Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Bouchra Guelib 
External Email - Use Caution

Firstly, thanks for your explanation, I didn't know that it would take less
than hours since I used recon-all to run 202 samples, I used parallel to
run 8 images at once and it took almost 13 hours, but at the end , you can
be sure of the results you have. Also it gives you a variety of  aseg
statistics for subcortical and cortex regions, which would be useful if you
want to use them as features for machine learning frameworks, so since you
don't have the same results each time recon-all would be better solution.

Le sam. 27 août 2022 à 12:47, Giulio Siracusano 
a écrit :

> External Email - Use Caution
>
> I've tested reproducibility of the results either using ASEG (therefore
> via recon-all -all) and also SAMSEG (via run_samseg).
>
> The methods are different either in terms of reproducibility of results.
>
> Multiple runs of ASEG (recon-all -all) provide the same result but it
> requires 8+ hours to be executed (each). By comparing the results of
> multiple runs using the file from a single patient, such results are
> exactly the same, no changes at all.
>
> If I use SAMSEG (which is a lot faster, execution time is less than 1h
> using multi-thread execution), I get overall slightly similar results
> (when compared to ASEG) except for the CSF which is very different.
>
> The problem I've found is that if I run SAMSEG on the same patient data
> and evaluate the results, these results (which I would expect they
> should be exactly the same), are slightly different. I've done multiple
> test, whether using single-thread or multi-thread execution. Every time
> I execute run_samseg the results express variability. I think this is
> because multiple calls to numpy.random in the python code of samseg.
> This problem should be fixed to ensure reproducibility of the data.
>
> I hope to be clear now.
>
> I just wanted to understand is the results from ASEG and SAMSEG (which
> is again, a lot faster) could be compared in terms of reproducibility,
> even if these results are not equivalent per se.
>
>
> Regards
>
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Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Bouchra Guelib 
External Email - Use Caution

Why you didn't run recon-all directly ?

Le sam. 27 août 2022 à 11:32, Giulio Siracusano 
a écrit :

> External Email - Use Caution
>
> Hello,
>
> this is true (i.e. reproducibility) for ASEG (when running recon-all -all).
>
> But, if you use SAMSEG (i.e. running run_samseg instead) you get
> slightly different results everytime. This is regardless you use
> -threads flag or not.
>
> My command line is (using the file I've provided in the link in my
> previous email):
>
> run_samseg --input ./I18211_ADNI_12M4_TS_2_20060706103342_2.nii --output
> /usr/local/freesurfer/7.2.0/subjects/002_S_0685-I18211/SAMSEG_NIF
>
> either using this version (1-thread) or a multi-thread
>
> run_samseg --input ./I18211_ADNI_12M4_TS_2_20060706103342_2.nii --output
> /usr/local/freesurfer/7.2.0/subjects/002_S_0685-I18211/SAMSEG_NIF -threads
> 6
>
>
> You get always slightly different results.
>
>
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Re: [Freesurfer] SAMSEG and statistics

2022-08-27 Thread Bouchra Guelib 
External Email - Use Caution

I used freesurfer for ADNI data, specifically MRI for AD/CN.  Even I run
segmentation many times , I always  having the same statistics. Would you
share with us the commend line you used !

Le sam. 27 août 2022 à 09:32, Giulio Siracusano 
a écrit :

> External Email - Use Caution
>
> Hi Douglas,
> I've investigated the use of SAMSEG for AD/MCI patients. I'm using the 7.2
> version of Freesurfer and I've realized that I get different results using
> the same data but when I run the SAMSEG multiple times (on the same
> patient).
>
> Differently from using ASEG, SAMSEG provides also the chance to execute
> the code using multiple threads.
>
> In the first run I've executed SAMSEG on ADNI patient id 002_S_0685 using
> the MP-RAGE series having ID I18211 (the link below provides the NIFTI
> version of the series which has been used for the processing). This
> patients is part of ADNI dataset.
>
> *MailScanner has detected a possible fraud attempt from
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>
> The first execution of SAMSEG was with default settings (1 thread) and
> results are attached, the second was using --threads 6.
>
> These results from the SAME series are similar but they are NOT the same.
>
> How can we explain that?
>
> Regards
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Re: [Freesurfer] PET-segmentattion

2022-08-10 Thread Bouchra Guelib 
External Email - Use Caution

I fix it by adding --id 'segmentation id'  to mri_segstats.
Thanx  Douglas.


Le mer. 10 août 2022 à 03:51, Douglas N. Greve  a
écrit :

> Can you send the terminal output and the petsuv.segstats.dat? How have you
> verified that the registration is correct? What version of FS are you
> running?
>
> On 8/5/2022 4:44 PM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> I want to segment registered PET to T1 MRI to 45 subcortical regions as
> the regions in aseg.stats of MRI.
> I used  mri_segstats --seg MRI-floder/mri/aparc+aseg.mgz --reg
> Pet2T1.register.dof12.lta  --sum petsuv.segstats.dat --i PET-SPM.mgh
>  --ctab-default
> into petsuv.segstats.dat, I found only 40 regions, not as aseg.stats
> what should I change in my commend?
>
> --
> *GUELIB Bouchra: *Ph.D. student
> *Lire *Laboratory
> University: Constantine 2-Abdelhamid Mehri- *Algeria *
> Alternative email: guelibbouc...@gmail.com
>
>
>
>
>
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Re: [Freesurfer] Fwd: eTIV

2022-08-07 Thread Bouchra Guelib 
External Email - Use Caution

I want to use eTIV to normalize also the  normDev, normMean of subcortical
regions as well as the morphological variables of cortical regions such as
gray matter volume, rectified mean curvature.
Should I devide them on eTIV ?

