Hi Anastasia,
Apologies this looks like an error on my part. I had edited the script to
specify --init-spm instead of --init-fsl but forgot to specify that this script
was to be used. It all seems to be looking good now which is fantastic- thanks
very much for all of your help!!
One last question, when using the command:
freeview -tv
$TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/merged_avg33_mni_bbr.mgz \
-v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz &
I am able to see all of the tracts clearly, except in some of the subjects the
Forceps Major seems to be missing. Changing the threshold doesn't seem to make
a difference. Do you have any ideas what the issue could be with this?
Thanks,
Amanda
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki
<ayend...@nmr.mgh.harvard.edu>
Sent: 11 February 2015 16:21
To: Freesurfer support list
Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error]
Hi Amanda - It doesn't look like the new registration was applied to the
aparc+aseg. Can you tell us the exact sequence of steps that you followed,
including your bbregister command line and the trac-all command lines that
you ran after running bbregister?
Thanks,
a.y
On Wed, 11 Feb 2015, Worker, Amanda wrote:
> Hi,
>
> Thanks for this. --init-spm does appear to work and when checking the
> registration using the instructions bbregister gives it all looks good to me.
> However, when I check the dtifit_FA and aparc+aseg.bbr.nii it still doesn't
> look too good. I've continued on with the next steps for reconstructing the
> pathways just to see what happens, but they don't come out well.
>
> I've attached a screenshot of the registration using --init-spm and then also
> a screenshot of the dmri/dtfit_FA.nii.gz alone and with aparc+aseg.bbri.nii
> overlayed.
>
> Best wishes,
>
> Amanda
>
>
>
>
> ________________________________________
> From: freesurfer-boun...@nmr.mgh.harvard.edu
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve
> <gr...@nmr.mgh.harvard.edu>
> Sent: 06 February 2015 19:15
> To: Bruce Fischl; Freesurfer support list
> Subject: Re: [Freesurfer] bbregister error [Was: TRACULA mask error]
>
> or --init-rr if you don't have matlab/spm
>
> On 02/06/2015 01:49 PM, Bruce Fischl wrote:
>> try --init-spm
>> On Fri, 6 Feb 2015, Anastasia Yendiki wrote:
>>
>>>
>>> Hi Amanda - So it looks like --init-header didn't work, and neither does
>>> --init-fsl. I'll defer to the father of bbregister, Doug, for clues
>>> about
>>> how to proceed.
>>>
>>> a.y
>>>
>>> On Wed, 21 Jan 2015, Worker, Amanda wrote:
>>>
>>>> Hi Anastasia,
>>>>
>>>> Yes I have done that. My command line was... " bbregister --s
>>>> PDPLUS010 --init-header --dti --mov
>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/dwi.nii.gz
>>>> --reg
>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/anatorig2diff.bbr.dat
>>>> --fslmat
>>>> /home/k1204763/images/PDPLUS_TRACULA/TRACULA_OUTPUT/PDPLUS010/dmri/xfms/diff2anatorig.bbr.mat
>>>> "
>>>>
>>>> Following the instructions printed I can only see a tiny bit of the
>>>> dwi.nii.gz, as attached.
>>>>
>>>> I've also tried substituting --dti for --t1 in the command line and
>>>> that doesn't make much difference.
>>>>
>>>> Do you have any other ideas?
>>>>
>>>> Thanks,
>>>>
>>>> Amanda
>>>>
>>>>
>>>>
>>>>
>>>> ________________________________________
>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia
>>>> Yendiki <ayend...@nmr.mgh.harvard.edu>
>>>> Sent: 15 January 2015 15:36
>>>> To: Freesurfer support list
>>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>>
>>>> Did you follow the instructions and the end of the output of the
>>>> bbregister command? What does that look like? See what I wrote below
>>>> about
>>>> looking for the bbregister command in trac-all.log, running it
>>>> separately
>>>> on one subject after changing that one option and looking at its
>>>> output.
>>>>
>>>> On Wed, 14 Jan 2015, Worker, Amanda wrote:
>>>>
>>>>> Sorry, I misunderstood.
>>>>>
>>>>> I've attached a screenshot of what I can see, it does look like
>>>>> there is probably a different problem now as both the
>>>>> dtifit_FA.nii.gz and aparc+aseg.bbr.nii are completely off centre.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Amanda
>>>>>
>>>>>
>>>>> ________________________________________
>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia
>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu>
>>>>> Sent: 13 January 2015 17:52
>>>>> To: Freesurfer support list
>>>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>>>
>>>>> It's impossible to know unless you actually check the registration.
