External Email - Use Caution
Thanks Doug,
The script works well for projfrac-avg. but the problem is: when i use mris_preproc to assemble my MWIs and put them on fsaverage, as .fsgd file is only the order of my controls and subjects and i would have the inflated cortex of MWI on fsaverage, then anyway i have to specify my volume and registration files (tkregister2 output). Then there’s an error: i shouldn’t use both -fsgd and - iv together. Then i decided not to use fsgd file for mris_preproc and only using that for mri_glmfit. In mris_preproc, i write all “-iv volumes and registration files” in the same order as in fsgd file but i don’t write -fsgd argument. Is this way correct?
Thanks, Reza
On 29 Jul 2019, at 23:32, Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
Oh, I guess that's a problem! I've created a new version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc See if that works. You should compare the output to using the max or -projfrac 0.5 to make sure they are at least similar since I have not run it even once:)
On 7/29/19 5:08 PM, Reza Rahmanzadeh wrote:
External Email - Use CautionThanks
But mris_prepoc will not accept “projfrac-avg” and there’s an error: argument unrecognized!
Then how can i compute the average via mris_preproc? As based on tutorial, first i used tkregister/bbregister to compute the registration matrix and then i should put input images with transformation matrix in mris_preproc. I mean i shouldn’t use mri_vol2surf (that allows me to use projfrac-avg) in group analysis and that’s the reason i have problem with mris_proproc to compute the average.
What should i do?
Thanks, Reza
On 29 Jul 2019, at 23:03, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use CautionDear Doug,
I appreciat if you reply my question in the previous e-mail with this:
can not i use projfrac-avg in mris_preproc? Is --projfrac-max min max delta just the same?
Best,
Reza
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Monday, July 29, 2019 11:37:46 AM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionDear Doug,
Thanks, the tutorial was super helpful. As i would compare the MWF value in cortex between control subjects and patients. Now my problem is how to make the contrast matrix for mris_preproc to do the comparison in both direction (in 1, the outcome should be voxels in which MWf value in control>patients & in 2, reversed).
The explanations in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
is for one group analysis and in https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis is not clear about contrast.
I remember for -randomise command-line, there was possibility to make contrast and design matrix (something like FSGD) via design_ttest2. Can i use still design_ttest2 for producing contrast and design matrix?
Best,
Reza
*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> *Sent:* Wednesday, July 17, 2019 5:31:27 PM *To:* Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help Ah, I see. Try this tutorial. It is for fMRI, but it applies to any modality https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriGroup_fre...
On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:
External Email - Use Cautionto clarify better, i need to compare myelin water fraction in cortex of control and patients to find out the areas with reduced MWF in patients cortex compared with controls, that is the reason i want to have cortex in inflated format.
For this reason i used bbregister to have register.dat, and then mri_vol2surf to resample MWI cortex to surface. As i need to have all surfaces in fsaverage space for group analysis, i am using mri_preproc7mri_surf2surf (according to the group analysis wiki you sent me).
*From:* freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza Rahmanzadeh
<reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch> *Sent:* Wednesday, July 17, 2019 4:26:21 PM *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] need for help
External Email - Use CautionI 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. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
*Sent:* Wednesday, July 17, 2019 4:14:41 PM *To:* Reza Rahmanzadeh; Freesurfer support list;
greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@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 CautionDear 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza
Rahmanzadeh <reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch
mailto:reza.rahmanzadeh@unibas.ch>
*Sent:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@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+ml@rcmd.org > mailto:ts+ml@rcmd.org
mailto:ts+ml@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.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@unibas.ch mailto:reza.rahmanzadeh@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. <DGREVE@mgh.harvard.edu >> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@mgh.harvard.edu>
>> Sent: Tuesday, July 16, 2019 10:01:15 PM >> To: Reza Rahmanzadeh; Freesurfer support list; greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu mailto:greve@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-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu
>>> <freesurfer-bounces@nmr.mgh.harvard.edu >>> mailto:freesurfer-bounces@nmr.mgh.harvard.edu
mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas
>>> N.,Ph.D. <DGREVE@mgh.harvard.edu >>> mailto:DGREVE@mgh.harvard.edu mailto:DGREVE@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
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. <DGREVE@mgh.harvard.edu >>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@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
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. <DGREVE@mgh.harvard.edu >>>>> mailto:DGREVE@mgh.harvard.edu
mailto: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 >>>>>> mailto:DGREVE@mgh.harvard.edu
mailto:DGREVE@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
mailto:Freesurfer@nmr.mgh.harvard.edu
>>>>>> *Cc:* greve@nmr.mgh.harvard.edu >>>>>> mailto:greve@nmr.mgh.harvard.edu
mailto: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 >>>>>>> >>>>>> >>>>>> 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 >>> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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 > Freesurfer@nmr.mgh.harvard.edu > mailto:Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer