There is a registration file that gets created by the longitudinal
processing that can be used with mri_vol2vol. I don't know where the LTA
file is, but maybe Martin can weigh in.


On 05/08/2018 12:31 PM, Abdullah Ishaque wrote:
>
>
> Hi,
>
> I figured that part out: I can't load surfaces as volumes in freeview,
> but rather i need to load them as an overlay to the subject white, or
> pial surfaces.
>
> I have another question for which I can't find an answer to. After
> registering myelin maps to the individual subjects, how do I
> register/transform them into the subjects' longitudinal T1s (obtained
> after the recon-all long command)?
>
> The broad goal that I am trying to achieve is longitudinal myelin
> analysis. Any feedback is appreciated. Thanks!
>
> On Tue, Apr 24, 2018 at 1:30 PM, Abdullah Ishaque
> <aishaque@ualberta.ca <mailto:aishaque@ualberta.ca>> wrote:
>
>     I did: mri_vol2surf --src Myelin_conformed.mgz --out
>     C01_myelin.mgz --regheader C01 --hemi lh --projfrac 0.5
>
>     Now I'm just getting the error "freadFloat: fread failed" a whole
>     bunch of times and the terminal gets stuck. Any suggestions?
>
>     I checked Myelin_conformed.mgz and loaded it with orig.mgz in
>     freeview and they look fine with great overlap and registration
>
>     Thanks!
>
>     On Tue, Apr 24, 2018 at 1:23 PM, Douglas Greve
>     <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>
>         Specify a file format for the output (eg, C01.mgz)
>
>
>         On 4/24/18 3:17 PM, Abdullah Ishaque wrote:
>>
>>
>>         Hi,
>>
>>         Thank you for the prompt response.
>>
>>         I used the following command:
>>
>>         mri_vol2surf --src Myelin_conformed.mgz (T1/T2 image after
>>         mri_vol2vol from the previous step) --out C01 --regheader C01
>>         --hemi lh --projfrac 0.5
>>
>>         This created two files called COR-.info and COR001. I tried
>>         loaded the COR001 file into freeview and tksurfer, but I keep
>>         the error "MRISalloc(8229512, 76): could allocated faces \
>>         cannot allocate memory
>>
>>         Am I making a mistake somewhere?
>>
>>         Thanks,
>>
>>         On Tue, Apr 24, 2018 at 11:34 AM, Douglas Greve
>>         <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>>
>>             That all looks correct. For the registration, just use
>>             --regheader C01
>>
>>
>>             On 4/24/18 11:12 AM, Abdullah Ishaque wrote:
>>>
>>>
>>>             Hi,
>>>
>>>             It's my first time using FreeSurfer and I'd like some
>>>             guidance regarding some of my steps.
>>>
>>>             I'm attempting to perform myelin mapping as outlined in
>>>             the paper by Righart (2017) Ann Neurol. Overall, I want
>>>             to calculate myelin maps from each subject, sample them
>>>             from the mid-cortical level to create cortical myelin
>>>             surface maps, and perform vertexwise and ROI based analyses.
>>>
>>>             Here's what I've done so far:
>>>
>>>             1. recon-all for all the subjects
>>>             2. Used bbregister to register the native T2 scans to
>>>             the conformed T1 scans using this command: bbregister
>>>             --s C01 --mov C01_T2.nii --init-fsl --reg register.dat
>>>             --t2 (my understanding here is that this generates the
>>>             .dat file that has the transformation to register the T2
>>>             image to the conformed orig.mgz file from subject C01)
>>>             3. Applied the register.dat file to the native T2 using
>>>             mri_vol2vol --mov C01_T2.nii --o T2_conformed.mgz
>>>             --fstarg --reg register.dat (this registers the T2 to
>>>             the orig.mgz file in the conformed space)
>>>
>>>             The next step for me is to perform mri_vol2surf. My
>>>             question here is, which file should I select for the
>>>             --srcreg flag and what should the --trgsubject input be?
>>>             Secondly, am I on the right track to complete the
>>>             analysis i.e., correct file types and my understanding
>>>             of the steps? Clarifications regarding these questions
>>>             and any suggestions for further directions will be very
>>>             helpful!
>>>
>>>             Let me know. Thanks!
>>>
>>>
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>>>             <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>>
>>
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>>
>>         --
>>         *Abdullah Ishaque, BSc.*
>>         MD/PhD Student, Neuroscience and Mental Health Institute
>>         Faculty of Medicine and Dentistry, University of Alberta
>>         aishaque@ualberta.ca <mailto:aishaque@ualberta.ca>
>>
>>
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>     --
>     *Abdullah Ishaque, BSc.*
>     MD/PhD Student, Neuroscience and Mental Health Institute
>     Faculty of Medicine and Dentistry, University of Alberta
>     aishaque@ualberta.ca <mailto:aishaque@ualberta.ca>
>
>
>
>
> --
> *Abdullah Ishaque, BSc.*
> MD/PhD Student, Neuroscience and Mental Health Institute
> Faculty of Medicine and Dentistry, University of Alberta
> aishaque@ualberta.ca <mailto:aishaque@ualberta.ca>
>
>
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