>>>>> See my
>>>>> previous email below on how to do that.
>>>>>
>>>>> On Tue, 13 Jan 2015, Worker, Amanda wrote:
>>>>>
>>>>>> I have edited the trac-preproc script to "--init-header" instead
>>>>>> of "--init-fsl" - hoping that this would fix the registration
>>>>>> problem. Perhaps this hasn't helped?
>>>>>> ________________________________________
>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia
>>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu>
>>>>>> Sent: 12 January 2015 19:58
>>>>>> To: Freesurfer support list
>>>>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>>>>
>>>>>> Have you checked that the registration has been fixed? It looks
>>>>>> like it
>>>>>> might not.
>>>>>>
>>>>>> On Mon, 12 Jan 2015, Worker, Amanda wrote:
>>>>>>
>>>>>>> Yes of course. Please find attached.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> Amanda
>>>>>>> ________________________________________
>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia
>>>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu>
>>>>>>> Sent: 12 January 2015 16:39
>>>>>>> To: Freesurfer support list
>>>>>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>>>>>
>>>>>>> Can you please attach the entire trac-all.log file? It's hard to
>>>>>>> tell just
>>>>>>> from the last few lines, the initial error may have happened much
>>>>>>> earlier.
>>>>>>>
>>>>>>> On Mon, 12 Jan 2015, Worker, Amanda wrote:
>>>>>>>
>>>>>>>> Hi Anastasia,
>>>>>>>>
>>>>>>>> Thank you for your response. I have made the changes that you
>>>>>>>> recommended and attempted to run trac-all -prep on one of the
>>>>>>>> subjects with errors. I am now getting the following error:
>>>>>>>>
>>>>>>>> Writing output files to
>>>>>>>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_*
>>>>>>>> Writing spline volumes to
>>>>>>>> /home/k1204763/images/bbreg_TRAC/TRACULA_OUTPUT/PDPLUS010/dlabel/mni/lh.cst_AS_avg33_mni_bbr_cpts_6.nii.gz
>>>>>>>> Segmentation fault
>>>>>>>>
>>>>>>>> trac-preproc-edit exited with ERRORS at Fri Jan
>>>>>>>>
>>>>>>>>
>>>>>>>> Do you have any idea what the problem could be now?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> Amanda
>>>>>>>>
>>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>>>>> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Anastasia
>>>>>>>> Yendiki [ayend...@nmr.mgh.harvard.edu]
>>>>>>>> Sent: 07 January 2015 17:11
>>>>>>>> To: Freesurfer support list
>>>>>>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>>>>>>
>>>>>>>> Hi Amanda - See attached screenshot of your data, there is a gross
>>>>>>>> misregistration (~45 degree angle rotation) between the
>>>>>>>> diffusion and
>>>>>>>> anatomical. You can check if this is the case for the rest of
>>>>>>>> your bad
>>>>>>>> cases by superimposing the FA map (dmri/dtifit_FA.nii.gz) and
>>>>>>>> anatomical
>>>>>>>> segmentation mapped to diffusion space
>>>>>>>> (dlabel/diff/aparc+aseg.bbr.nii).
>>>>>>>>
>>>>>>>> According to bbregister czar Doug, a big error like this in
>>>>>>>> bbregister
>>>>>>>> happens when the initialization of the registration fails. If the
>>>>>>>> diffusion and T1 were acquired in the same session, you can try
>>>>>>>> initializing the registration from the headers of the images, by
>>>>>>>> running
>>>>>>>> bbregister with "--init-header" instead of "--init-fsl".
>>>>>>>>
>>>>>>>> You can try it on one of your subjects first. Search for the
>>>>>>>> bbregister
>>>>>>>> command line in trac-all.log of this subject and rerun
>>>>>>>> bbregister with the
>>>>>>>> changed option. Follow the instructions that bbregister prints
>>>>>>>> out when
>>>>>>>> it's done to check the registration.
>>>>>>>>
>>>>>>>> To change how tracula does this, you'll have to edit the script
>>>>>>>> $FREESURFER_HOME/bin/trac-preproc
>>>>>>>> Search for "bbregister" and edit the --init-fsl option. Then rerun
>>>>>>>> trac-all for the subjects that had this problem. You can skip
>>>>>>>> the first 2
>>>>>>>> steps of the preprocessing, i.e., do trac-all -prep -nocorr -noqa.
