Re: [Freesurfer] MeanItensities- PET

[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
>> 
>> ?
>>
>> best regards.
>>
>>
>> --
>> *GUELIB Bouchra: *Ph.D. student
>> *Lire *Laboratory
>> University: Constantine 2-Abdelhamid Mehri- *Algeria *
>> Alternative email: guelibbouc...@gmail.com
>>
>>
>>
>>
>>
>> ___
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>> detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
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>>  
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Re: [Freesurfer] MeanItensities- PET

[Douglas N. Greve]

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 applymri_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://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer


?


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] MeanItensities- PET

[Douglas N. Greve]

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 applymri_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://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer


?


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] Freeview GUI overlay and registration

[Douglas N. Greve]

On 6/15/2022 1:26 PM, Kuo, Yi-Ling wrote:


Hello,

The below solutions sounded like data need to be analyzed with 
Freesurfer individually to get the registration file?


The anatomical  must be analyzed in FS, but not the fMRI. See eg 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview


I realized that the stats can be presented in Freeview with the 
correct locations in T1, but when it comes to inflated surface, the 
BOLD signals always present in a specific location regardless of 
dataset (please see the attached figure, looks like it’s a 
registration issue). I wonder if the data were already analyzed by FSL 
in group level, is it possible to present the analyzed group data on 
inflated surface in Freeview?



Yes, see web page above


Thank you again for helping,

Irene

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Date: *Wednesday, June 8, 2022 at 11:15 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Freeview GUI overlay and registration

You will need an lta file that maps from the anatomical to the fmri. 
You can get this with something

bbregister --mov template.nii.gz --s subject --t2 --reg reg.lta
where template.nii.gz is the fmri motion correction template or the 
mean fmri (I forgot what it is called in FSL)


On 6/3/2022 5:12 PM, Kuo, Yi-Ling wrote:

Hi Freesurfer experts,

I am trying to use the Freeview GUI to load fMRI BOLD activation
data (analyzed in FSL) and project on the inflated surface. I used
the feature “Overlay/Load generic” and was prompted to select
overlay file and/or apply registration. The selected overlay file
didn’t seem to project on the right spot on the inflated surface
as would be seen in T1. If registration was the issue, what
registration file should be selected in the Freeview GUI?

My Freeview was updated. Thank you very much for helping.

Irene



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Re: [Freesurfer] SPM to FreeSurfer

[Douglas N. Greve]

That page is  way out of date. Try this one 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview


On 6/15/2022 5:47 PM, Rachel Wagner wrote:


External Email - Use Caution

Apologies for repeat email – I’m getting the following error message, 
is there something I should add?


developer@developer-VirtualBox:~$ mri_convert i.mgz i.img

mri_convert i.mgz i.img

reading from i.mgz...

error: mghRead(/home/developer/i.mgz, -1): could not open file

developer@developer-VirtualBox:~$

*From: *Rachel Wagner 
*Sent: *June 15, 2022 5:04 PM
*To: *Freesurfer@nmr.mgh.harvard.edu
*Subject: *SPM to FreeSurfer

Hello,

I am trying to take my SPM images and cortically project them with 
free surfer (SpmPainting - Free Surfer Wiki (harvard.edu) 
. 
As it might be quite obvious, I have very little experience using 
these softwares.


I am typing in the suggested code as follows:

developer@developer-VirtualBox:~$ mri_convert 
$SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img


mri_convert 
/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz brain.img


reading from 
/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz...


error: 
mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, 
-1): could not open file


developer@developer-VirtualBox:~$ ^C

developer@developer-VirtualBox:~$

Is there something I am doing incorrectly?

Thank you!

Rachel


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The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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receiving this message means you understand and accept this risk and wish to 
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Re: [Freesurfer] mris_label2annot seed not set

[Douglas N. Greve]

You can ignore that. That was put in by a contractor who put it into 
every source file that did not set the random see. No randomness is used 
in this program, so you are safe


On 6/16/2022 9:58 AM, Benjamin Deck wrote:


External Email - Use Caution

Hi Freesurfer experts,

While trying to create a custom annotation file I get the following 
warning:


mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab 
sub-DAEK_yeoLUT.txt --ldir 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ 
--hemi rh