Le jeu. 28 juil. 2022 à 18:24, Douglas N. Greve  a
écrit :

> I usually just divide the volume by the eTIV (you can do this in
> asegstats2table with the --etiv flag). Some people will use it as a
> nuisance regressor in the GLM
>
> On 7/27/2022 3:11 PM, Bouchra Guelib wrote:
>
> External Email - Use Caution
>
> -- Forwarded message -
> De : Bouchra Guelib 
> Date: mer. 27 juil. 2022 à 19:28
> Subject: eTIV
> To: 
>
>
> I hope you can help me with this  point
> I extracted the measures in 'aseg.stats', 'lh.aparc.stats',and
> 'rh.aparc.stats'. Now I want to use these measures as input data for my
> model. However, I read that we need to normalize this data using eTIV. Can
> you tell me how?
>
> --
> *GUELIB Bouchra: *Ph.D. student
> *Lire *Laboratory
> University: Constantine 2-Abdelhamid Mehri- *Algeria *
> Alternative email: guelibbouc...@gmail.com
>
>
>
>
>
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[Freesurfer] PET-segmentattion

2022-08-05 Thread Bouchra Guelib 
External Email - Use Caution

I want to segment registered PET to T1 MRI to 45 subcortical regions as the
regions in aseg.stats of MRI.
I used  mri_segstats --seg MRI-floder/mri/aparc+aseg.mgz --reg
Pet2T1.register.dof12.lta  --sum petsuv.segstats.dat --i PET-SPM.mgh
 --ctab-default
into petsuv.segstats.dat, I found only 40 regions, not as aseg.stats
what should I change in my commend?

-- 
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com
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[Freesurfer] Fwd: eTIV

2022-07-27 Thread Bouchra Guelib 
External Email - Use Caution

-- Forwarded message -
De : Bouchra Guelib 
Date: mer. 27 juil. 2022 à 19:28
Subject: eTIV
To: 


I hope you can help me with this  point
I extracted the measures in 'aseg.stats', 'lh.aparc.stats',and
'rh.aparc.stats'. Now I want to use these measures as input data for my
model. However, I read that we need to normalize this data using eTIV. Can
you tell me how?

-- 
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com
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Re: [Freesurfer] ERROR: Talairach failed

2022-07-27 Thread Bouchra Guelib 
External Email - Use Caution

It is clear now thank you.

Le mer. 27 juil. 2022 à 14:13, Douglas N. Greve  a
écrit :