>>>>>>>>
>>>>>>>> Hope this helps,
>>>>>>>> a.y
>>>>>>>>
>>>>>>>> PS: Yes, when you send something with filedrop that I should
>>>>>>>> look at, give
>>>>>>>> my email address as the recipient.
>>>>>>>>
>>>>>>>>
>>>>>>>> On Wed, 7 Jan 2015, Worker, Amanda wrote:
>>>>>>>>
>>>>>>>>> Hi Anastasia,
>>>>>>>>>
>>>>>>>>> Thanks for your response. I have sent over a zip file via the
>>>>>>>>> filedrop
>>>>>>>>> portal, it seemed to fail each time I tried to send it to
>>>>>>>>> freesurfer@nmr.mgh.harvard.edu so I've sent it over to your email
>>>>>>>>> address - hopefully you have received this.
>>>>>>>>>
>>>>>>>>> I've had a look at the segmentations and they look ok, so I
>>>>>>>>> think there
>>>>>>>>> may be an issue with registrating between the T1 and diffusion.
>>>>>>>>> Anyway I
>>>>>>>>> have sent an example over, hopefully this will give you some
>>>>>>>>> idea of
>>>>>>>>> what has gone wrong.
>>>>>>>>>
>>>>>>>>> Thanks,
>>>>>>>>>
>>>>>>>>> Amanda
>>>>>>>>>
>>>>>>>>> ________________________________________
>>>>>>>>> From: freesurfer-boun...@nmr.mgh.harvard.edu
>>>>>>>>> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia
>>>>>>>>> Yendiki <ayend...@nmr.mgh.harvard.edu>
>>>>>>>>> Sent: 11 December 2014 19:37
>>>>>>>>> To: Freesurfer support list
>>>>>>>>> Subject: Re: [Freesurfer] TRACULA mask error
>>>>>>>>>
>>>>>>>>> Hi Amanda - The final masks used by tracula are derived from the
>>>>>>>>> structural and not the diffusion data, i.e., they are the
>>>>>>>>> whole-brain
>>>>>>>>> FreeSurfer segmentations (from mri/aparc+aseg.mgz) mapped onto
>>>>>>>>> diffusion
>>>>>>>>> space and dilated slightly. It may be that there was something
>>>>>>>>> wrong with
>>>>>>>>> the FreeSurfer reconstructions of those subjects (if, for
>>>>>>>>> example, the T1
>>>>>>>>> contrast was poorer in part of the brain and the part was not
>>>>>>>>> included in
>>>>>>>>> the brain mask), or that there was misregistration between the
>>>>>>>>> T1 and
>>>>>>>>> diffusion. You can troubleshoot this by looking at the
>>>>>>>>> aparc+aseg in
>>>>>>>>> diffusion space (from the dlabel/diff directory, over the FA
>>>>>>>>> map (from the
>>>>>>>>> dmri directory).
>>>>>>>>>
>>>>>>>>> If you still have trouble deciding what went wrong, you can
>>>>>>>>> upload a zip
>>>>>>>>> file for me with all the directories created by trac-all (dmri,
>>>>>>>>> dlabel,
>>>>>>>>> etc) for one of these subjects, here:
>>>>>>>>> https://gate.nmr.mgh.harvard.edu/filedrop2/
>>>>>>>>>
>>>>>>>>> Best,
>>>>>>>>> a.y
>>>>>>>>>
>>>>>>>>> On Thu, 27 Nov 2014, Worker, Amanda wrote:
>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Dear All,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> I have run all of the pre-processing steps on my DTI data and
>>>>>>>>>> as I am
>>>>>>>>>> checking my nodif_brain_mask I have realised that some of the
>>>>>>>>>> masks have
>>>>>>>>>> become distorted and twisted in some way. I have attached
>>>>>>>>>> screenshots of
>>>>>>>>>> both the raw data (which looks fine) and the white mask (which is
>>>>>>>>>> distorted). In addition, as I have read that it is important
>>>>>>>>>> to check the
>>>>>>>>>> dtifit_V1 and dtifit_FA I have also included these in the word
>>>>>>>>>> document,
>>>>>>>>>> incase this helps.
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> This distortion has occured for approximately a quarter of the
>>>>>>>>>> subjects that
>>>>>>>>>> I have processed and the rest look good. Please can you let me
>>>>>>>>>> know if you
>>>>>>>>>> have any ideas about what has gone wrong and how to fix this?
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Thanks in advance for your help,
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> Amanda
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>> _______________________________________________
>>>>>> 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
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> 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
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>
>>
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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