External Email - Use Caution
I am trying to compare MWI(sampled on the surface) between couple patients and
controls using group analysis, therefore i need to have all inflated
surface_on_same space (according to the wiki of group analysis you sent me, i
should use mris_preproc to put my data on fsaverage).
Could you now tell me whether my mris_prepoc is right? and one other question i
have asked in last email?
Thanks a lot,
Reza
________________________________
From: Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>
Sent: Wednesday, July 17, 2019 4:14:41 PM
To: Reza Rahmanzadeh; Freesurfer support list; gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] need for help
It is not clear to me what you are trying to do. Do you want to do a
morphometry study (ie, comparing thickness, area, and/or volume across
subjects)? Or do you want to compare MWI (sampled on the surface) across
subjects?
On 7/17/19 10:09 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear Doug,
I took the back slash away and ran
mris_preproc --target fsaverage --hemi lh --s FSP010 --out lh.FSP10.white.mgh
--meas white
but i got error:
Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white
MRISreadBinaryCurvature: incompatible vertex number in file
/usr/local/freesurfer/subjects/FSP010/surf/lh.white
ERROR: reading curvature file
Then i changed it to --meas : mris_preproc --target fsaverage --hemi lh --s
FSP010 --out lh.FSP10.white.mgz --meas area
Then, as i need to register my the inflated cortex of myelin water image (MWI)
to the surface_registered_on_fsaverage (could it be the output of command-line
above?), should i use this output "lh.FSP10.white.mgz" and the output of
mri_vol2surf (resampling myelin water image to lh.white of my subject FSP10
before registration to fsaverage) for mri_surf2surf (to resample the latter to
the former, to have MWI to surface_fsaverage)
Looking forward to answers
Thanks
Reza
________________________________
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Reza Rahmanzadeh
<reza.rahmanza...@unibas.ch><mailto:reza.rahmanza...@unibas.ch>
Sent: Wednesday, July 17, 2019 9:56:00 AM
To: Freesurfer support list
Cc: dgr...@mgh.harvard.edu<mailto:dgr...@mgh.harvard.edu>
Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Thanks Tim,
Then if i would resample my data to fsaverage and surfaces are of main
importance to my work, what should i use for -meas ?
Reza
> On 17 Jul 2019, at 09:39, Tim Schäfer <ts...@rcmd.org><mailto:ts...@rcmd.org>
> wrote:
>
> External Email - Use Caution
>
> I guess '-meas' expects a measure (like 'thickness' or 'area'), not a surface
> (like 'white').
>
> Best,
>
> Tim
>
>> On July 17, 2019 at 9:03 AM Reza Rahmanzadeh
>> <reza.rahmanza...@unibas.ch><mailto:reza.rahmanza...@unibas.ch> wrote:
>>
>>
>> External Email - Use Caution
>>
>> I removed the back slash and the command line i executed is:
>>
>>
>> mris_preproc --target fsaverage --hemi lh --s FSP010 --out
>> lh.FSP10.white.mgh --meas white
>>
>>
>> but i got the error:
>>
>> Reading curvature file /usr/local/freesurfer/subjects/FSP010/surf/lh.white
>> MRISreadBinaryCurvature: incompatible vertex number in file
>> /usr/local/freesurfer/subjects/FSP010/surf/lh.white
>> ERROR: reading curvature file
>>
>> I have added --srcfmt mgh as the last argument, but again i got the error:
>> Reading source surface reg
>> /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg
>> Loading source data
>> No such file or directory
>> ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as
>> type 3
>>
>>
>> What is wrong with my mris_prepoc command line?
>>
>> Reza
>>
>>
>> ________________________________
>> From: Greve, Douglas N.,Ph.D.
>> <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
>> Sent: Tuesday, July 16, 2019 10:01:15 PM
>> To: Reza Rahmanzadeh; Freesurfer support list;
>> gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
>> Subject: Re: need for help
>>
>> don't include the back slash (ie, fsaverage not fsaverage/ same for FSP010)
>>
>>> On 7/16/19 3:07 PM, Reza Rahmanzadeh wrote:
>>>
>>> External Email - Use Caution
>>>
>>> Thanks a lot Doug,
>>>
>>>
>>> I started to proceed with FS group analysis wiki you sent to me.
>>> Accordingly, i have to resample all my data (output of recon-all for a
>>> given subject for example) into fsaverage using mris_preproc. My
>>> commandline for a subject was:
>>>
>>> mris_preproc --target fsaverage/ --hemi lh --s FSP010/ --out
>>> lh.FSP10.white.mgh --meas white
>>>
>>>
>>> and i got the error:
>>>
>>> *
>>> *
>>> *Reading source surface reg
>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory
>>> mri_surf2surf: could not read surface
>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.fsaverage/.sphere.reg
>>> No such file or directory*
>>> *
>>> *
>>> As there was no**lh.fsaverage/.sphere.reg* *folder, i found one file
>>> in fsaverage/surf: lh.fsaverage_sym.sphere.reg. i created a folder
>>> with the name lh.fsaverage and i copied/pasted the mentiomed file into
>>> this folder and i changed the file name to: ./sphere.reg. I got the
>>> error:
>>> *
>>> *
>>> *Reading curvature file
>>> /usr/local/freesurfer/subjects/FSP010//surf/lh.sphere
>>> MRISreadBinaryCurvature: incompatible vertex number in file
>>> /usr/local/freesurfer/subjects/FSP025//surf/lh.sphere*
>>> *
>>> *
>>> *
>>> *
>>> What is the problem with my mris_preproc command-line?
>>>
>>> Reza
>>>
>>> ------------------------------------------------------------------------
>>> *From:*
>>> freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>> <freesurfer-boun...@nmr.mgh.harvard.edu><mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
>>> on behalf of Greve, Douglas
>>> N.,Ph.D. <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
>>> *Sent:* Tuesday, July 16, 2019 7:01:30 PM
>>> *To:* Reza Rahmanzadeh;
>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> *Subject:* Re: [Freesurfer] need for help
>>>
>>>
>>>> On 7/16/19 12:57 PM, Reza Rahmanzadeh wrote:
>>>>
>>>> External Email - Use Caution
>>>>
>>>> (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.
>>>>
>>> QDEC is no longer being supported. Use the command line stream
>>> (mri_surf2surf, mri_glmfit, mri_glmfit-sim).
>>> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis
>>>>
>>>>
>>>> 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?
>>>>
>>> Run mri_vol2surf with --help and look for --projfrac-avg
>>>>
>>>>
>>>> thanks a lot,
>>>>
>>>> Reza
>>>>
>>>>
>>>> ------------------------------------------------------------------------
>>>> *From:* Greve, Douglas N.,Ph.D.
>>>> <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
>>>> *Sent:* Tuesday, July 16, 2019 6:22:56 PM
>>>> *To:* Reza Rahmanzadeh;
>>>> freesurfer@nmr.mgh.harvard.edu<mailto: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.
>>>>> <dgr...@mgh.harvard.edu><mailto:dgr...@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.
>>>>>> <dgr...@mgh.harvard.edu><mailto:dgr...@mgh.harvard.edu>
>>>>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM
>>>>>> *To:* Reza Rahmanzadeh;
>>>>>> Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> *Cc:* gr...@nmr.mgh.harvard.edu<mailto:gr...@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
>>>>>>>
>>>>>>
>>>>>> 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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>>
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>
> --
> Dr. Tim Schäfer
> Postdoc Computational Neuroimaging
> Department of Child and Adolescent Psychiatry, Psychosomatics and
> Psychotherapy
> University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany
>
> _______________________________________________
> Freesurfer mailing list
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