Problem with freesurfer measures

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Alberto Del Cerro Leon

8 Mar 2021 8 Mar '21

7:01 a.m.

External Email - Use Caution

Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures: 1. Gray and White Matter Volume 2. Folding Index 3. Curvature measures 4. Thickness However I don't know what surface in the surf folder of each subject I have to use. Could u help me?

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Fischl, Bruce

8 Mar 8 Mar

10:02 a.m.

Hi Alberto

1. And 4. Are not properties of single surfaces – they are computed from the white and the pial. For 2 and 3 that is really up to you Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alberto Del Cerro Leon Sent: Monday, March 8, 2021 7:02 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Problem with freesurfer measures

External Email - Use Caution Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures: 1. Gray and White Matter Volume 2. Folding Index 3. Curvature measures 4. Thickness However I don't know what surface in the surf folder of each subject I have to use. Could u help me?

Alberto Del Cerro Leon

11:40 a.m.

External Email - Use Caution

I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow.

1. Convert the annotation file to each subject space using mri_sur2surf and using mri_anatomical_stats in each subject 2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (BFISCHL@mgh.harvard.edu) escribió:

...

Hi Alberto

And 4. Are not properties of single surfaces – they are computed

from the white and the pial. For 2 and 3 that is really up to you

Cheers Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro Leon *Sent:* Monday, March 8, 2021 7:02 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Problem with freesurfer measures
   External Email - Use Caution        *
Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures:

Gray and White Matter Volume

Folding Index

Curvature measures

Thickness

However I don't know what surface in the surf folder of each subject I have to use. Could u help me? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5...

Douglas N. Greve

16 Mar 16 Mar

11:59 a.m.

I think they will give very similar results, but my guess is that #1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:

...

External Email - Use Caution

I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow.

Convert the annotation file to each subject space using

mri_sur2surf and using mri_anatomical_stats in each subject 2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (<BFISCHL@mgh.harvard.edu mailto:BFISCHL@mgh.harvard.edu>) escribió:
Hi Alberto

 1. And 4. Are not properties of single surfaces – they are
    computed from the white and the pial. For 2 and 3 that is
    really up to you

Cheers
Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
<freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> *On Behalf Of
*Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject:* [Freesurfer] Problem with freesurfer measures

*        External Email - Use Caution *

Hello Freesurfer team, I am using an annotation file that i've
created previously to obtain the measures of some ROIs. To do that
i am using de commands mri_surf2surf and mri_segstats. I want to
obtain the following measures:

1. Gray and White Matter Volume

2. Folding Index

3. Curvature measures

4. Thickness

However I don't know what surface in the surf folder of each
subject I have to use. Could u help me?

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
*MailScanner has detected a possible fraud attempt from
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Alberto Del Cerro Leon

22 Mar 22 Mar

9:06 a.m.

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Thanks!, how can I obtain the white matter volume stats using my annotation file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

...

I think they will give very similar results, but my guess is that #1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow.

Convert the annotation file to each subject space using mri_sur2surf

and using mri_anatomical_stats in each subject 2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (BFISCHL@mgh.harvard.edu) escribió:

...
Hi Alberto

And 4. Are not properties of single surfaces – they are computed

from the white and the pial. For 2 and 3 that is really up to you

Cheers Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro Leon *Sent:* Monday, March 8, 2021 7:02 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Problem with freesurfer measures
   External Email - Use Caution        *
Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures:

Gray and White Matter Volume

Folding Index

Curvature measures

Thickness

However I don't know what surface in the surf folder of each subject I have to use. Could u help me? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnqe... https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Douglas N. Greve

25 Mar 25 Mar

9:59 a.m.

Look in recon-all.log to find the command that creates the wmparc.mgz. Run that command changing the aparc annot to your annot and the output to a new file name. Look in wmparc.stats; at the top will be an mri_segstats command line. Copy that command line changing the file names as needed.

On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:

...

External Email - Use Caution

Thanks!, how can I obtain the white matter volume stats using my annotation file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (<dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>) escribió:

I think they will give very similar results, but my guess is that
#1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:

...

        External Email - Use Caution

I want to use the annotation file created by myself in fsaverage
to calculate the anatomical stats, but i dont know what is the
best workflow.

