Dear Doug,

I have to come back to you for helps as yet i did not find a solution for Group analysis of inflated cortex for NDI and ODI maps of NODDI. What i know is:

1- when i load the output of mris_preproc (regardless of using the old and new versions or having arguments --projfrac 0.5 or projfracavg 0 1 0.25) in freeview and scroll through my images in Configure, i could not see any value in any subjects. and when i uae this mris_preproc output as the input of mri_glmfit, there will be one error:

ERROR: no voxels found in the mask

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

2- I checked the registration done via bbregister. that looks like perfect for all subjects.

3-I have run mri_vol2surf individually for subjects, again it seems that the output of mri_vol2surf looks like good and the resampled volume has non-zero values.

In the mris_preproc, beside the steps outlined above, we have the registration to fsaverage. As the output of mris_preproc even for one subject does not have non-zero voxels, then i think perhaps the problem is perhaps in the registration of my NDI maps to fsaverage.

What is your idea? If so, what should i do?

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: Thursday, August 8, 2019 1:35:20 PM
To: Greve, Douglas N.,Ph.D.
Cc: Freesurfer support list
Subject: Re: [Freesurfer] [WARNING: UNSCANNABLE EXTRACTION FAILED]Re: need for help

External Email - Use Caution

Dear Doug,

Please find the enclosed the output of mris_preproc and .log output of terminal. I viewed the output in freevew as overlay, and again it seems that values getting 0 after mris_preproc.

Thanks,

Reza

From: Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu>
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, Reza Rahmanzadeh wrote:
>          External Email - Use Caution
>
> Yes, i checked -projfrac 0.5 with old or new mris_preproc but didn’t work. I checked all registration, they are perfect.
>
>> On 7 Aug 2019, at 17:29, Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
>>
>> If you do not specify --projfrac-avg, does it come 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 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 <reza.rahmanzadeh@unibas.ch> wrote:
>>>>
>>>>         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 <my ndi map_for controls and patients> <registration.lta for that subjects>
>>>>
>>>>> On 7 Aug 2019, at 17:14, Reza Rahmanzadeh <reza.rahmanzadeh@unibas.ch> wrote:
>>>>>
>>>>> mris_preproc --target fsaverage --hemi lh --projfrac-avg 0 1 0.25 --out lh.NDI_inflated.avg.mgh
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