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I have rerun xtract. This time xtract_stats gives me the same previous error but in this case it makes total sense. Every tract is empty. So waytotal or sumwaytotal is always 0. I don't knkow if I am doing something wrong but I called xtract this way this time

xtract -bpx 25633.bedpostX -out 25633.xtract -species HUMAN -gpu -stdwarp '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx_xtract/25633.bedpostX/xfms/std2diff.nii.gz' '/media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx_xtract/25633.bedpostX/xfms/diff2std.nii.gz'

where warps are from convertwarp from mat files as I mentioned earlier.

Is there somethig I am missing ? Is it normal to have no tract. Like all the folders and the files are in it but is like everything is empty somehow.

Best,

RA.

De: FSL - FMRIB's Software Library <[log in to unmask]> en nombre de Andrade Rey René <[log in to unmask]>
Enviado: martes, 13 de diciembre de 2022 13:00
Para: [log in to unmask] <[log in to unmask]>
Asunto: Re: [FSL] xtract_stats ERROR empty mask image

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.

Oh so sorry I thought it was only for other parts of xtract and not for all of them. I will re do this step and get back to you.

On 13 Dec 2022, at 12:22, Shaun Warrington <[log in to unmask]> wrote:

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.
Nope, as Saad previously said:

“

Xtract does not accept FLIRT matrices as diff2standard or standard2diff warps. You would need to convert them to warp fields. You can do that using convertwarp. For example:

> convertwarp -m diff2std.mat -o diff2std.nii.gz -r <standard space volume>
> convertwarp -m std2diff.mat -o std2diff.nii.gz -r <diffusion space volume>

"
On 13 Dec 2022, at 10:05, Andrade Rey René <[log in to unmask]> wrote:
Just to make sure I called xtract this way

xtract -bpx 25633.bedpostX -out 25633.xtract -species HUMAN -gpu -stdwarp 25633.bedpostx/xfms/standard2diff.mat 25633.bedpostx/xfms/diff2standard.mat

Is it correct?

In the case of the mat files I obtained them via the GUI with FDT DIffusion > Registration > 12 DOF bedpostx directory etc.

In case all the previous is ok I will send screenshots of some tracts.

Best,

RA.

De: FSL - FMRIB's Software Library <[log in to unmask]> en nombre de Shaun Warrington <[log in to unmask]>
Enviado: martes, 13 de diciembre de 2022 10:23
Para: [log in to unmask] <[log in to unmask]>
Asunto: Re: [FSL] xtract_stats ERROR empty mask image
ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.
Screenshots of some tracts.

Registration: transform a subject FA map to standard space and check alignment.

-----------------------------------------------------------
Shaun Warrington
Research Fellow

Division of Clinical Neuroscience, School of Medicine
University of Nottingham

w: https://swarrington1.github.io/
-----------------------------------------------------------
On 12 Dec 2022, at 10:05, Andrade Rey René <[log in to unmask]> wrote:
I can send screenshots. Let me know if there is something specific to be shown.

About quality of data I can say dwi is of 30 gradient directions. 3T.

Bad registration? How can I check for that? Is it the warp images?

If xtract failed which should be highly unlikely as it should be thorough for every subject and therefore should give the exact error for every one of them. As all of them fail in the same manner.

I wonder two things. Warp images or data quality and lastly perhaps xtract failure.

Best,
RA.

On 12 Dec 2022, at 10:31, Shaun Warrington <[log in to unmask]> wrote:
ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.
Hi,

Your results won’t exactly like the example - that’s the average across 1000 HCP (high-resolution) subjects with spline interpolation.

However, the shape of the tracts should resemble what is exampled.

Missing tracts (sounds like MCP is missing) suggests either poor quality data, bad registrations, or xtract failed.

You need to visually check the tracts more closely and send a couple of screenshots.

Thanks,

Shaun.
-----------------------------------------------------------
Shaun Warrington
Research Fellow

Division of Clinical Neuroscience, School of Medicine
University of Nottingham

w: https://swarrington1.github.io/
-----------------------------------------------------------
On 11 Dec 2022, at 19:49, Andrade Rey René <[log in to unmask]> wrote:
I insist as I have not received any answer yet. Sorry for my insistence.
On 8 Dec 2022, at 09:53, Andrade Rey René <[log in to unmask]> wrote:
See answers interspersed below.

On 7 Dec 2022, at 15:23, Shaun Warrington <[log in to unmask]> wrote:

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.

Hi Andrade,

Hi Shaun Warrington.

Your command call looks OK to me.

Ok thanks for that part.

Just to confirm, is dwi_den_preproc_FA.nii.gz in the native diffusion space?

Yes it is. It is the dti_FA output of dtifit.

I remember you previously had some issues with the warp fields. Is this with correct warp fields now?

I guess so. These are the warp fields I was recommended.

You should visually check the quality of the tracts. Empty mask images most likely arise due to xtract failing to reconstruct the tract, potentially due to registration issues.