> recon-all does not change the space to mni305 (it just "conforms" it).
>
> On 7/26/2022 10:22 AM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> The problem was That I transferred my MRI to mni 305 space before the
> recon-all. Still, when I read the documentation on your website, I found
> that changing the space is a step of the recon-all, so I used recon-all
> directly on my original data without any space changing. Thank you so
> much for your answer.
>
> Le lun. 25 juil. 2022 à 03:40, Douglas N. Greve 
> a écrit :
>
>> did you see where it said "see *MailScanner has detected a possible
>> fraud attempt from "secure-web.cisco.com" claiming to be*
>> http://secure-web.cisco.com/1Gz_6qC6AfoxAkFmHB1wHgUcoxuYfNh7T2q2fiAktR1qt2txv5liygRCoYcH__ASEFBrgsa-YCgdFD1qAo6qPxc9L3tXuWvoXnpwd42oq1fWCXinQXrRQEgTP0zPGXqoTnWE8Plnm8xYtffeS1VyozB_L12jfeV0PLZOwcNbjyb6dBArvo9G7O5dsjRS8jV8nqdo4dA6olahBYSdqOsDOfWOPOyn-KljS3ZsPcE6uiR-5RTA3pOTcpwZSNh5fx77aPPeh2FmklfUXTFcjY03jnMfBvN_N0pQpqtARGooSXPgnX1Ir0pYqsgzF78EzCuZ3X8gi_WYpcu3PxKYOEWoahg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
>> <http://secure-web.cisco.com/11upxJF_-cI-E4FBY17KCMERFQk_Wf_2bOtw3CCmUNLSGGVrK54gr2EM9fpqEmsCTWzXs7Ea1kbTxQ4kSg8DwV8yfE1xjTDkl-LLzn9Xox5LSosY9ER1OQNAcvutPc-I5EDdB8Z8uw2r645Hw5srMmxgOldyyzqllkGGNsDM2M8aT1rn76eT5yvnpU6sDeNDgBlh2NfiAGzPRENkH5mFVjPEhDHfsT7T6QI89p3wCpxfDMhTdj9jbi0X_6Lvc71RT1iz1OsYv_FfIIsS4Sg2lrk9kW9DqS8VPrNO92qqcsr72sgIQlqObGlYyHXxpZ1McV516rU2J7prI3GaF2LtgdA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach>"?
>> Try following those instructions.
>>
>> On 7/22/2022 7:00 AM, Bouchra Guelib wrote:
>>
>> External Email - Use Caution
>> I have a nifty MRI, converted to mni 305 space when I apply recon-all, I
>> have this error:
>> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
>> ***FAILED*** (p=0.0525, pval=0.0034 < threshold=0.0050)
>> Command exited with non-zero status 1
>> @#@FSTIME  2022:07:22:11:11:46 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P
>> 100% M 6628 F 0 R 266 W 0 c 0 w 1 I 0 O 0 L 2.89 2.56 1.45
>> @#@FSLOADPOST 2022:07:22:11:11:46 talairach_afd N 4 2.89 2.56 1.45
>>
>> Manual Talairach alignment may be necessary, or
>> include the -notal-check flag to skip this test,
>> making sure the -notal-check flag follows -all
>> or -autorecon1 in the command string.
>> see
>> *MailScanner has detected a possible fraud attempt from
>> "secure-web.cisco.com" claiming to be*
>> http://secure-web.cisco.com/1Gz_6qC6AfoxAkFmHB1wHgUcoxuYfNh7T2q2fiAktR1qt2txv5liygRCoYcH__ASEFBrgsa-YCgdFD1qAo6qPxc9L3tXuWvoXnpwd42oq1fWCXinQXrRQEgTP0zPGXqoTnWE8Plnm8xYtffeS1VyozB_L12jfeV0PLZOwcNbjyb6dBArvo9G7O5dsjRS8jV8nqdo4dA6olahBYSdqOsDOfWOPOyn-KljS3ZsPcE6uiR-5RTA3pOTcpwZSNh5fx77aPPeh2FmklfUXTFcjY03jnMfBvN_N0pQpqtARGooSXPgnX1Ir0pYqsgzF78EzCuZ3X8gi_WYpcu3PxKYOEWoahg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
>> <http://secure-web.cisco.com/11upxJF_-cI-E4FBY17KCMERFQk_Wf_2bOtw3CCmUNLSGGVrK54gr2EM9fpqEmsCTWzXs7Ea1kbTxQ4kSg8DwV8yfE1xjTDkl-LLzn9Xox5LSosY9ER1OQNAcvutPc-I5EDdB8Z8uw2r645Hw5srMmxgOldyyzqllkGGNsDM2M8aT1rn76eT5yvnpU6sDeNDgBlh2NfiAGzPRENkH5mFVjPEhDHfsT7T6QI89p3wCpxfDMhTdj9jbi0X_6Lvc71RT1iz1OsYv_FfIIsS4Sg2lrk9kW9DqS8VPrNO92qqcsr72sgIQlqObGlYyHXxpZ1McV516rU2J7prI3GaF2LtgdA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach>
>> ERROR: Talairach failed!
>> what should I do?
>>
>> --
>> *GUELIB Bouchra: *Ph.D. student
>> *Lire *Laboratory
>> University: Constantine 2-Abdelhamid Mehri- *Algeria *
>> Alternative email: guelibbouc...@gmail.com
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
>> https://secure-web.cisco.com/1ahdoMxlvGh9dGzvkN-ECv_JsRsWMQVdwmGQ6hSvLvzHj6nfHx0K2y2fM0IFdv-MSgUdOcUPOqgzF3_OgrlOs5ATpCh_KNXtnnUQ6wixkZgGscYZBxd7SA2yJpphjQL1Qq8tq5HdS2SLiv0rWKa0pKMbGXavH7NeaVr52yECqF44BNcweenYfuXPDDzu_mB0MtYABYspgKQD3k01WFR7zWr-OxIszzI7HR2zpyG3jTn9ZtG5hsZ3gc1oHAwcDWQTMPuK5P0kVYy9wovLWUG_YIsbZCIiPN20Jjdzz9_SNgzmkpNZOlEcXtl4FZIeyvHI97FCU2TVctSxrdqxUGQT8HA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>>  
>> <https://secure-web.cisco.com/1JbeOES1Op3Y2eFoH0AGZ79blJxSr89RAASmMIwvW5FhxbUyslkD82E-GIyAc3Ujn_egXzYji2WtvLlV7G024sKxiAsTXekV6WCFt_1t_E2_oro5vwaYLdXopGRcP8ZUnubK6CgFgh0lW3j

Re: [Freesurfer] ERROR: Talairach failed

2022-07-26 Thread Bouchra Guelib 
External Email - Use Caution

The problem was That I transferred my MRI to mni 305 space before the
recon-all. Still, when I read the documentation on your website, I found
that changing the space is a step of the recon-all, so I used recon-all
directly on my original data without any space changing. Thank you so
much for your answer.

Le lun. 25 juil. 2022 à 03:40, Douglas N. Greve  a
écrit :

