no idea until you tell me what you did, including command lines and
terminal output

On 8/7/19 11:08 AM, Reza Rahmanzadeh wrote:

        External Email - Use Caution

Thanks, I saw that before, what could be the reason for that and how could i do mris_preproc correctly for NDI maps?

Thanks,

Reza

On 7 Aug 2019, at 17:05, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:

Every vertex of every subject is 0 in lh.NDI_inflated.avg.05.mgh

On 8/6/19 6:30 AM, Reza Rahmanzadeh wrote:

        External Email - Use Caution

Hi Doug,

When i click on the link you sent me for uploading the files, there is

no bottom/way to upload something there. That is why i attached the

outputs.

My command lines sequentially for the analysis are: ( I have done just

the same command lines for MWF maps and it worked very good, but for

NDI and ODI maps of NODDI does not work).

1-mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25

--out lh.NDI_inflated.avg.mgh (i used the new mris_preproc you sent me).

2-mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex --sval

lh.NDI_inflated.avg.mgh --tval lh.NDI_inflated.avg.05.mgh

3-mri_glmfit --y lh.NDI_inflated.avg.05.mgh --surf fsaverage lh --C

contrast --fsgd fsgd.fsgd --cortex --glmdir lh.NDI_inflated.avg.05.glmdir

The outputs of all three steps are attached.

Looking forward for your helps

Reza

------------------------------------------------------------------------

*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>

*Sent:* Monday, August 5, 2019 5:55:18 PM

*To:* Reza Rahmanzadeh; Freesurfer support list

*Cc:* greve@nmr.mgh.harvard.edu

*Subject:* Re: [Freesurfer] need for help

Can you upload the input (ie, argument to --y) here:

ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming

Also, send your mri_glmfit command line.

On 8/2/2019 9:41 AM, Reza Rahmanzadeh wrote:

        External Email - Use Caution

yes, I have the page below for all patients.

I think it means all values are zero. My registration for bbregister

is fine and i wrote my mris_preproc the same as MWF maps.

Thanks,

Reza

------------------------------------------------------------------------

*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>

*Sent:* Friday, August 2, 2019 3:35:45 PM

*To:* Reza Rahmanzadeh; Freesurfer support list

*Cc:* greve@nmr.mgh.harvard.edu

*Subject:* Re: [Freesurfer] need for help

did you check each subject to make sure they had a non-zero map?

On 8/2/2019 6:25 AM, Reza Rahmanzadeh wrote:

        External Email - Use Caution

Dear Doug,

NODDI is diffusion imaging and we have vakue regarding neurite

density (NDI in NDI map) and orientation dispersion (ODI value in

ODI map). I do not know why mris_preproc works well on MWI maps but

not on NODDI maps (both NDI and ODI maps). Beside using projfrac-avg

0 1 0.25 , i have run mris_preproc with projfrac 0.5 but again i got

this error:

ERROR: no voxels found in the mask

  make sure at least one voxel has a non-zero value for each input

I have run mris_preproc on three patients that i am sure about

registration quality, again when i scroll through them , there is no

value in none of them. How that is possible?

NODDI does not have a lot of zero value but all values in cortex are

between 0.2-0.4.

Thanks,

Reza

------------------------------------------------------------------------

*From:* Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>

*Sent:* Wednesday, July 31, 2019 12:50:45 AM

*To:* Reza Rahmanzadeh; Freesurfer support list

*Cc:* greve@nmr.mgh.harvard.edu

*Subject:* Re: [Freesurfer] need for help

I don't know what is in the NODDI maps. The way mri_glmfit works is

that

if any subject has a 0-value at a vertex, then it will mask out that

vertex for all subjects. Is NODDI something that might have a lot of

0-values? It also may be that one subject has all 0s (eg, if the

regitration was really bad), so you can check the map created by

mris_preproc (load it in as an overlay, then hit the configure button,

then change the frame number to scroll through your subjects)

On 7/30/19 12:46 PM, Reza Rahmanzadeh wrote:

        External Email - Use Caution

(sorry for bombaeding you with e-mails)

It seems that the error happens only when i use NODDI diffusion image

e.g. NDI map i get that error, but for MWIs the new mris_preproc

works

well.

Should i do anything special for NODDI images? BTW, the bbregister

works well for NODDI and i entered the correct registration file into

mris_preproc.

Thanks,

Reza

------------------------------------------------------------------------

*From:* Reza Rahmanzadeh

*Sent:* Tuesday, July 30, 2019 6:17:22 PM

*To:* Greve, Douglas N.,Ph.D.; Freesurfer support list

*Cc:* greve@nmr.mgh.harvard.edu

*Subject:* Re: [Freesurfer] need for help

... One problem when i use the new mris_preproc:

Always the output of mri_glmfit when the input is the result of new

mris_preproc is:

*F**ound 0 voxels in mask

ERROR: no voxels found in the mask

  make sure at least one voxel has a non-zero value for each input*

*

*

*

*

I think it means that something is perhaps wrong with the script. I

tried both projfrac 0.5 and projfrac-avg 0 1 0.25 and i got the same

error.  I did not get the error when i used old mris_preproc using

projfrac 0.5.*

*

*

*

*The other thing that could be the reason is my fsgd file. I have

problem how to specify the name of subjects,

*

Now it is sth like:

GroupDescriptorFile 1

Class Group1

CLASS Group2

Input FSC001 Group1

Input FSC002 Group1

Input FSC003 Group1

.

.

.

Input FSP001 Group2

Input FSP002 Group2

Input FSP003 Group2

.

.

The oeder is thew same with mris_preproc, now the subject name is

FSC0xx for controls and FSP00x for patients, these are the name of

folders containing FS outputs, but my input volume is MWIs and the

registration files are not stored in this folder. Does it matter how

to name subjects when i am using fsgd file only in mri_glmfit ( to

get

aware of order)?

Thanks,

Reza

------------------------------------------------------------------------

*From:* freesurfer-bounces@nmr.mgh.harvard.edu

<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Reza

Rahmanzadeh

<reza.rahmanzadeh@unibas.ch>

*Sent:* Tuesday, July 30, 2019 2:44:25 PM

*To:* Greve, Douglas N.,Ph.D.

*Cc:* Freesurfer support list; greve@nmr.mgh.harvard.edu

*Subject:* Re: [Freesurfer] need for help

        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 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 <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 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

<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 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>

<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_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>

<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 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>

<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 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>

<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

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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

<http://www.partners.org/complianceline> . If the e-mail was

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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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