1. Convert the annotation file to each subject space using
mri_sur2surf and using mri_anatomical_stats in each subject
2. Convert the surface of each subject to fsaverage space and use
mri_segstats to obtain the data, in this case i dont know what
surface i have to convert to fsaverage space to do it (i can see
thickness (lh/rh.thickness) and volume (lh/rh.volume) but not
folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
(<BFISCHL@mgh.harvard.edu <mailto:BFISCHL@mgh.harvard.edu>>)
escribió:

    Hi Alberto

     1. And 4. Are not properties of single surfaces – they are
        computed from the white and the pial. For 2 and 3 that is
        really up to you

    Cheers
    Bruce

    *From:* freesurfer-bounces@nmr.mgh.harvard.edu
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
    <freesurfer-bounces@nmr.mgh.harvard.edu
    <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> *On Behalf
    Of *Alberto Del Cerro Leon
    *Sent:* Monday, March 8, 2021 7:02 AM
    *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
    <mailto:freesurfer@nmr.mgh.harvard.edu>>
    *Subject:* [Freesurfer] Problem with freesurfer measures

    *        External Email - Use Caution *

    Hello Freesurfer team, I am using an annotation file that
    i've created previously to obtain the measures of some ROIs.
    To do that i am using de commands mri_surf2surf and
    mri_segstats. I want to obtain the following measures:

    1. Gray and White Matter Volume

    2. Folding Index

    3. Curvature measures

    4. Thickness

    However I don't know what surface in the surf folder of each
    subject I have to use. Could u help me?

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>
    *MailScanner has detected a possible fraud attempt from
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Alberto Del Cerro Leon

26 Mar 26 Mar

10:09 a.m.

External Email - Use Caution

Hello Douglas, i tried but when i look at the wmparc.mgz created by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names from FreeSurferColorLUT instead of the names in the colorLUT associated with myAAL.annot then the ROIs are disorganized. Could you help me with this problem?

El jue, 25 mar 2021 a las 14:59, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

...

Look in recon-all.log to find the command that creates the wmparc.mgz. Run that command changing the aparc annot to your annot and the output to a new file name. Look in wmparc.stats; at the top will be an mri_segstats command line. Copy that command line changing the file names as needed.

On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
Thanks!, how can I obtain the white matter volume stats using my annotation file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

...
I think they will give very similar results, but my guess is that #1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow.

Convert the annotation file to each subject space using mri_sur2surf

and using mri_anatomical_stats in each subject 2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (BFISCHL@mgh.harvard.edu) escribió:

...
Hi Alberto

And 4. Are not properties of single surfaces – they are computed

from the white and the pial. For 2 and 3 that is really up to you

Cheers Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro Leon *Sent:* Monday, March 8, 2021 7:02 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Problem with freesurfer measures
   External Email - Use Caution        *
Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures:

Gray and White Matter Volume

Folding Index

Curvature measures

Thickness

However I don't know what surface in the surf folder of each subject I have to use. Could u help me? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG9... https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Douglas N. Greve

28 Mar 28 Mar

11:21 p.m.

You'll need to create your own color table by adding 3000 to the left hemi structures and 4000 to the right hemi structures. Look at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt

On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:

...

External Email - Use Caution

El jue, 25 mar 2021 a las 14:59, Douglas N. Greve (<dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>) escribió:

Look in recon-all.log to find the command that creates the
wmparc.mgz. Run that command changing the aparc annot to your
annot and the output to a new file name. Look in wmparc.stats; at
the top will be an mri_segstats command line. Copy that command
line changing the file names as needed.

On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:

...

        External Email - Use Caution

Thanks!, how can I obtain the white matter volume stats using my
annotation file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve
(<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió:

    I think they will give very similar results, but my guess is
    that #1 is a little better

    On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:

...

            External Email - Use Caution

    I want to use the annotation file created by myself in
    fsaverage to calculate the anatomical stats, but i dont know
    what is the best workflow.

    1. Convert the annotation file to each subject space using
    mri_sur2surf and using mri_anatomical_stats in each subject
    2. Convert the surface of each subject to fsaverage space
    and use mri_segstats to obtain the data, in this case i
    dont know what surface i have to convert to fsaverage space
    to do it (i can see thickness (lh/rh.thickness) and volume
    (lh/rh.volume) but not folding index and white matter volume)

    Any idea?

