Re: [Freesurfer] Problem with freesurfer measures
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
*On Behalf Of *Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list
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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Re: [Freesurfer] Problem with freesurfer measures
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 () 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 () > 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 (< >> dgr...@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 (< >>> dgr...@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 () >>>> 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-boun...@nmr.mgh.harvard.edu < >>>>>
Re: [Freesurfer] Problem with freesurfer measures
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
(mailto:dgr...@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
(mailto:dgr...@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
(mailto:dgr...@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
(mailto:bfis...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
*On Behalf Of *Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list
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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Re: [Freesurfer] Problem with freesurfer measures
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 () 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 () > 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 (< >> dgr...@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 () >>> 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-boun...@nmr.mgh.harvard.edu < >>>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del >>>> Cerro Leon >>>> *Sent:* Monday, March 8, 2021 7:02 AM >>>> *To:* Freesurfer support list >>>> *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 >>>> *MailScanner has detected a possible fraud attempt from >>>> "secure-web.cisco.com" claiming to be* >>>> https://secure-web.cisco.com/1wwKasfUxceW84pkucUGkmsYQ_veBEUDGdn4KBJ5uoTfR9QEXcl20ViD3v1z-M2EnYwrZWMYqvtsknqADt-sYTrwIi7
Re: [Freesurfer] Problem with freesurfer measures
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
(mailto:dgr...@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
(mailto:dgr...@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
(mailto:bfis...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On
Behalf Of *Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list
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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Re: [Freesurfer] Problem with freesurfer measures
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 () 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 () > 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 () >> 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-boun...@nmr.mgh.harvard.edu < >>> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del >>> Cerro Leon >>> *Sent:* Monday, March 8, 2021 7:02 AM >>> *To:* Freesurfer support list >>> *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 >>> *MailScanner has detected a possible fraud attempt from >>> "secure-web.cisco.com" claiming to be* >>> https://secure-web.cisco.com/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG91AjL1ZBmUrTsH4uVppkOxMsSjpGieAeNogSOH-B4xx5g9unahzAc5C3ej66181XPQbOyF-QGM3IiysY85C2K3kUDwUnIZU0bpa6puHpvIZjLD3nhAp5OfMoayKhs_3KQu2Of-pNFnkKv4aCDH5bgpGDz9VcW-tGQIUIAt172I-tNHanxfB2OHj9nNbVaEInREVZwtxJM_jFMf0lLIXT5gJHIRKX0q_RgpAUoygww/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >>> <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> >> >> >> ___ >> 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/1ekuMRUoFakA2GcA-HAYdzP-YJXE02k2qNXi0TJVuyogwG91AjL1ZBmUrTsH4uVppkOxMsSjpGieAeNogSOH-B4xx5g9unahzAc5C3ej66181XPQbOyF-QGM3IiysY85C2K3kUDwUnIZU0bpa6puHpvIZjLD3nhAp5Of
Re: [Freesurfer] Problem with freesurfer measures
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
(mailto:dgr...@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
(mailto:bfis...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf
Of *Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list 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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Re: [Freesurfer] Problem with freesurfer measures
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 () 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 () > 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-boun...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro >> Leon >> *Sent:* Monday, March 8, 2021 7:02 AM >> *To:* Freesurfer support list >> *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 >> *MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to be* >> https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnqexfnx4M_Pdm9J5uI07IHMoSLX06nTKmLoGpCM__s_0BMxj3yFWmG-DrcG6_hwmbQ4lmwutoIJ7LgzXFCY1kq67Vh2ew-rSx7g1EsGVdqylYYD-iDG_k-YXsbd2bEshDXD1Qem3t3Vtnd2vU-YadqAhVEksxzWDJrWr5lnPwyL89yQGUfLXDJIiRGxyCQZxSHNkSoSCXq9BCZ85lPb6M33BVmSYeBvf-nyCBHvN7NQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> <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> > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://secure-web.cisco.com/1G_h97ZZmS1M3Mu1WvIxpTpCamKUMZrdeii7Mb-_WyhLnqexfnx4M_Pdm9J5uI07IHMoSLX06nTKmLoGpCM__s_0BMxj3yFWmG-DrcG6_hwmbQ4lmwutoIJ7LgzXFCY1kq67Vh2ew-rSx7g1EsGVdqylYYD-iDG_k-YXsbd2bEshDXD1Qem3t3Vtnd2vU-YadqAhVEksxzWDJrWr5lnPwyL89yQGUfLXDJIiRGxyCQZxSHNkSoSCXq9BCZ85lPb6M33BVmSYeBvf-nyCBHvN7NQ/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with freesurfer measures
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
(mailto:bfis...@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-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> *On Behalf Of
*Alberto Del Cerro Leon
*Sent:* Monday, March 8, 2021 7:02 AM
*To:* Freesurfer support list 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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Re: [Freesurfer] Problem with freesurfer measures
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 () 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-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Alberto Del Cerro > Leon > *Sent:* Monday, March 8, 2021 7:02 AM > *To:* Freesurfer support list > *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 > 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problem with freesurfer measures
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-boun...@nmr.mgh.harvard.edu On Behalf Of Alberto Del Cerro Leon Sent: Monday, March 8, 2021 7:02 AM To: Freesurfer support list 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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
