Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
wb_command -file-information on the .dlabel.nii file should do the trick.
Matt.
From: on behalf of Alina Rojas
Reply-To: Freesurfer support list
Date: Monday, July 20, 2020 at 6:13 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Thank you for the quick answer! For the archive and my understanding…the
pscalar gives out a column with 360 values, these values are the average
thickness of my one subject and finally, the data I was searching for: cortical
thickness values from my subject obtained with Freesurfer but with the
parcellation of the HCP-MMP1. Is there a document or a command where I can
correlate these values with the name/number of cortical area?
Regards,
Alina
Am 20.07.2020 um 11:32 schrieb Alina Rojas
mailto:alinacol...@gmail.com>>:
Thank you, the ciftify was run successfully! But now I have questions to the
wb-command -cifti-parcellate:
wb_command -cifti-parcellate
- the cifti file to parcellate
- a cifti label file to use for the parcellation
- which mapping to parcellate (integer, ROW, or COLUMN)
- output - output cifti file
I understand that should be
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
but what should I use as label? The
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii
from https://balsa.wustl.edu/WN56? And the output from the -cifty-parcellate is
.pscalar.nii..how do I get from there to GIFTI?
And for the GIFTY to .annot I would do:
mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer
example)
Thank you,
Alina
Am 14.07.2020 um 16:17 schrieb Glasser, Matthew
mailto:glass...@wustl.edu>>:
External Email - Use Caution
I would find using something like ciftify (https://github.com/edickie/ciftify)
potentially more straightforward (and then you can just use wb_command
-cifti-parcellate on
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
It is possible to go the other direction too (e.g. using this link:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
and then perhaps someone on the list can explain how to go from GIFTI on
fsaverage to .annot on the native meshes and extract the stats.
Matt.
On 7/14/20, 8:54 AM,
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Alina Rojas"
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:
* External Email - Caution *
External Email - Use Caution
Hello Freesurfer support list,
I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
subjects to get the values of the parcellation, like aparc.stats but aparc
being HCP-MMP1. The aim ist to compare the cortical thickness of the
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
archive and didn’t find the solution. It would be so great if you could help me!
Thank you and regards,
Alina Rojas
___
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The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
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The materials in this message are private and may contain Protected Healthcare
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or the taking of any action in reliance on the contents of this information is
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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Thank you for the quick answer! For the archive and my understanding…the
pscalar gives out a column with 360 values, these values are the average
thickness of my one subject and finally, the data I was searching for: cortical
thickness values from my subject obtained with Freesurfer but with the
parcellation of the HCP-MMP1. Is there a document or a command where I can
correlate these values with the name/number of cortical area?
Regards,
Alina
> Am 20.07.2020 um 11:32 schrieb Alina Rojas :
>
> Thank you, the ciftify was run successfully! But now I have questions to the
> wb-command -cifti-parcellate:
> wb_command -cifti-parcellate
>- the cifti file to parcellate
>- a cifti label file to use for the parcellation
>- which mapping to parcellate (integer, ROW, or COLUMN)
>- output - output cifti file
> I understand that should be
> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
> but what should I use as label? The
> Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii
> from https://balsa.wustl.edu/WN56? And the
> output from the -cifty-parcellate is .pscalar.nii..how do I get from there to
> GIFTI?
>
> And for the GIFTY to .annot I would do:
>
> mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer
> example)
>
> Thank you,
>
> Alina
>
>> Am 14.07.2020 um 16:17 schrieb Glasser, Matthew > >:
>>
>>External Email - Use Caution
>>
>> I would find using something like ciftify
>> (https://github.com/edickie/ciftify )
>> potentially more straightforward (and then you can just use wb_command
>> -cifti-parcellate on
>> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
>> It is possible to go the other direction too (e.g. using this link:
>> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
>>
>>
>> and then perhaps someone on the list can explain how to go from GIFTI on
>> fsaverage to .annot on the native meshes and extract the stats.
>>
>> Matt.
>>
>> On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu
>> on behalf of Alina Rojas"
>> > on behalf of
>> alinacol...@gmail.com > wrote:
>>
>>* External Email - Caution *
>>
>>External Email - Use Caution
>>
>>Hello Freesurfer support list,
>>
>>I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
>> subjects to get the values of the parcellation, like aparc.stats but aparc
>> being HCP-MMP1. The aim ist to compare the cortical thickness of the
>> Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
>> archive and didn’t find the solution. It would be so great if you could help
>> me!