    El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
    (<BFISCHL@mgh.harvard.edu <mailto:BFISCHL@mgh.harvard.edu>>)
    escribió:

        Hi Alberto

         1. And 4. Are not properties of single surfaces – they
            are computed from the white and the pial. For 2 and
            3 that is really up to you

        Cheers
        Bruce

        *From:* freesurfer-bounces@nmr.mgh.harvard.edu
        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
        <freesurfer-bounces@nmr.mgh.harvard.edu
        <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> *On
        Behalf Of *Alberto Del Cerro Leon
        *Sent:* Monday, March 8, 2021 7:02 AM
        *To:* Freesurfer support list
        <freesurfer@nmr.mgh.harvard.edu
        <mailto:freesurfer@nmr.mgh.harvard.edu>>
        *Subject:* [Freesurfer] Problem with freesurfer measures

        *        External Email - Use Caution *

        Hello Freesurfer team, I am using an annotation file
        that i've created previously to obtain the measures of
        some ROIs. To do that i am using de commands
        mri_surf2surf and mri_segstats. I want to obtain the
        following measures:

        1. Gray and White Matter Volume

        2. Folding Index

        3. Curvature measures

        4. Thickness

        However I don't know what surface in the surf folder of
        each subject I have to use. Could u help me?

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Alberto Del Cerro Leon

30 Mar 30 Mar

5:24 a.m.

External Email - Use Caution

Thanks a lot, It works!, now I have obtained values to ctx and wm volumes for each area. However when I look at the gray matter volume values calculated by mri_anatomical stats, the results are pretty similar to the ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In that case what measure will be more suitable?

El lun, 29 mar 2021 a las 5:22, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

...

You'll need to create your own color table by adding 3000 to the left hemi structures and 4000 to the right hemi structures. Look at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt

On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
Hello Douglas, i tried but when i look at the wmparc.mgz created by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names from FreeSurferColorLUT instead of the names in the colorLUT associated with myAAL.annot then the ROIs are disorganized. Could you help me with this problem?

El jue, 25 mar 2021 a las 14:59, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

...
Look in recon-all.log to find the command that creates the wmparc.mgz. Run that command changing the aparc annot to your annot and the output to a new file name. Look in wmparc.stats; at the top will be an mri_segstats command line. Copy that command line changing the file names as needed.

On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
Thanks!, how can I obtain the white matter volume stats using my annotation file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:

...
I think they will give very similar results, but my guess is that #1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow.

Convert the annotation file to each subject space using mri_sur2surf

and using mri_anatomical_stats in each subject 2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (BFISCHL@mgh.harvard.edu) escribió:

...
Hi Alberto

And 4. Are not properties of single surfaces – they are computed

from the white and the pial. For 2 and 3 that is really up to you

Cheers Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro Leon *Sent:* Monday, March 8, 2021 7:02 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Problem with freesurfer measures
   External Email - Use Caution        *
Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures:

Gray and White Matter Volume

Folding Index

Curvature measures

Thickness

However I don't know what surface in the surf folder of each subject I have to use. Could u help me? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9Q... https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Douglas N. Greve

5 Apr 5 Apr

9:49 a.m.

What are your command lines?

On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:

...

External Email - Use Caution

El lun, 29 mar 2021 a las 5:22, Douglas N. Greve (<dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>) escribió:

You'll need to create your own color table by adding 3000 to the
left hemi structures and 4000 to the right hemi structures. Look
at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt


On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:

...

        External Email - Use Caution

Hello Douglas, i tried but when i look at the wmparc.mgz created
by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm
--rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes
the index and the names from FreeSurferColorLUT instead of the
names in the colorLUT associated with myAAL.annot then the ROIs
are disorganized. Could you help me with this problem?

El jue, 25 mar 2021 a las 14:59, Douglas N. Greve
(<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió:

    Look in recon-all.log to find the command that creates the
    wmparc.mgz. Run that command changing the aparc annot to your
    annot and the output to a new file name. Look in
    wmparc.stats; at the top will be an mri_segstats command
    line. Copy that command line changing the file names as needed.

    On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:

...

            External Email - Use Caution

    Thanks!, how can I obtain the white matter volume stats
    using my annotation file?

