viewed the tract. The tract was in the 
>>> wrong area of the brain.
>>>
>>> So, I think this may have something to do with the transfromation matrices 
>>> I gave it via tracula.
>>>
>>> *FSL asks for the seed to diffusion transformation matrix so that it can 
>>> convert your seed masks from MNI space to diffusion space. I gave the 
>>> transformation matrix  in the dmri folder under xfms, titled 
>>> mni2diff.bbr.mat. I have a feeling this may be the issue.
>>>
>>> * I then tried to use the FLIRT registration tool through FSL to get the 
>>> appropriate transformation matrices.  It asks for the bedpost directory. I 
>>> got an error saying it could not read my no_dif_brain_mask.nii.
>>>
>>> I am not sure what transformation matrix to give and was wondering if you 
>>> could give me some guidance.
>>>
>>> Thanks,
>>>
>>> Emily
>>>
>>>
>>> ___
>>> 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.
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
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>
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>
>
>
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Re: [Freesurfer] Tracula

[Emily Louise Belleau]

Hi Anastasia,

I am still having a bit of trouble understanding how to properly view my tract 
through fsl view.

What is the appropriate underlay to use/settings?

Thanks again for your continued help!

Emily

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Anastasia Yendiki 

Sent: Thursday, September 04, 2014 4:54 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Tracula

Certainly you can, and it's a good idea for troubleshooting this. In FSL
you can do it with:

flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz 
-ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp 
nearestneighbour

Then you can overlay the transformed label on some of the other inputs
that you're giving probtrackx (e.g. a volume from the bedpostx directory)
to make sure they look right in fslview.


On Thu, 4 Sep 2014, Emily Louise Belleau wrote:

> Hi Anastasia,
>
> Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat 
> file in the dmri folder and placed it into FSL's probtractx, I developed a 
> track that was in the wrong area of the brain, so I am thinking there is 
> something wrong happening with the transformation to diffusion space.
>
> Can I transform the amygdala mask into diffusion space prior to putting it 
> into FSL's probtrackx viz bb register. If so, how might I go about doing that?
>
> Thanks so much for your help,
>
> Emily
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Anastasia Yendiki 
> 
> Sent: Thursday, September 04, 2014 4:26 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] Tracula
>
> Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the
> seed-to-diffusion transformation would be the MNI-to-diffusion
> transformation.
>
> a.y
>
> On Wed, 3 Sep 2014, Emily Louise Belleau wrote:
>
>> Hello,
>>
>> I did all of my DTI preprocessing through tracula.  I now am using FSL 
>> probtractx (which utilizes the bedpost stage output) to explore pathways 
>> from the amygdala to the ventromedial prefontal cortex.
>>
>> When I used FSL's probtractx, when I viewed the tract. The tract was in the 
>> wrong area of the brain.
>>
>> So, I think this may have something to do with the transfromation matrices I 
>> gave it via tracula.
>>
>> *FSL asks for the seed to diffusion transformation matrix so that it can 
>> convert your seed masks from MNI space to diffusion space. I gave the 
>> transformation matrix  in the dmri folder under xfms, titled 
>> mni2diff.bbr.mat. I have a feeling this may be the issue.
>>
>> * I then tried to use the FLIRT registration tool through FSL to get the 
>> appropriate transformation matrices.  It asks for the bedpost directory. I 
>> got an error saying it could not read my no_dif_brain_mask.nii.
>>
>> I am not sure what transformation matrix to give and was wondering if you 
>> could give me some guidance.
>>
>> Thanks,
>>
>> Emily
>>
>>
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>>
>>
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Re: [Freesurfer] trac-all -prep error field map error

[Eileen Moore]

Hi - I still have not been able to apply the field map correction within
tracula. Tracula does not appear to recognize the format of my field maps
in either dicom or nifti formats. However, as a work around I first did the
field map correction outside tracula (using our wrapper script for
epidewarp). Next I used this field map corrected image as the input
diffusion image for tracula and set  dob0 = 0 in my  dmrirc file (so as to
skip tracula's field map correction). This appears to be working.

Eileen.


