.
What is your idea? If so, what should i do?
Best,
Reza
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Reza Rahmanzadeh
Sent: Thursday, August 8, 2019 1:35:20 PM
To: Greve, Douglas N.,Ph.D.
Cc: Freesurfer support list
Subject: Re: [Freesurfer
From: Greve, Douglas N.,Ph.D.
Sent: Wednesday, August 7, 2019 6:03:58 PM
To: Reza Rahmanzadeh
Cc: Freesurfer support list
Subject: Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for
help
Run mris_preproc with a single subject and send the terminal output
On 8/7/19 11:47 AM
e out as non-zero? If
> so, I would think that it is a problem with the registration. Have you
> checked the registrations?
>
>> On 8/7/19 11:25 AM, Reza Rahmanzadeh wrote:
>> External Email - Use Caution
>>
>> It means that for any given subjects i’ve had
External Email - Use Caution
It means that for any given subjects i’ve had one -iv argument and then for
mri_glmfit i used .fsgd file with the same order.
> On 7 Aug 2019, at 17:23, Reza Rahmanzadeh wrote:
>
>External Email - Use Caution
>
External Email - Use Caution
Yes, for mris_preproc:
mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out
lh.NDI_inflated.avg.mgh --iv
> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh wrote:
>
> mris_preproc --target fsaverage --hemi lh --projfrac-avg
From: Greve, Douglas N.,Ph.D.
Sent: Tuesday, August 6, 2019 6:40:28 PM
To: Reza Rahmanzadeh; Freesurfer support list
Cc: gr...@nmr.mgh.harvard.edu
Subject: Re: [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: [Freesurfer] need for
help
Sorry, that should be
ftp
:50:45 AM
To: Reza Rahmanzadeh; Freesurfer support list
Cc: gr...@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
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: gr...@nmr.mgh.harvard.edu
Subject: Re
of order)?
Thanks,
Reza
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Reza Rahmanzadeh
Sent: Tuesday, July 30, 2019 2:44:25 PM
To: Greve, Douglas N.,Ph.D.
Cc: Freesurfer support list; gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] need for
/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 wrot
...@nmr.mgh.harvard.edu
on behalf of Reza Rahmanzadeh
Sent: Monday, July 29, 2019 11:37:46 AM
To: Greve, Douglas N.,Ph.D.; Freesurfer support list; gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] need for help
External Email - Use Caution
Dear Doug,
Thanks, the tutorial was super
: Greve, Douglas N.,Ph.D.
mailto:dgr...@mgh.harvard.edu>>
Sent: Wednesday, July 17, 2019 5:31:27 PM
To: Reza Rahmanzadeh; Freesurfer support list;
gr...@nmr.mgh.harvard.edu<mailto:gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] need for help
Ah, I see. Try this tutorial. It is for f
: Greve, Douglas N.,Ph.D.
Sent: Wednesday, July 17, 2019 5:31:27 PM
To: Reza Rahmanzadeh; Freesurfer support list; gr...@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
).
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Reza Rahmanzadeh
Sent: Wednesday, July 17, 2019 4:26:21 PM
To: Greve, Douglas N.,Ph.D.; Freesurfer support list; gr...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] need for help
External Email - Use Caution
I am trying to compare
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.
Sent: Wednesday, July 17, 2019 4:14:41 PM
To: Reza Rahmanzadeh
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
on behalf of Reza Rahmanzadeh
Sent: Wednesday, July 17, 2019 9:5
>
> 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
>> wrote:
>>
>>
>>
To: Reza Rahmanzadeh; Freesurfer support list; 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
command-line?
Reza
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Greve, Douglas N.,Ph.D.
Sent: Tuesday, July 16, 2019 7:01:30 PM
To: Reza Rahmanzadeh; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] need for help
On 7/16/19 12:57 PM, Reza
From: Greve, Douglas N.,Ph.D.
Sent: Tuesday, July 16, 2019 6:22:56 PM
To: Reza Rahmanzadeh; 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
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
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