    El mar, 16 mar 2021 a las 16:59, Douglas N. Greve
    (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>)
    escribió:

        I think they will give very similar results, but my
        guess is that #1 is a little better

        On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:

...

                External Email - Use Caution

        I want to use the annotation file created by myself in
        fsaverage to calculate the anatomical stats, but i
        dont know what is the best workflow.

        1. Convert the annotation file to each subject space
        using mri_sur2surf and using mri_anatomical_stats in
        each subject
        2. Convert the surface of each subject to fsaverage
        space and use mri_segstats to obtain the data, in this
        case i dont know what surface i have to convert to
        fsaverage space to do it (i can see thickness
        (lh/rh.thickness) and volume (lh/rh.volume) but not
        folding index and white matter volume)

        Any idea?

        El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
        (<BFISCHL@mgh.harvard.edu
        <mailto:BFISCHL@mgh.harvard.edu>>) escribió:

            Hi Alberto

             1. And 4. Are not properties of single surfaces –
                they are computed from the white and the pial.
                For 2 and 3 that is really up to you

            Cheers
            Bruce

            *From:* freesurfer-bounces@nmr.mgh.harvard.edu
            <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
            <freesurfer-bounces@nmr.mgh.harvard.edu
            <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
            *On Behalf Of *Alberto Del Cerro Leon
            *Sent:* Monday, March 8, 2021 7:02 AM
            *To:* Freesurfer support list
            <freesurfer@nmr.mgh.harvard.edu
            <mailto:freesurfer@nmr.mgh.harvard.edu>>
            *Subject:* [Freesurfer] Problem with freesurfer
            measures

            *        External Email - Use Caution *

            Hello Freesurfer team, I am using an annotation
            file that i've created previously to obtain the
            measures of some ROIs. To do that i am using de
            commands mri_surf2surf and mri_segstats. I want to
            obtain the following measures:

            1. Gray and White Matter Volume

            2. Folding Index

            3. Curvature measures

            4. Thickness

            However I don't know what surface in the surf
            folder of each subject I have to use. Could u help me?

            _______________________________________________
            Freesurfer mailing list
            Freesurfer@nmr.mgh.harvard.edu
            <mailto:Freesurfer@nmr.mgh.harvard.edu>
            *MailScanner has detected a possible fraud attempt
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Alberto Del Cerro Leon

11:47 a.m.

External Email - Use Caution

To obtain de stats from mri_anatomical stats i used *>>mris_anatomical_stats -a /usr/local/freesurfer/subjects/218/label/rh.myAAL.annot -f* */usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats -b 218 rh* In another hand, the workflow to obatian the stats from mri_segstats was:

...

...
*mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask

--o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz **--annot myAAL* *>>**mri_segstats --seg /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz* *--ctab /home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum /usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats * *-**-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0 --brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in /usr/local/freesurfer/subjects/218/mri/norm.mgz* *--in-intensity-name norm --in-intensity-units MR --subject 218 --surf-wm-vol --etiv*

El lun, 5 abr 2021 a las 15:50, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

...

What are your command lines?

On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
Thanks a lot, It works!, now I have obtained values to ctx and wm volumes for each area. However when I look at the gray matter volume values calculated by mri_anatomical stats, the results are pretty similar to the ctx-ROIs calculated by mri_segstats, but not the same. It is normal? In that case what measure will be more suitable?

El lun, 29 mar 2021 a las 5:22, Douglas N. Greve (dgreve@mgh.harvard.edu) escribió:

...
You'll need to create your own color table by adding 3000 to the left hemi structures and 4000 to the right hemi structures. Look at the 3000s and 4000s in $FREESURFER_HOME/FreeSurferColorLUT.txt

On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
Hello Douglas, i tried but when i look at the wmparc.mgz created by the code >>mri_aparc2aseg --s 215 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --annot myAAL it takes the index and the names from FreeSurferColorLUT instead of the names in the colorLUT associated with myAAL.annot then the ROIs are disorganized. Could you help me with this problem?

El jue, 25 mar 2021 a las 14:59, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:

...
Look in recon-all.log to find the command that creates the wmparc.mgz. Run that command changing the aparc annot to your annot and the output to a new file name. Look in wmparc.stats; at the top will be an mri_segstats command line. Copy that command line changing the file names as needed.

On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
Thanks!, how can I obtain the white matter volume stats using my annotation file?

