External Email - Use Caution        

Thanks 

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> wrote:

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_freeview
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_freeview


On 7/17/19 10:58 AM, Reza Rahmanzadeh wrote:

        External Email - Use Caution

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:

        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-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:

        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>> 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>>
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


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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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