>>
>>Thank you and regards,
>>
>>Alina Rojas
>>
>>___
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
I would use https://balsa.wustl.edu/file/show/3VLx which is the CIFTI label
file. The pscalar is not a label file, but rather the average thicknesses in
each cortical area. You can view the average thicknesses in Connectome
Workbench or print out the results with wb_command -cifti-convert -to-text.
Matt.
From: on behalf of Alina Rojas
Reply-To: Freesurfer support list
Date: Monday, July 20, 2020 at 4:32 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Thank you, the ciftify was run successfully! But now I have questions to the
wb-command -cifti-parcellate:
wb_command -cifti-parcellate
- the cifti file to parcellate
- a cifti label file to use for the parcellation
- which mapping to parcellate (integer, ROW, or COLUMN)
- output - output cifti file
I understand that should be
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
but what should I use as label? The
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii
from https://balsa.wustl.edu/WN56? And the output from the -cifty-parcellate is
.pscalar.nii..how do I get from there to GIFTI?
And for the GIFTY to .annot I would do:
mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer
example)
Thank you,
Alina
Am 14.07.2020 um 16:17 schrieb Glasser, Matthew
mailto:glass...@wustl.edu>>:
External Email - Use Caution
I would find using something like ciftify (https://github.com/edickie/ciftify)
potentially more straightforward (and then you can just use wb_command
-cifti-parcellate on
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
It is possible to go the other direction too (e.g. using this link:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
and then perhaps someone on the list can explain how to go from GIFTI on
fsaverage to .annot on the native meshes and extract the stats.
Matt.
On 7/14/20, 8:54 AM,
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Alina Rojas"
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:
* External Email - Caution *
External Email - Use Caution
Hello Freesurfer support list,
I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
subjects to get the values of the parcellation, like aparc.stats but aparc
being HCP-MMP1. The aim ist to compare the cortical thickness of the
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
archive and didn’t find the solution. It would be so great if you could help me!
Thank you and regards,
Alina Rojas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Thank you, the ciftify was run successfully! But now I have questions to the
wb-command -cifti-parcellate:
wb_command -cifti-parcellate
- the cifti file to parcellate
- a cifti label file to use for the parcellation
- which mapping to parcellate (integer, ROW, or COLUMN)
- output - output cifti file
I understand that should be
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
but what should I use as label? The
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii
from https://balsa.wustl.edu/WN56? And the
output from the -cifty-parcellate is .pscalar.nii..how do I get from there to
GIFTI?
And for the GIFTY to .annot I would do:
mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer
example)
Thank you,
Alina
> Am 14.07.2020 um 16:17 schrieb Glasser, Matthew :
>
>External Email - Use Caution
>
> I would find using something like ciftify
> (https://github.com/edickie/ciftify) potentially more straightforward (and
> then you can just use wb_command -cifti-parcellate on
> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
> It is possible to go the other direction too (e.g. using this link:
> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
> and then perhaps someone on the list can explain how to go from GIFTI on
> fsaverage to .annot on the native meshes and extract the stats.
>
> Matt.
>
> On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Alina Rojas" alinacol...@gmail.com> wrote:
>
>* External Email - Caution *
>
>External Email - Use Caution
>
>Hello Freesurfer support list,
>
>I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
> subjects to get the values of the parcellation, like aparc.stats but aparc
> being HCP-MMP1. The aim ist to compare the cortical thickness of the
> Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
> archive and didn’t find the solution. It would be so great if you could help
> me!
>
>Thank you and regards,
>
>Alina Rojas
>
>___
>Freesurfer mailing list
>Freesurfer@nmr.mgh.harvard.edu
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you are
> not the intended recipient, be advised that any unauthorized use, disclosure,
> copying or the taking of any action in reliance on the contents of this
> information is strictly prohibited. If you have received this email in error,
> please immediately notify the sender via telephone or return mail.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
They didn’t have that data either. So perhaps there is some possibility of a
.gcs having improved performance over a simple surface registration depending
on how this was done (e.g. if the MSMAll registration were used to get the
individual lables and there are “modes” of folding that correlate with “modes”
of areal size, shape, and positions). Certainly no one has worked with us on
actually validating this approach though (e.g. comparing the output of the .gcs
to the “gold standard” multi-modal areal classifier outputs generated on
individual subjects). So I would use with caution.
Matt.