Reading ctab sub-DAEK_yeoLUT.txt
Number of ctab entries 105
INFO: no labels specified, generating from ctab
mris_label2anno supposed to be reproducible but seed not set
51 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label
52 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label
53 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label
54 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label
55 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label
56 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label
57 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label
58 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label
59 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label
60 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label
61 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label
62 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label
63 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label
64 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label
65 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label
66 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label
67 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label
68 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label
69 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label
70 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label
71 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label
72 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label
73 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label
74 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label
75 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label
76 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_19_ROIs_1_rh_native.label
77 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_1_rh_native.label
78 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_2_ROIs_2_rh_native.label
79 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_1_rh_native.label
80 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_2_rh_native.label
81 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_3_ROIs_3_rh_native.label
82 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_4_ROIs_1_rh_native.label
83 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_1_rh_native.label
84 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_2_rh_native.label
85 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_3_rh_native.label
86 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_5_ROIs_4_rh_native.label
87 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_1_rh_native.label
88 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_2_rh_native.label
89 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_6_ROIs_3_rh_native.label
90 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_1_rh_native.label
91 
/mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_7_ROIs_2_rh_native.label
92 

Re: [Freesurfer] mris_label2annot seed not set

[Benjamin Deck]

External Email - Use Caution

Awesome, thank you for the information!

Ben


Virus-free.
http://secure-web.cisco.com/1e-cB1nd2aKMFiuZelF1bCq3dmr3UhHo2Ab50rlwBX1UzypHv0kB5HalQpgqrb_keEnQQPO_JsOgNFerd1RSOk6oshlHecObgAOXmo2CSMxzvfOhDEof3o4Jmh7Icxvla4sQ8izffvae66U6LqLTVbZci3LJUQ2FTKNXUbQdAqK9d_Tyo79Jwp73hYEqOtafVmzXP6uXaCPQ0Te4F-TxeRTyPqOeJ_mJFgWSgrFVTpuA2v9wCcYCsPpNMmZQrCzJ25JCKpIj-ZHFJIPH_K9VVeGw1I5YZUiPu2FShsl16FNTrOtZovF5hvR3do8GYbrM2/http%3A%2F%2Fwww.avast.com

<#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

On Sun, Jun 19, 2022 at 11:06 AM Douglas N. Greve 
wrote:

> You can ignore that. That was put in by a contractor who put it into every
> source file that did not set the random see. No randomness is used in this
> program, so you are safe
>
> On 6/16/2022 9:58 AM, Benjamin Deck wrote:
>
> External Email - Use Caution
> Hi Freesurfer experts,
>
> While trying to create a custom annotation file I get the following
> warning:
>
> mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab
> sub-DAEK_yeoLUT.txt --ldir
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels/ --hemi rh
> Reading ctab sub-DAEK_yeoLUT.txt
> Number of ctab entries 105
> INFO: no labels specified, generating from ctab
> mris_label2anno supposed to be reproducible but seed not set
> 51
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_10_ROIs_1_rh_native.label
> 52
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_11_ROIs_1_rh_native.label
> 53
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_1_rh_native.label
> 54
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_12_ROIs_2_rh_native.label
> 55
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_1_rh_native.label
> 56
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_2_rh_native.label
> 57
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_3_rh_native.label
> 58
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_13_ROIs_4_rh_native.label
> 59
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_1_rh_native.label
> 60
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_2_rh_native.label
> 61
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_3_rh_native.label
> 62
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_4_rh_native.label
> 63
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_14_ROIs_5_rh_native.label
> 64
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_15_ROIs_1_rh_native.label
> 65
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_1_rh_native.label
> 66
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_2_rh_native.label
> 67
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_16_ROIs_3_rh_native.label
> 68
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_1_rh_native.label
> 69
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_2_rh_native.label
> 70
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_3_rh_native.label
> 71
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_17_ROIs_4_rh_native.label
> 72
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_1_rh_native.label
> 73
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_2_rh_native.label
> 74
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_3_rh_native.label
> 75
> /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_labels//rh.Net_18_ROIs_4_rh_native.label
> 76
> 

Re: [Freesurfer] Incorporating samseg segmentation into the recon-all pipeline

[Douglas N. Greve]

You can run something like
samseg --t1w /path/to/input/volume --s subject --recon
This will run recon-all but using samseg to do the initial steps, 
including the segmentation of course
We don't have a lot of experience using this as preprocessing to the 
surface-based analysis, so look at your results carefully


On 6/10/2022 4:18 AM, Julian McGinnis wrote:


External Email - Use Caution

/Hello everyone,/

/We have been utilizing freesurfer for our brain morphometry and 
processing pipelines, and have recently tested the samseg segmentation 
algorithm on a clinical cohort./


/With respect to some regions, we currently prefer its results to the 
ones generated by the standard freesurfer segmentation algorithm.