El mar, 16 mar 2021 a las 16:59, Douglas N. Greve (< dgreve@mgh.harvard.edu>) escribió:

...
I think they will give very similar results, but my guess is that #1 is a little better

On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:
    External Email - Use Caution
I want to use the annotation file created by myself in fsaverage to calculate the anatomical stats, but i dont know what is the best workflow.

Convert the annotation file to each subject space using mri_sur2surf

and using mri_anatomical_stats in each subject 2. Convert the surface of each subject to fsaverage space and use mri_segstats to obtain the data, in this case i dont know what surface i have to convert to fsaverage space to do it (i can see thickness (lh/rh.thickness) and volume (lh/rh.volume) but not folding index and white matter volume)

Any idea?

El lun, 8 mar 2021 a las 16:04, Fischl, Bruce (BFISCHL@mgh.harvard.edu) escribió:

...
Hi Alberto

And 4. Are not properties of single surfaces – they are

computed from the white and the pial. For 2 and 3 that is really up to you

Cheers Bruce

*From:* freesurfer-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro Leon *Sent:* Monday, March 8, 2021 7:02 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Problem with freesurfer measures
   External Email - Use Caution        *
Hello Freesurfer team, I am using an annotation file that i've created previously to obtain the measures of some ROIs. To do that i am using de commands mri_surf2surf and mri_segstats. I want to obtain the following measures:

Gray and White Matter Volume

Folding Index

Curvature measures

Thickness

However I don't know what surface in the surf folder of each subject I have to use. Could u help me? _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu *MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1ig2ol_YfPL7vkGsCqXX1xseLR5cg4PLQwrszsbYhNdPL0F... https://secure-web.cisco.com/1YJFf9_v-FCEIEML34ObuC19lwndNnPr3qXQ27W-KJa3aD5cHD7GRwSEtVGA5l0wVfI-qwadg-4V9ONf5EZ0kiLcRjW6DVI_Rd2ZeqiMxXTIBEnUxA3T9NzdNSt8iXVZ7cyXIzeEsQeBhrig9ume-iTSL61o9NJ8xeYD0zqzkN5beVGaw6yxXpHYMufcuWsp7li3hf1daYTVoJEiUno9_8hA_Q7xVe54KZ585zoXC2r43bYx3pxJ56xQU1iAEqLf5WArPGhqVAV_6TmQ9v8C2Xw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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Douglas N. Greve

6 Apr 6 Apr

9:28 a.m.

It is normal that those give different results. I would expect them to be extremely close to each other, so small that the difference does not matter. But if you had to take one, I'd take the output of mris_anatomical_stats

On 4/5/2021 11:47 AM, Alberto Del Cerro Leon wrote:

...

External Email - Use Caution

To obtain de stats from mri_anatomical stats i used />>mris_anatomical_stats -a /usr/local/freesurfer/subjects/218/label/rh.myAAL.annot -f///usr/local/freesurfer/subjects/218/stats/rh.myAAL.stats -b 218 rh/ In another hand, the workflow to obatian the stats from mri_segstats was:

...

...
/mri_aparc2aseg --s 218 --labelwm --hypo-as-wm --rip-unknown --volmask

--o /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz //--annot myAAL/ />>//mri_segstats --seg /usr/local/freesurfer/subjects/218/mri/wmmyAAL.mgz//--ctab /home/neuroimage/fsl/FreeSurfer/wmAALColorLUT.txt --sum /usr/local/freesurfer/subjects/218/stats/wmmyAAL.stats / /-//-pv /usr/local/freesurfer/subjects/218/mri/norm.mgz --excludeid 0 --brainmask /usr/local/freesurfer/subjects/218/mri/brainmask.mgz --in /usr/local/freesurfer/subjects/218/mri/norm.mgz/ /--in-intensity-name norm --in-intensity-units MR --subject 218 --surf-wm-vol --etiv/

El lun, 5 abr 2021 a las 15:50, Douglas N. Greve (<dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu>) escribió:

What are your command lines?

On 3/30/2021 5:24 AM, Alberto Del Cerro Leon wrote:

...

        External Email - Use Caution

Thanks a lot, It works!, now I have obtained values to ctx and wm
volumes for each area. However when I look at the gray matter
volume values calculated by mri_anatomical stats, the results are
pretty similar to the ctx-ROIs calculated by mri_segstats, but
not the same. It is normal? In that case what measure will be
more suitable?