I was able to open xtract_viewer but I’m not sure if what I am seeing is correct or there is any problem with tract reconstruction. It doesn’t look like the example showned in your tutorial of xtract here https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT#XTRACT_-_a_command-line_tool_for_automated_tractography. It seems less smoothed and more filled with squares, like voxels missing in certain tracts. For example I couldn’t see MCP. May be I’m overstating facts but It might be better if you guide me somehow.

Thanks,

Shaun.

Best,

Rene.
-----------------------------------------------------------
Shaun Warrington
Research Fellow

Division of Clinical Neuroscience, School of Medicine
University of Nottingham

w: https://swarrington1.github.io/
-----------------------------------------------------------

On 6 Dec 2022, at 15:40, Andrade Rey René <[log in to unmask]> wrote:

I insist just in case it has been marked as spam. So I keep having the issue with xtract_stats

De: Andrade Rey René
Enviado: Viernes, 11 de Noviembre de 2022 18:56
Para: FSL - FMRIB's Software Library
Asunto: Re: [FSL] xtract_stats ERROR empty mask image

I am afraid I won’t be able to receive any answer on this subject. I think I will have to compute FA measures from the tracts of xtract via fslmaths multiplying for each tract for each subject if there is no other way out.

On 9 Nov 2022, at 12:51, Andrade Rey René <[log in to unmask]> wrote:

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.

I have tried every possibility that I might come up with and still I don't know how to figure it out.

De: FSL - FMRIB's Software Library <[log in to unmask]> en nombre de Andrade Rey René <[log in to unmask]>
Enviado: martes, 8 de noviembre de 2022 6:33
Para: [log in to unmask] <[log in to unmask]>
Asunto: [FSL] xtract_stats ERROR empty mask image

ATENCIÓN: Este correo electrónico se envió desde fuera de la UAH. No haga clic en enlaces ni abra archivos adjuntos a menos que reconozca al remitente y sepa que el contenido es seguro.

Dear experts:

I am getting in touch this time because of an error like I mention in the subject. I copy and paste the error. I try different options of xtract_stats and all show the same error.

All the best,

Rene Andrade.

xtract_stats -d /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/dtifit/25633/dwi_den_preproc_ -xtract /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25633.xtract -w /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25633.bedpostX/xfms/std2diff.nii.gz -r /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/dtifit/25633/dwi_den_preproc_FA.nii.gz

__ _______ ____ _ ____ _____ _ _

\ \/ /_ _| _ \ / \ / ___|_ _|__| |_ __ _| |_ ___

\ / | | | |_) | / _ \| | | |/ __| __/ _ | __/ __|

/ \ | | | _ < / ___ \ |___ | |\__ \ || (_| | |_\__ \

/_/\_\ |_| |_| \_\/_/ \_\____| |_||___/\__\__ _|\__|___/

Getting summary stats for: vol prob length FA MD

Running for all tracts under /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25633.xtract/tracts

Processing ac

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing af_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing af_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing ar_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing ar_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing atr_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing atr_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cbd_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cbd_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cbp_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cbp_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cbt_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cbt_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cst_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing cst_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing fa_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing fa_r

another different call of xtract_stats

xtract_stats -d /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25633.bedpostX/mean_ -xtract /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25633.xtract -w /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25633.bedpostX/xfms/std2diff.nii.gz -r /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/dtifit/25633/dwi_den_preproc_FA.nii.gz -meas vol,f1samples,f2samples

__ _______ ____ _ ____ _____ _ _

\ \/ /_ _| _ \ / \ / ___|_ _|__| |_ __ _| |_ ___

\ / | | | |_) | / _ \| | | |/ __| __/ _ | __/ __|

/ \ | | | _ < / ___ \ |___ | |\__ \ || (_| | |_\__ \

/_/\_\ |_| |_| \_\/_/ \_\____| |_||___/\__\__ _|\__|___/

Getting summary stats for: vol f1samples f2samples

Running for all tracts under /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25633.xtract/tracts

Processing ac

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing af_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing af_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing ar_l

OF ANOTHER SUBJECT

xtract_stats -d /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/dtifit/25634/dwi_den_preproc_ -xtract /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25634.xtract -w /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25634.bedpostX/xfms/std2diff.nii.gz -r /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/dtifit/25634/dwi_den_preproc_FA.nii.gz

__ _______ ____ _ ____ _____ _ _

\ \/ /_ _| _ \ / \ / ___|_ _|__| |_ __ _| |_ ___

\ / | | | |_) | / _ \| | | |/ __| __/ _ | __/ __|

/ \ | | | _ < / ___ \ |___ | |\__ \ || (_| | |_\__ \

/_/\_\ |_| |_| \_\/_/ \_\____| |_||___/\__\__ _|\__|___/

Getting summary stats for: vol prob length FA MD

Running for all tracts under /media/andraderenew/Elements/backup_1TB/image_databases/anorexia/results/Diffusion/bedpostx/25634.xtract/tracts

Processing ac

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing af_l

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing af_r

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

ERROR:: Empty mask image

Processing ar_l

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