/

/As SAMSEG only provides volume calculation (please correct me if I am 
wrong) and does not feature cortical thickness measurements,/


/I was wondering if the recon-all pipeline can be modified to utilize 
the samseg segmentation instead, and if so, which script(s) or chain 
of commands would be a good starting point to implement this./


/Looking forward to your feedback,/

/Julian
/

Julian McGinnis

PhD Candidate
TUM-Neuroimaging Center, School of Medicine, Technical University of Munich, 
Munich, Germany
Department of Computer Science, Technical University of Munich, Munich, Germany

Email:julian.mcgin...@tum.de

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Re: [Freesurfer] How is cache.th40.pos.sig.voxel.mgh computed, exactly?

[Douglas N. Greve]

from mri_glmfit-sim --help

csdbase.sig.voxel.mgh - the sig volume corrected for multiple 
comparisons on a voxel-wise basis. The threshhold and sign are 
irrelevant. The value at each voxel is the corrected -log10(p-value) for 
that voxel.


It is computed from a simulation in which gaussian noise is smoothed, 
then converted to p-values (log10(p)), then the maximum log10(p) is 
found. This is repeated 10,000 times to give 10k maximums. A corrected 
p-value for each voxel is then computed based upon the rank of the raw 
pvalue in this list of 10k.



On 6/10/2022 4:14 PM, Mark Ebden wrote:


External Email - Use Caution

Hi,

I was wondering if anyone knows how the numbers 
incache.th40.pos.sig.voxel.mghare computed, or where I'd look to learn 
this. There is a one-liner in the documentation 
 
but I'd like the mathematical details of the correction etc. so I can 
determine what the final numbers (from 0 to 1) represent. I've noticed 
from browsing the plot in FreeView that significant areas have values 
close to 1, which is puzzling.


Thanks if you could point me in the right direction.

Kind regards,

Mark

Mar

**



*Mark Ebden**, D.Phil *

(Pronouns: He/Him)

Research Analyst

**

The Hospital for Sick Children

555 University Ave, Toronto ON M5G 1X8

P 416.888.0841

**







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Re: [Freesurfer] recon-all -s exited with ERRORS

[Douglas N. Greve]

It looks like there are a lot of defects as I see a lot of these messages

An extra large defect has been detected...
This often happens because cerebellum or dura has not been removed from 
wm.mgz.

This may cause recon-all to run very slowly or crash.
if so, see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview


Try following those instructions


On 6/14/2022 5:37 PM, Wang, Yu wrote:


External Email - Use Caution

Hi, FreeSurfer Developers,

 I am attempting to use the recon-all to reconstruction, I 
successfully run this command in some subjects, but it also failed in 
around 1/3 of subjects. And after running the recon-all of this 1/3 
subjects. It will show “mri_watershed error:GLOBAL region of the brain 
empty” and I already solve this with the command “recon-all 
-skullstrip -no-wsgcaatlas -s smwrc1NT816”. And after working with 
this, I tried to use the command “recon-all -autorecon2 -autorecon3 -s 
smwrc1NT816” and it shows the output as without given some detailed 
reasons:


*recon-all -s smwrc1NT816 exited with ERRORS at Mon Jun 13 13:54:10 
CDT 2022*


**

*For more details, see the log file 
/Applications/freesurfer/7.2.0/subjects/smwrc1NT816/scripts/recon-all.log*


*To report a problem, see*MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 
*


I’ve searched over the internet and did not find the reasons and 
solutions of my problems. And I will attached the recon-all.log in 
case it's of any use.


I try to work out on two machine, and they show the same problems :

 1. FreeSurfer version: freesurfer-darwin-macOS-7.2.0-20210713-aa8f76b
and freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b
 2. Platform: MacOs 11.4 and ubantu 20.04.4
 3. uname -a:Darwin WANGs-MBP.attlocal.net 20.5.0 Darwin Kernel
Version 20.5.0: Sat May8 05:10:31 PDT 2021;
root:xnu-7195.121.3~9/RELEASE_ARM64_T8101 arm64

or:Linux sulu 5.4.0-113-lowlatency #127-Ubuntu SMP PREEMPT Wed May 18 
15:12:18 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux


 4. recon-all.log: see attached (this one is run by macOS)

I will be appreciated if you can give me a hand with these problems. 
And looking forward to your reply.