> did you see where it said "see *MailScanner has detected a possible fraud
> attempt from "secure-web.cisco.com" claiming to be*
> http://secure-web.cisco.com/1I4T0PsjF4_Bgt2OJNZh8UJ9TkQcYqnPTMVBdfZvdcE5XxJF9DoyJ_26yhCZyv6rHBBFLfKFslJN4cWeRCqAu5RkUdH7dLsq_Z3CmrgEC-Cgy9gERRKjj6dNLTIFkYyNsVmhYxw8CCgZjeE4zSmivuvV13f0yDKg2NlJkVSFIDBq2_Yqbn_TBvPPWSAl1PzGYRD1dIUQSyGTvqxb2yAiv0u9ZanuNIGkEgNLgAVg0_PpmKF8w4OhcWxfIekDarhLqu-2YfhjbE2dAGaauICVx1qwn-0LgAj-plFQJMmr-NwCu39B4hvIyaxkKsBoYlr1fvvTwolIhzWt4NLmDgOURgg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
> <http://secure-web.cisco.com/11upxJF_-cI-E4FBY17KCMERFQk_Wf_2bOtw3CCmUNLSGGVrK54gr2EM9fpqEmsCTWzXs7Ea1kbTxQ4kSg8DwV8yfE1xjTDkl-LLzn9Xox5LSosY9ER1OQNAcvutPc-I5EDdB8Z8uw2r645Hw5srMmxgOldyyzqllkGGNsDM2M8aT1rn76eT5yvnpU6sDeNDgBlh2NfiAGzPRENkH5mFVjPEhDHfsT7T6QI89p3wCpxfDMhTdj9jbi0X_6Lvc71RT1iz1OsYv_FfIIsS4Sg2lrk9kW9DqS8VPrNO92qqcsr72sgIQlqObGlYyHXxpZ1McV516rU2J7prI3GaF2LtgdA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach>"?
> Try following those instructions.
>
> On 7/22/2022 7:00 AM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> I have a nifty MRI, converted to mni 305 space when I apply recon-all, I
> have this error:
> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
> ***FAILED*** (p=0.0525, pval=0.0034 < threshold=0.0050)
> Command exited with non-zero status 1
> @#@FSTIME  2022:07:22:11:11:46 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P
> 100% M 6628 F 0 R 266 W 0 c 0 w 1 I 0 O 0 L 2.89 2.56 1.45
> @#@FSLOADPOST 2022:07:22:11:11:46 talairach_afd N 4 2.89 2.56 1.45
>
> Manual Talairach alignment may be necessary, or
> include the -notal-check flag to skip this test,
> making sure the -notal-check flag follows -all
> or -autorecon1 in the command string.
> see
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be*
> http://secure-web.cisco.com/1I4T0PsjF4_Bgt2OJNZh8UJ9TkQcYqnPTMVBdfZvdcE5XxJF9DoyJ_26yhCZyv6rHBBFLfKFslJN4cWeRCqAu5RkUdH7dLsq_Z3CmrgEC-Cgy9gERRKjj6dNLTIFkYyNsVmhYxw8CCgZjeE4zSmivuvV13f0yDKg2NlJkVSFIDBq2_Yqbn_TBvPPWSAl1PzGYRD1dIUQSyGTvqxb2yAiv0u9ZanuNIGkEgNLgAVg0_PpmKF8w4OhcWxfIekDarhLqu-2YfhjbE2dAGaauICVx1qwn-0LgAj-plFQJMmr-NwCu39B4hvIyaxkKsBoYlr1fvvTwolIhzWt4NLmDgOURgg/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
> <http://secure-web.cisco.com/11upxJF_-cI-E4FBY17KCMERFQk_Wf_2bOtw3CCmUNLSGGVrK54gr2EM9fpqEmsCTWzXs7Ea1kbTxQ4kSg8DwV8yfE1xjTDkl-LLzn9Xox5LSosY9ER1OQNAcvutPc-I5EDdB8Z8uw2r645Hw5srMmxgOldyyzqllkGGNsDM2M8aT1rn76eT5yvnpU6sDeNDgBlh2NfiAGzPRENkH5mFVjPEhDHfsT7T6QI89p3wCpxfDMhTdj9jbi0X_6Lvc71RT1iz1OsYv_FfIIsS4Sg2lrk9kW9DqS8VPrNO92qqcsr72sgIQlqObGlYyHXxpZ1McV516rU2J7prI3GaF2LtgdA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach>
> ERROR: Talairach failed!
> what should I do?
>
> --
> *GUELIB Bouchra: *Ph.D. student
> *Lire *Laboratory
> University: Constantine 2-Abdelhamid Mehri- *Algeria *
> Alternative email: guelibbouc...@gmail.com
>
>
>
>
>
> ___
> Freesurfer mailing 
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[Freesurfer] ERROR: Talairach failed

2022-07-22 Thread Bouchra Guelib 
External Email - Use Caution

I have a nifty MRI, converted to mni 305 space when I apply recon-all, I
have this error:
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm
***FAILED*** (p=0.0525, pval=0.0034 < threshold=0.0050)
Command exited with non-zero status 1
@#@FSTIME  2022:07:22:11:11:46 talairach_afd N 4 e 0.00 S 0.00 U 0.00 P
100% M 6628 F 0 R 266 W 0 c 0 w 1 I 0 O 0 L 2.89 2.56 1.45
@#@FSLOADPOST 2022:07:22:11:11:46 talairach_afd N 4 2.89 2.56 1.45

Manual Talairach alignment may be necessary, or
include the -notal-check flag to skip this test,
making sure the -notal-check flag follows -all
or -autorecon1 in the command string.
see
http://secure-web.cisco.com/11upxJF_-cI-E4FBY17KCMERFQk_Wf_2bOtw3CCmUNLSGGVrK54gr2EM9fpqEmsCTWzXs7Ea1kbTxQ4kSg8DwV8yfE1xjTDkl-LLzn9Xox5LSosY9ER1OQNAcvutPc-I5EDdB8Z8uw2r645Hw5srMmxgOldyyzqllkGGNsDM2M8aT1rn76eT5yvnpU6sDeNDgBlh2NfiAGzPRENkH5mFVjPEhDHfsT7T6QI89p3wCpxfDMhTdj9jbi0X_6Lvc71RT1iz1OsYv_FfIIsS4Sg2lrk9kW9DqS8VPrNO92qqcsr72sgIQlqObGlYyHXxpZ1McV516rU2J7prI3GaF2LtgdA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FTalairach
ERROR: Talairach failed!
what should I do?

