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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
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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 CautionYes, 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 CautionYes, 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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