Sincerely,

Yu


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Re: [Freesurfer] mri_label2vol misaligned for subcortical atlas

[Douglas N. Greve]

How was H-O_subcortical_parcellation_thr50.nii  created? Those 
instructions are for when you have a segmentation in the FS conformed 
space and you want to get them back to the native space. So your 
segmentation must be in FS conformed space of the individual


On 6/10/2022 6:49 PM, Christopher Pirrung wrote:


External Email - Use Caution

Hi Freesurfer Devs,

I’m attempting to transform the Harvard-Oxford subcortical atlas 
(obtained from https://neurovault.org/collections/262/) to my 
subjects’ native anatomical space to create individualized versions of 
this atlas.  To do so I used the line:


mri_label2vol --seg H-O_subcortical_parcellation_thr50.nii --temp 
rawavg.mgz --o HO-subcort.mgz --regheader 
H-O_subcortical_parcellation_thr50.nii


based on the recommendation from *MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat 
. 
However, when I load the rawavg.mgz and individualized atlas in 
freeview, the atlas is ~30 mm away from being aligned.  Do you have 
any idea why this might be the case or recommendations to get a better 
alignment?


Thanks!

Chris


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Re: [Freesurfer] -hires flag sometimes breaks recon-all

[Douglas N. Greve]

The -hires performs all operations in 0.7mm space whereas leaving it off 
causes recon-all to "conform" the volume so that it is 256^3 and 1mm^3. 
If you want more help with this, send the log file


On 6/10/2022 6:58 PM, Schneider, Christoph wrote:


Hi,

I have 7T MP2RAGE data of 25 individuals with an isotropic 0.7mm voxel 
resolution. I initially ran FS with the -hires flag to preserve the 
additional detail, but in 4 cases this crashed the process, while 
running the same image without the -hires flag works fine (surfaces 
visually inspected). I just wanted to know what could be the cause for 
this difference in behavior between the two options.


Many thanks in advance,
Chris

Christoph Schneider, PhD
Postdoctoral Research Fellow

Harvard Medical School

Massachusetts General Hospital

Gordon Center for Medical Imaging


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Re: [Freesurfer] mri_aparc2aseg bad incorrect ROIs

[Douglas N. Greve]

I'm not sure what is happening. Does cortex have label value that are 
just not in the LUT or are the values 0?

Try adding --aseg aseg.presurf.hypos
If you need more help,make sure to include the full terminal output

On 6/13/2022 4:49 PM, Benjamin Deck wrote:


External Email - Use Caution

Hi Freesurfer experts,

I am attempting to turn my surface-based parcellation into a 
segmentation file using the following command:


mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table 
sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask


However, when I load the resulting volume using my custom LUT the ROIs 
get labeled to the white matter and subcortical structures leaving the 
grey matter unlabeled.


When I examine the annotation files, they look appropriate and there 
isn't any overlap.


Do I need to include the subcortical structures in my custom LUT to 
avoid this from happening or is there a better solution?


Thank you!

--
*Benjamin L. Deck*
/Doctoral Student/
/Applied Cognitive and Brain Sciences/
/Department of Psychological and Brain Sciences/
/Drexel University/

 
	Virus-free. *MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* www.avast.com 
 




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Re: [Freesurfer] MeanItensities- PET

[Douglas N. Greve]

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 
https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer ?



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

[Douglas N. Greve]

You should be able to run 7.2 on top of the 5.3 and at will take all 
your edits (make a copy of your 5.3 data first:)



On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:


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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Re: [Freesurfer] Problem with longitudinal processing

[Douglas N. Greve]

When you say they are growing rather than shrinking, do you mean in the 
longitudnial recon-all run? The reason I ask is that you only mention 
the base and cross. When you do the longitudinal analysis, you need to 
do cross, then base, then long.


On 6/15/2022 11:43 AM, Wittayer, Matthias wrote:


External Email - Use Caution

Dear community,

I tried to process MS- patient’s MRIs (mostly same scanner, same 
settings) Longitudinally over a long period of time. I first processed 
all timeponits crosssectionally and then initialised  the base image 
by recon- all – base TP1 TP2 TP3 etc. Now I am trying to run label 
based morphometry and it seems some areas are growing rather than 
shrinking. Which is highly unlikely. I tried to exclude timepoint of a 
relapse to rule out perifocal edema interfering with measures but the 
problem remains.


Did anybody have the same problem?

Is it a potential bug or just a garbage in garbage out problem (though 
I don’t know what would be wrong with our scans)?


Does it make sense to make an intermediate template for two timeponits 
only? I.e. recon- all –base TP1 TP2; recon –all –base TP2 TP3 … and 
use them for longitudinal runs?


Thanks for your opinions. Best

Matthias


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