El lun, 29 mar 2021 a las 5:22, Douglas N. Greve
(<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>) escribió:

    You'll need to create your own color table by adding 3000 to
    the left hemi structures and 4000 to the right hemi
    structures. Look at the 3000s and 4000s in
    $FREESURFER_HOME/FreeSurferColorLUT.txt


    On 3/26/2021 10:09 AM, Alberto Del Cerro Leon wrote:

...

            External Email - Use Caution

    Hello Douglas, i tried but when i look at the wmparc.mgz
    created by the code >>mri_aparc2aseg --s 215 --labelwm
    --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz
    --annot myAAL it takes the index and the names from
    FreeSurferColorLUT instead of the names in the colorLUT
    associated with myAAL.annot then the ROIs are disorganized.
    Could you help me with this problem?

    El jue, 25 mar 2021 a las 14:59, Douglas N. Greve
    (<dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>)
    escribió:

        Look in recon-all.log to find the command that creates
        the wmparc.mgz. Run that command changing the aparc
        annot to your annot and the output to a new file name.
        Look in wmparc.stats; at the top will be an mri_segstats
        command line. Copy that command line changing the file
        names as needed.

        On 3/22/2021 9:06 AM, Alberto Del Cerro Leon wrote:

...

                External Email - Use Caution

        Thanks!, how can I obtain the white matter volume stats
        using my annotation file?

        El mar, 16 mar 2021 a las 16:59, Douglas N. Greve
        (<dgreve@mgh.harvard.edu
        <mailto:dgreve@mgh.harvard.edu>>) escribió:

            I think they will give very similar results, but my
            guess is that #1 is a little better

            On 3/8/2021 11:40 AM, Alberto Del Cerro Leon wrote:

...

                    External Email - Use Caution

            I want to use the annotation file created by
            myself in fsaverage to calculate the anatomical
            stats, but i dont know what is the best workflow.

            1. Convert the annotation file to each subject
            space using mri_sur2surf and using
            mri_anatomical_stats in each subject
            2. Convert the surface of each subject to
            fsaverage space and use mri_segstats to obtain the
            data, in this case i dont know what surface i have
            to convert to fsaverage space to do it (i can see
            thickness (lh/rh.thickness) and volume
            (lh/rh.volume) but not folding index and white
            matter volume)

            Any idea?

            El lun, 8 mar 2021 a las 16:04, Fischl, Bruce
            (<BFISCHL@mgh.harvard.edu
            <mailto:BFISCHL@mgh.harvard.edu>>) escribió:

                Hi Alberto

                 1. And 4. Are not properties of single
                    surfaces – they are computed from the
                    white and the pial. For 2 and 3 that is
                    really up to you

                Cheers
                Bruce

                *From:* freesurfer-bounces@nmr.mgh.harvard.edu
                <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>
                <freesurfer-bounces@nmr.mgh.harvard.edu
                <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>
                *On Behalf Of *Alberto Del Cerro Leon
                *Sent:* Monday, March 8, 2021 7:02 AM
                *To:* Freesurfer support list
                <freesurfer@nmr.mgh.harvard.edu
                <mailto:freesurfer@nmr.mgh.harvard.edu>>
                *Subject:* [Freesurfer] Problem with
                freesurfer measures

                *        External Email - Use Caution *

                Hello Freesurfer team, I am using an
                annotation file that i've created previously
                to obtain the measures of some ROIs. To do
                that i am using de commands mri_surf2surf and
                mri_segstats. I want to obtain the following
                measures:

                1. Gray and White Matter Volume

                2. Folding Index

                3. Curvature measures

                4. Thickness

                However I don't know what surface in the surf
                folder of each subject I have to use. Could u
                help me?

                _______________________________________________
                Freesurfer mailing list
                Freesurfer@nmr.mgh.harvard.edu
                <mailto:Freesurfer@nmr.mgh.harvard.edu>
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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1882

Age (days ago)

1911

Last active (days ago)

freesurfer@nmr.mgh.harvard.edu

11 comments

3 participants

tags (0)

participants (3)

Alberto Del Cerro Leon
Douglas N. Greve
Fischl, Bruce