>
> --
>
> Message: 5
> Date: Wed, 27 Aug 2014 13:51:06 -0700
> From: Eileen Moore 
> Subject: Re: [Freesurfer] trac-all -prep error field map error
> To: "freesurfer@nmr.mgh.harvard.edu" 
> Message-ID:
>  lvufckbs+_061v7dctfc5t11pn0k4g9d-c...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Anastasia, I'm not sure how I can give tracula the phase difference maps,
> can you provide an example?
>
> As a reminder, I've run a wrapper script around epidewarp which takes our
> dicom images and converts them into a phase difference map (it is based on
> the script that was authored by Doug Greve for the fBIRN consortium).
>
> In the tutorial dmrirc example I see only the 'set b0mlist' and 'set
> b0plist' options, and am unsure where I could give it the phase difference
> map.
>
> I've also tried converting the dicom magnitude and phase maps to nifti
> format and inputting these into the dmrirc file but I am still getting an
> error. (See attached log file).
>
> Thanks,
> Eileen.
>
>
>
> > --
> >
> > Message: 10
> > Date: Thu, 17 Jul 2014 04:14:16 -0400 (EDT)
> > From: Anastasia Yendiki 
> > Subject: Re: [Freesurfer] trac-all -prep error field map error
> > To: Freesurfer support list 
> > Message-ID: 
> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> >
> >
> > Hi Eileen - All image formats that mri_convert (and thus any freesurfer
> > program) can read will do, you don't need dicom. Try giving trac-all the
> > phase difference maps you have and let's see what happens.
> >
> > Best,
> > a.y
> >
> > On Wed, 16 Jul 2014, Eileen Moore wrote:
> >
> > > Hi Anastasia,
> > >
> > > OK - our imaging physicists had developed a wrapper script around
> > epidewarp
> > > which takes our dicom images and converts them into the phase
> difference
> > map
> > > (it is based on the script that was authored by Doug Greve for the
> fBIRN
> > > consortium). It looks like the tracula script requires dicom images. Is
> > > there a way for me to do epidewarp manually and then follow through
> with
> > the
> > > remaining steps using trac-all?
> > >
> > > Thanks,
> > > Eileen.
> > >
> > >
> > >   Date: Mon, 14 Jul 2014 11:23:47 -0400 (EDT)
> > >   From: Anastasia Yendiki 
> > >   Subject: Re: [Freesurfer] trac-all -prep error field map error
> > >   To: Freesurfer support list 
> > >   Message-ID:
> > >   
> > >   Content-Type: text/plain; charset="utf-8"
> > >
> > >
> > >   Hi Eileen - That step is run with the program epidewarp.fsl,
> > >   which you can
> > >   run on the command line to see the available options. The input
> > >   phase map
> > >   volume is expected to have either 2 frames (2 separate phase
> > >   maps) or 1
> > >   frame (the difference phase map). This error from trac-all means
> > >   that it
> > >   found that your input phase map has something other than 1 or 2
> > >   frames, so
> > >   it doesn't know how to handle it.
> > >
> > >   Hope this helps,
> > >   a.y
> > >
> > >   On Sat, 12 Jul 2014, Eileen Moore wrote:
> > >
> > >   > Hi - I'm using freesurfer 5.3 on an Ubuntu operating system.
> > >   I'm tyring to
> > >   > run tracula on some? images acquired from a GE scanner. I am
> > >   running into
> > >   > problems when I try to perform the registration-based
> > >   B0-inhomogeneity
> > >   > compensation, getting an error in the terminal output: "ERROR:
> > >   Unrecognized
> > >   > format of phase map". However, trac-all -prep runs fine when I
> > >   skip the
> > >   > B0-inhomogeneity compensation step. Is there something else I
> > >   need to do to
> > >   > use field map correction?
> > >   >
> > >   > I've attached the trac-all.log and a copy of the terminal
> > >   output.
> > >   >
> > >   > Thanks,
> > >   > Eileen.
> > >   >
> > >   >
> > >   >
> > >   >
> > >
> > >
> > >
> > >
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Re: [Freesurfer] tracula: bvec-error

[Robby De Pauw]

Hi Anastasia and Barbara

I updated Tracula and now everything is running fine.

Thx,

Robby

Robby De Pauw, drs.
Ghent University
Department of Physiotherapy and Rehabilitation Sciences
3B3
De Pintelaan 185
B-9000 Ghent

robby.dep...@ugent.be






On 04 Sep 2014, at 22:01, Anastasia Yendiki  
wrote:

> 
> Hi Robby - The option to specify a different gradient table for each scan 
> (with bveclist) was introduced more recently. See:
>   http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates
> 
> The version that you're using doesn't recognize bveclist.
> 
> Hope this helps,
> a.y
> 
> On Tue, 26 Aug 2014, Robby De Pauw wrote:
> 
>> Hi Anastasia,
>> 
>> I’m using this version of tracula.
>> 
>> trac-all,v 1.22.2.12 2013/02/23 02:01:02 ayendiki Exp
>> 
>> I’ve attached the log-file you requested.
>> 
>> Robby De Pauw, dra.
>> Ghent University
>> Department of Physiotherapy and Rehabilitation Sciences
>> 3B3
>> De Pintelaan 185
>> B-9000 Ghent
>> 
>> robby.dep...@ugent.be
>> 
>> 
>> 
>> 
>> 
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