-- 
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com
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Re: [Freesurfer] MeanItensities- PET

2022-06-24 Thread Bouchra Guelib 
External Email - Use Caution

I would like to follow the documentation, however I need all 45 subcortical
regions which I can't get them using mri_gtmpvc

Le ven. 24 juin 2022 à 15:32, Douglas N. Greve  a
écrit :

> This is not the workflow that we support. Follow the workflow in the
> petsurfer documentation is you want assistance.
>
> On 6/21/2022 4:40 AM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> Hi,
> I want to register PET to T1 MRI using FSL dof12
> then I want to extract the SUV.
> I would like you to help me on these lines
> Firstly I converted my MRI named ADNI.nii T1 to min305 space then I
> applied recon-all. The output is the Folder ADNI
> Then I want to register my PET to T1 MRI so I use these line
> bbregister --s ADNI --init-fsl --t2 --mov PET.nii --reg
> Pet2T1.register.dof12.dat --lta Pet2T1.register.dof12.lta --init-reg-out
> Pet2T1
> here I want to extract SUV so used this commend
> mri_segstats --seg ADNI/mri/aparc+aseg.mgz  --sum petsuv.segstats.dat --i
> PET.nii  --ctab-default
> the CMD displays
> ERROR: dimension mismatch between input volume and seg
>   input 128 128 90
>   seg   256 256 256
> Would tell me where is my mistakes
>
>
> Le dim. 19 juin 2022 à 22:43, Douglas N. Greve  a
> écrit :
>
>> You can try removing --default-seg-merge, but it may fail.
>> It can compute a relative SUV (relative to a give n ROI). By default,
>> this will be pons, but you can chose others. SUV requires knowing things
>> like the patients weight.
>>
>> On 6/19/2022 4:15 PM, Bouchra Guelib wrote:
>>
>> External Email - Use Caution
>> mri_gtmpvc --i ADNI-PET.nii --reg template.reg.lta --psf 6 --seg
>> gtmseg.mgz --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o
>> gtmpvc.output
>> I am trying to do like that.
>> I tried to change the --seg gtmseg.mgz by aparc+aseg.mgz to obtain the 45
>> subcortical regions but it doesn't work
>> PS: does  mri_gtmpvc compute SUV? or the mean intensity?
>>
>> Le dim. 19 juin 2022 à 20:55, Douglas N. Greve 
>> a écrit :
>>
>>> what is your mri_gtmpvc command line?
>>>
>>> On 6/19/2022 2:22 PM, Bouchra Guelib wrote:
>>>
>>> External Email - Use Caution
>>> These are the missing regions in which I want to obtain their SUVr.
>>> Left-Lateral-Ventricle, Left-Inf-Lat-Vent,
>>> 3rd-Ventricle, 4th-Ventricle, Left-vessel,  Right-Lateral-Ventricle, 
>>> Right-Inf-Lat-Vent, 5th-Ventricle, WM-hypointensities, 
>>> Left-WM-hypointensities,
>>> Right-WM-hypointensities, non-WM-hypointensities, 
>>> Left-non-WM-hypointensities, Right-non-WM-hypointensities, Optic-Chiasm, 
>>> CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,  CC_Anterior.
>>>
>>> This is what I get when I apply mri_gtmpvc.
>>> I already followed the link that you submitted to me.
>>>
>>>
>>> Le dim. 19 juin 2022 à 15:54, Douglas N. Greve 
>>> a écrit :
>>>
>>>>
>>>>
>>>> On 6/15/2022 7:40 AM, Bouchra Guelib wrote:
>>>>
>>>> External Email - Use Caution
>>>> Hi,
>>>> I wonder if someone can help me to do  something similar to that:
>>>> "  the mean intensity of each FreeSurfer region (ROI) for the 45
>>>> subcortical and the 68 cortical regions were assessed the mean
>>>> intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68
>>>> cortical regions were assessed to obtain  SVU".
>>>> Also, I found an article that mentioned that " the estimated total
>>>> intracranial volume (eTIV) is calculated, which is used later for
>>>> normalization of the volumetric measures".
>>>> My questions are:
>>>> 1) In "  gtm.stats.dat" not all subcortical regions are mentioned, why?
>>>>
>>>> which ones are missing?
>>>>
>>>> 2) I applied "mri_getmpc" to obtain the mean intensity, however, I
>>>> could not figure out what I should do after this step to obtain the mean
>>>> intensity and compute SVU.
>>>>
>>>> Do you mean mri_gtmpvc? the values will be in the gtm.stats.dat file
>>>>
>>>> 3) why do they use eTIV, should I use it, and if yes how!
>>>>
>>>> I don't know. It does not make sense to correct an intensity with eTIV.
>>>> btw, I assume  you've seen this page *MailScanner has detected a
>&

Re: [Freesurfer] 7z virtualbox passcode request

2022-06-22 Thread Bouchra Guelib 
External Email - Use Caution

Hi,
I already used VMware as virtual machine to install Freesurfer, I would
advice you to change your OS to linux or Mac , it won't take the same time
as you run Freesurfer on VM, also the installation is easy, just download
the freesurfer and use tar commend line to install it.
Please let me know if you face problem

Le mer. 22 juin 2022 à 17:27, Gregori, Johannes, Prof. Dr. <
johannes.greg...@h-da.de> a écrit :

