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(I assume now we are discussing in FS list, if no please let me how possible?)


Thanks Doug, now i could see the inflate surface, this means that my mri_vol2surf works well. As i would do GLM  analysis over inflated cortex of patients and controls in Qdec,


1- should i input my surfaces to Qdec as inflated surface or just inputting the output_of_vol2surf.mgz to Qdec?

if inflated one is the input, then how could i get them? mris_inflate gives error.


2- should i input all patients and controls surfaces in standard surface before entering to Qdec?


3- I would like to resample whole cortex (whole cortical thickness, in other words: the average of all projfrac between 0 and 1), is it possible? or i am limited to resample one given depth of cortex into inflated surface only?


thanks a lot,

Reza


From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
Sent: Tuesday, July 16, 2019 6:22:56 PM
To: Reza Rahmanzadeh; freesurfer@nmr.mgh.harvard.edu
Subject: Re: need for help
 
The command should be something like
tksurfer mysubject lh inflated -overlay output_of_vol2surf.mgz
Also, tksurfer is also obsolete (but should work). You should be using
freeview (or tksurferfv, a freeview front end that takes the same
command line args as tksurfer)
Also, please remember to respond to the fs list

On 7/16/19 12:12 PM, Reza Rahmanzadeh wrote:
>
>         External Email - Use Caution
>
> I got the mri_vol2surf output with .mgz:
>
>
> my tksurfer command:
>
> tksurfer FSP010/ (my subject) lh inflated_MWI.mgz (output of
> mri_vol2surf was lh.inflated_MWI.mgz)
>
>
> and the error i got:
>
> *freadFloat: fread failed**
> No such file or directory*
>
> To me, opening the surfer in tksurfer is only a way to get sure my
> vol2surf worked well. the main problem is i got this error for all
> mris_smooth, mris_inflate, mris_sphere ...
>
>
> Do you think that means the output of mri_vol2surf is not correct, or
> otherwise i could proceed with that , even when tksurfer could not
> open it, for GLM in Qdec?
>
>
> Thanks,
>
> Reza
>
> ------------------------------------------------------------------------
> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
> *Sent:* Tuesday, July 16, 2019 6:01:15 PM
> *To:* Reza Rahmanzadeh
> *Subject:* Re: need for help
> what is your tksurfer command line? Also, the .w file is somewhat
> obsolete (it should still work); instead you can use .mgz file (and
> don't spec --paint)
>
> On 7/16/2019 11:53 AM, Reza Rahmanzadeh wrote:
>>
>>         External Email - Use Caution
>>
>> Thanks Doug,
>>
>>
>> I used the one without --inflated also, again the tksurfer could not
>> open it and i got the same error. Where is the problem with my cmd.?
>>
>>
>> In addition, i wanted to make the output of mri_vol2surf inflated
>> using mris_inflate but i got the same error:
>>
>> *freadFloat: fread failed
>> No such file or directory*
>> *
>> *
>> *could you let me know what is the problem in registering my mwi
>> volumes to surface that i getonly such errors.*
>> *
>> *
>> *Thanks,*
>> *reza
>> *
>>
>> ------------------------------------------------------------------------
>> *From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM
>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu
>> *Cc:* greve@nmr.mgh.harvard.edu
>> *Subject:* Re: need for help
>> Don't use --inflated. The inflated surface is not a biological
>> surface. The default is the white surface, which is the one you want
>> (--projfrac 0.5 will project it to the middle between the white and pial)
>>
>> On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote:
>>>
>>>         External Email - Use Caution
>>>
>>> Dear Freesurfer,
>>>
>>> I have a batch of myelin water image (MWI) from patients and
>>> controls, and trying to have inflated cortex registered on standard
>>> surface for GLM (Qdec).
>>>
>>> With the commandlines below i get my inflated surface of MWI map of
>>> my patients and controls.
>>>
>>> 1-using bbregister to put MWI into FS space and to calculate
>>> register.dat:
>>> bbregister --s FSP042/ --mov mwf.nii --init-fsl --reg register.dat
>>> --o mwf_FS --t1
>>>
>>> 2-using mri_vol2surf to extract inflated surface of MWI:
>>> mri_vol2surf --mov mwf.nii --reg register.dat --projfrac 0.5
>>> --interp nearest --hemi lh --o lh.inflated_MWI.w --out_type
>>> paint--inflated (*or*--surf sphere)
>>>
>>> However the tksurfer could not open the inflated surface and the
>>> error message is:
>>> *ERROR: MRISread: file 'inflated.lh.mwf.mgh' has 0 vertices!
>>> Probably trying to use a scalar data file as a surface!*
>>>
>>> I used the commandline below for #2:
>>> mri_vol2surf --src mwf.nii --srcreg register.dat --hemi lh --o
>>> mwf-lh.w --out_type paint
>>> and i got the error:
>>>
>>> *ERROR: MRISread: file
>>> '/usr/local/freesurfer/subjects/FSP010//surf/lh.mwf-lh.w' has many
>>> more faces than vertices!**
>>> Probably trying to use a scalar data file as a surface!*
>>> *
>>> *
>>> As tksurfer could not open my surfaces with errors above, i think
>>> perhaps the vol2surf procedure is not done properly. Where is the
>>> problem? i need to get the inflated cortex and then putting ob
>>> sphere (using mris_sphere) and the registering to standard surface
>>> using mris_register for GLM in Qdec, right?
>>>
>>>
>>> It is two weeks i am struggling with these commands, any helps
>>> highly appreciated. *
>>> *
>>> *
>>> *
>>> *
>>> *
>>> Best,
>>> Reza
>>>
>>
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