one computes the average, the other computes the maximum
On 7/29/19 9:03 AM, Reza Rahmanzadeh wrote:
External Email - Use Caution
Dear 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 freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Reza Rahmanzadeh 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 *Subject:* Re: [Freesurfer] need for help
External Email - Use Caution
Dear 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> *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 *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:
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to 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
<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:* 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 *Subject:* Re: [Freesurfer] need for help
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. <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
*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:
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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-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:* Wednesday, July 17, 2019 9:56:00 AM *To:* Freesurfer support list *Cc:* 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> wrote:
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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> wrote:
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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>
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
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
<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> *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. <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
> *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>
>> *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>
>>> *Sent:* Tuesday, July 16, 2019 5:37:17 PM >>> *To:* Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu
mailto:Freesurfer@nmr.mgh.harvard.edu
>>> *Cc:* 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. >>> >> >
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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
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