> External Email - Use Caution
>
> Hello
>
>
> I would like to try out th 7z virtual machine image containing freesurfer.
> Could you send me the passcode?
>
>
> Thanks in advance
>
> mit freundlichen Grüßen / best regards
>
>
> Johannes
>
>
>
>
>
>
> *Prof. Dr. Johannes Gregori *
>
>
> *h**_*
> *da *Hochschule Darmstadt
> University of Applied Sciences
>
>
>
> Fachbereich Mathematik und Naturwissenschaften
>
>
> Schöfferstr. 3
> D-64295 Darmstadt
>
>
> *MailScanner has detected a possible fraud attempt from
> "secure-web.cisco.com" claiming to be* 
> https://secure-web.cisco.com/1BkMPnXcFBLh3S3zWrwrgV8kvHfY8C77xtIaDNAy5whgUZ91mDKkXT-vwEHrnZRBntwu8KVXmGcnR8KBOsBKXigxysmTnw1ezli5Fk8CwGjZSuIeyZKSCF5MrhZZ873PTuKXIkfh-ni9mzf4ZB1FqqAFVORJyOAskvMTbc6HZG1yQK7XmXU1C2jZj0mplhVwbva8_ZqeSOeil6V3Jo7oFpcjRWrbKXtczPF3Rj8T_Otv4cWE0k_BqxFTGCTfpuJLSHkq4C5xBiuaZ5Rob0uTxQhvAxEvtqljlYkp1B9uZaNHMf97jkyRGYzqvCi6fzBlUMm00WsMxsR3FSgKORhr1ug/https%3A%2F%2Ffbmn.h-da.de
> 
>
>
>
> ___
> Freesurfer mailing list
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> risk and wish to continue to communicate over unencrypted e-mail.
>
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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 Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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Re: [Freesurfer] MeanItensities- PET

2022-06-21 Thread Bouchra Guelib 
External Email - Use Caution

Hi,
I want to register PET to T1 MRI using FSL dof12
then I want to extract the SUV.
I would like you to help me on these lines
Firstly I converted my MRI named ADNI.nii T1 to min305 space then I applied
recon-all. The output is the Folder ADNI
Then I want to register my PET to T1 MRI so I use these line
bbregister --s ADNI --init-fsl --t2 --mov PET.nii --reg
Pet2T1.register.dof12.dat --lta Pet2T1.register.dof12.lta --init-reg-out
Pet2T1
here I want to extract SUV so used this commend
mri_segstats --seg ADNI/mri/aparc+aseg.mgz  --sum petsuv.segstats.dat --i
PET.nii  --ctab-default
the CMD displays
ERROR: dimension mismatch between input volume and seg
  input 128 128 90
  seg   256 256 256
Would tell me where is my mistakes


Le dim. 19 juin 2022 à 22:43, Douglas N. Greve  a
écrit :

> You can try removing --default-seg-merge, but it may fail.
> It can compute a relative SUV (relative to a give n ROI). By default, this
> will be pons, but you can chose others. SUV requires knowing things like
> the patients weight.
>
> On 6/19/2022 4:15 PM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> mri_gtmpvc --i ADNI-PET.nii --reg template.reg.lta --psf 6 --seg
> gtmseg.mgz --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o
> gtmpvc.output
> I am trying to do like that.
> I tried to change the --seg gtmseg.mgz by aparc+aseg.mgz to obtain the 45
> subcortical regions but it doesn't work
> PS: does  mri_gtmpvc compute SUV? or the mean intensity?
>
> Le dim. 19 juin 2022 à 20:55, Douglas N. Greve  a
> écrit :
>
>> what is your mri_gtmpvc command line?
>>
>> On 6/19/2022 2:22 PM, Bouchra Guelib wrote:
>>
>> External Email - Use Caution
>> These are the missing regions in which I want to obtain their SUVr.
>> Left-Lateral-Ventricle, Left-Inf-Lat-Vent,
>> 3rd-Ventricle, 4th-Ventricle, Left-vessel,  Right-Lateral-Ventricle, 
>> Right-Inf-Lat-Vent, 5th-Ventricle, WM-hypointensities, 
>> Left-WM-hypointensities,
>> Right-WM-hypointensities, non-WM-hypointensities, 
>> Left-non-WM-hypointensities, Right-non-WM-hypointensities, Optic-Chiasm, 
>> CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,  CC_Anterior.
>>
>> This is what I get when I apply mri_gtmpvc.
>> I already followed the link that you submitted to me.
>>
>>
>> Le dim. 19 juin 2022 à 15:54, Douglas N. Greve 
>> a écrit :
>>
>>>
>>>
>>> On 6/15/2022 7:40 AM, Bouchra Guelib wrote:
>>>
>>> External Email - Use Caution
>>> Hi,
>>> I wonder if someone can help me to do  something similar to that:
>>> "  the mean intensity of each FreeSurfer region (ROI) for the 45
>>> subcortical and the 68 cortical regions were assessed the mean
>>> intensity of each FreeSurfer region (ROI) for the 45 subcortical and the 68
>>> cortical regions were assessed to obtain  SVU".
>>> Also, I found an article that mentioned that " the estimated total
>>> intracranial volume (eTIV) is calculated, which is used later for
>>> normalization of the volumetric measures".
>>> My questions are:
>>> 1) In "  gtm.stats.dat" not all subcortical regions are mentioned, why?
>>>
>>> which ones are missing?
>>>
>>> 2) I applied "mri_getmpc" to obtain the mean intensity, however, I could
>>> not figure out what I should do after this step to obtain the mean
>>> intensity and compute SVU.
>>>
>>> Do you mean mri_gtmpvc? the values will be in the gtm.stats.dat file
>>>
>>> 3) why do they use eTIV, should I use it, and if yes how!
>>>
>>> I don't know. It does not make sense to correct an intensity with eTIV.
>>> btw, I assume  you've seen this page *MailScanner has detected a
>>> possible fraud attempt from "secure-web.cisco.com" claiming to be*
>>> https://secure-web.cisco.com/10fgLPhblHyLRZyALSM0tAKzNc2G6ixaXzYKhQAoYy_4gCxeIFcHjDNJDh0_0b9RAJpUY3tC2iVevmJcXLbZDp2rOTrLM_ZXD-UZaJKREQRKhy4jwSLFgP5OXiQxr6Fyxjh_Iut61PEpOVtB4y_6bNKRHf63iz9cNLKpr9Xm-kAEioeAva4kSnUb4OQ1cUCS1a6KHPGPMutLN2O4QGGircynJDMcoGkoVP_Gm0Y-xUbIWpxIMuOQa5o0Fe7HiwqBqSK5Z3IP6Tw1iL8zXbNsHk2Ze1C14dtY3v96XmpVMjudyd_AfwPZ8BgqxaGY9ShkHgUVyU4WxfHboYHTKNJQXxQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
>>> <https://secure-web.cisco.com/11lfuSnUl9w3h9Z18W6RjGbXg4yDv-3fW_VwCgPcK0MKpqIEgwfHSpVaj1YEx5PJfyFc68G0JtWihX6t3diQDXq8yaFQO9Je6SCNJYp-EeRtsGEzqIgHqfAOD0k51ASu89BiIu9TkU8w64pAJ6IAJBkfKYKW4qnakZIHQwje9eQRI80k8Lf_Y85maOKCcT0MNsdkyXw3wTk0fbbLy2z3bf6yDl7hz3Gjaz9i1azyger-vXc5sW10n9afmkMiMHj3-NxiHVryG3AqHBkAJgVSKoy3ZmHET

Re: [Freesurfer] MeanItensities- PET

2022-06-19 Thread Bouchra Guelib 
External Email - Use Caution

mri_gtmpvc --i ADNI-PET.nii --reg template.reg.lta --psf 6 --seg gtmseg.mgz
--default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output
I am trying to do like that.
I tried to change the --seg gtmseg.mgz by aparc+aseg.mgz to obtain the 45
subcortical regions but it doesn't work
PS: does  mri_gtmpvc compute SUV? or the mean intensity?

Le dim. 19 juin 2022 à 20:55, Douglas N. Greve  a
écrit :

> what is your mri_gtmpvc command line?
>
> On 6/19/2022 2:22 PM, Bouchra Guelib wrote:
>
> External Email - Use Caution
> These are the missing regions in which I want to obtain their SUVr.
> Left-Lateral-Ventricle, Left-Inf-Lat-Vent,
> 3rd-Ventricle, 4th-Ventricle, Left-vessel,  Right-Lateral-Ventricle, 
> Right-Inf-Lat-Vent, 5th-Ventricle, WM-hypointensities, 
> Left-WM-hypointensities,
> Right-WM-hypointensities, non-WM-hypointensities, 
> Left-non-WM-hypointensities, Right-non-WM-hypointensities, Optic-Chiasm, 
> CC_Posterior, CC_Mid_Posterior, CC_Central, CC_Mid_Anterior,  CC_Anterior.
>
> This is what I get when I apply mri_gtmpvc.
> I already followed the link that you submitted to me.
>
>
> Le dim. 19 juin 2022 à 15:54, Douglas N. Greve  a
> écrit :
>
>>
>>
>> On 6/15/2022 7:40 AM, Bouchra Guelib wrote:
>>
>> External Email - Use Caution
>> Hi,
>> I wonder if someone can help me to do  something similar to that:
>> "  the mean intensity of each FreeSurfer region (ROI) for the 45
>> subcortical and the 68 cortical regions were assessed the mean intensity
>> of each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical
>> regions were assessed to obtain  SVU".
>> Also, I found an article that mentioned that " the estimated total
>> intracranial volume (eTIV) is calculated, which is used later for
>> normalization of the volumetric measures".
>> My questions are:
>> 1) In "  gtm.stats.dat" not all subcortical regions are mentioned, why?
>>
>> which ones are missing?
>>
>> 2) I applied "mri_getmpc" to obtain the mean intensity, however, I could
>> not figure out what I should do after this step to obtain the mean
>> intensity and compute SVU.
>>
>> Do you mean mri_gtmpvc? the values will be in the gtm.stats.dat file
>>
>> 3) why do they use eTIV, should I use it, and if yes how!
>>
>> I don't know. It does not make sense to correct an intensity with eTIV.
>> btw, I assume  you've seen this page *MailScanner has detected a
>> possible fraud attempt from "secure-web.cisco.com" claiming to be*
>> https://secure-web.cisco.com/1Uwp6lqNIFYyMl7qCT0DRzJdCfBXpZ_PqAT03oufoXMOCmfTKDsgNj8jaC1dzep1pBNeDYtES5H43hYZqCXRTuwkwkNjW1h6Q_wu8-UxFbYj24MFG9t15d2quQ6cR_oqdhLCx07J6NItrM-3lPFByjlqKUC_X072lDVhi--_w6wOkewwapm5ZOY7dK7A9EBflGMt0rP7TpMKGZ0MBVi9SxsMILPX8bKSnZYCopBXMx4Qw-ti9VRoZy6_CVKH5M9oTPjl8hKGUs67IdktWXOdXVU2WmfhChGienWTmQopA_xq1hPHUkt_pHqhCWJmpP4BJshihlu1HvHAY7_AHiF3L_A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer
>> <https://secure-web.cisco.com/11lfuSnUl9w3h9Z18W6RjGbXg4yDv-3fW_VwCgPcK0MKpqIEgwfHSpVaj1YEx5PJfyFc68G0JtWihX6t3diQDXq8yaFQO9Je6SCNJYp-EeRtsGEzqIgHqfAOD0k51ASu89BiIu9TkU8w64pAJ6IAJBkfKYKW4qnakZIHQwje9eQRI80k8Lf_Y85maOKCcT0MNsdkyXw3wTk0fbbLy2z3bf6yDl7hz3Gjaz9i1azyger-vXc5sW10n9afmkMiMHj3-NxiHVryG3AqHBkAJgVSKoy3ZmHETymKPmXmWNOpt3OdL7H_LaYVYsA6ZbQ6MgzhA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer>
>> ?
>>
>> best regards.
>>
>>
>> --
>> *GUELIB Bouchra: *Ph.D. student
>> *Lire *Laboratory
>> University: Constantine 2-Abdelhamid Mehri- *Algeria *
>> Alternative email: guelibbouc...@gmail.com
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing listfreesur...@nmr.mgh.harvard.edu*MailScanner has 
>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
>> be* 
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>>  
>> <https://secure-web.cisco.com/1tJiVW4DA6nl89NLr1MA90ucm75k1Qj4zjYs9bBZl9TfjL89btPtk52_q-FUE52664jSIoJsQQo_HNgJEyTaHCUEMFub25rNL8Yash3BD9qNu_EMdV0MsltQdlNnvVuhGOcs-RNOeKx6-4LpVpjY3BAXxMfpVYgNx3vFjZHe8yM3TZUuk5pxkvIWJOQZZWYcNBuy5WBrwp6fDiyWfXcMVE3laalCdbzmiXk11yZ6Vb27DMnuAhY

[Freesurfer] (no subject)

2022-06-18 Thread Bouchra Guelib 
External Email - Use Caution

Hi,
I try to do something like that, Would anyone help me

-- 
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com
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contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

2022-06-15 Thread Bouchra Guelib 
External Email - Use Caution

Actually, I didn't try this idea and also I don't know what's the
difference between brain mask from previous versions.

Le mar. 14 juin 2022 à 22:39, Aaron Tanenbaum 
a écrit :

> External Email - Use Caution
>
> Great. glad I was of some help. I still need my questions answered.
>
> On Tue, Jun 14, 2022 at 4:33 PM Bouchra Guelib <
> bouchra.gue...@univ-constantine2.dz> wrote:
>
>> External Email - Use Caution
>>
>> The problem is solved, I just changed the freesurfer version , thnx for
>> your help
>>
>> Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum <
>> aaron.b.tanenb...@gmail.com> a écrit :
>>
>>> External Email - Use Caution
>>>
>>> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
>>> to do.  I see that you can give freesurfer a brainmask. I was thinking of
>>> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
>>> wise idea? Do you have any objections?
>>> ___
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[Freesurfer] MeanItensities- PET

2022-06-15 Thread Bouchra Guelib 
External Email - Use Caution

Hi,
I wonder if someone can help me to do  something similar to that:
"  the mean intensity of each FreeSurfer region (ROI) for the 45
subcortical and the 68 cortical regions were assessed the mean intensity of
each FreeSurfer region (ROI) for the 45 subcortical and the 68 cortical
regions were assessed to obtain  SVU".
Also, I found an article that mentioned that " the estimated total
intracranial volume (eTIV) is calculated, which is used later for
normalization of the volumetric measures".
My questions are:
1) In "  gtm.stats.dat" not all subcortical regions are mentioned, why?
2) I applied "mri_getmpc" to obtain the mean intensity, however, I could
not figure out what I should do after this step to obtain the mean
intensity and compute SVU.
3) why do they use eTIV, should I use it, and if yes how!
best regards.


-- 
*GUELIB Bouchra: *Ph.D. student
*Lire *Laboratory
University: Constantine 2-Abdelhamid Mehri- *Algeria *
Alternative email: guelibbouc...@gmail.com
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Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

2022-06-14 Thread Bouchra Guelib 
External Email - Use Caution

The problem is solved, I just changed the freesurfer version , thnx for
your help

Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum 
a écrit :

> External Email - Use Caution
>
> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
> to do.  I see that you can give freesurfer a brainmask. I was thinking of
> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
> wise idea? Do you have any objections?
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1MkjLfq-0LdmcCfYdV5NcT8yAoB2BE40dzzC_MoD-rkVBPdua6CFc5zuW22ZDsJQueMEBZCnW70AX1EA9jL95dEKdpGZbsJ4inOEKlO5dVFFF4PkJlpbut1xTLLHc17yBoB5G2KkBi1k3LLzxB5-bVlsKznWsIwTb7Iwelti7C1g5YI2vaZnrUhNYGrRASi4CsPMwBwFmo9P3VtXJadCivfSb3WGEvHlSCDA3UmJnguymAeZ-E8RuL-O9fiYD-f63cCgviLqzOeYlBCkowJTn74foJCctednnrv9ihTACvrglGjnB-z6jFzaRU5ZY1WjVjSmfwrDNGg9hp3pUBtqfiA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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