From: on behalf of Álvaro Deleglise
Reply-To: Freesurfer support list
Date: Tuesday, July 14, 2020 at 10:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
I found the .gcs files in a git repo: https://github.com/faskowit/multiAtlasTT
El mar., 14 jul. 2020 a las 11:58, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
External Email - Use Caution
So how exactly did you make a .gcs without the individual subject parcellations
or the multi-modal features used for classifying cortical areas? Note that we
are working on a tool for folks to do this.
Matt.
From:
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
on behalf of Álvaro Deleglise
mailto:alvarodelegl...@gmail.com>>
Reply-To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Date: Tuesday, July 14, 2020 at 9:49 AM
To: Freesurfer support list
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Hi Alina and Matthew,
I think there is a simple solution to the problem. You can use the .gcs files
of the parcellation you are interested in! You have to run the mris_ca_label
command to apply the parcellation in individual subject space and get de .annot
files of each hemisphere. Then, you can use mris_anatomical_stats to get the
.stats files from these annot files. Finally, you can use aparcstats2table to
get the metrics of your parcellation.
Here's and example:
mris_ca_label -l $SUBJECTS_DIR//label/?h.cortex.label \
lh $SUBJECTS_DIR//surf/?h.sphere.reg \
/?h.parcellation_X.gcs \
$SUBJECTS_DIR//label/?h.parcellation_X.annot
mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f
stats/?h.parcellation_X.stats -b -a label/?h.parcellation_X.annot -c
label/aparc.parcellation_X.ctab ?h
If you want to, I can provide you the .gcs files of the HCP-MMP1-Atlas.
El mar., 14 jul. 2020 a las 11:19, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
External Email - Use Caution
I would find using something like ciftify (https://github.com/edickie/ciftify)
potentially more straightforward (and then you can just use wb_command
-cifti-parcellate on
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
It is possible to go the other direction too (e.g. using this link:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
and then perhaps someone on the list can explain how to go from GIFTI on
fsaverage to .annot on the native meshes and extract the stats.
Matt.
On 7/14/20, 8:54 AM,
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Alina Rojas"
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:
* External Email - Caution *
External Email - Use Caution
Hello Freesurfer support list,
I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
subjects to get the values of the parcellation, like aparc.stats but aparc
being HCP-MMP1. The aim ist to compare the cortical thickness of the
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
archive and didn’t find the solution. It would be so great if you could help me!
Thank you and regards,
Alina Rojas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in rel
Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
I found the .gcs files in a git repo:
https://github.com/faskowit/multiAtlasTT
El mar., 14 jul. 2020 a las 11:58, Glasser, Matthew ()
escribió:
> External Email - Use Caution
>
> So how exactly did you make a .gcs without the individual subject
> parcellations or the multi-modal features used for classifying cortical
> areas? Note that we are working on a tool for folks to do this.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Álvaro
> Deleglise
> *Reply-To: *Freesurfer support list
> *Date: *Tuesday, July 14, 2020 at 9:49 AM
> *To: *Freesurfer support list
> *Subject: *Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for
> stats
>
>
>
> *External Email - Use Caution*
>
> Hi Alina and Matthew,
>
> I think there is a simple solution to the problem. You can use the .gcs
> files of the parcellation you are interested in! You have to run the
> mris_ca_label command to apply the parcellation in individual subject space
> and get de .annot files of each hemisphere. Then, you can use
> mris_anatomical_stats to get the .stats files from these annot files.
> Finally, you can use aparcstats2table to get the metrics of your
> parcellation.
>
>
>
> Here's and example:
>
> mris_ca_label -l $SUBJECTS_DIR//label/?h.cortex.label \
>lh $SUBJECTS_DIR//surf/?h.sphere.reg \
> /?h.parcellation_X.gcs \
> $SUBJECTS_DIR//label/?h.parcellation_X.annot
>
>
>
> mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f
> stats/?h.parcellation_X.stats -b -a label/?h.parcellation_X.annot -c
> label/aparc.parcellation_X.ctab ?h
>
>
>
> If you want to, I can provide you the .gcs files of the HCP-MMP1-Atlas.
>
>
>
>
>
> El mar., 14 jul. 2020 a las 11:19, Glasser, Matthew ()
> escribió:
>
> External Email - Use Caution
>
> I would find using something like ciftify (
> https://github.com/edickie/ciftify) potentially more straightforward (and
> then you can just use wb_command -cifti-parcellate on
> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
> It is possible to go the other direction too (e.g. using this link:
> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
> and then perhaps someone on the list can explain how to go from GIFTI on
> fsaverage to .annot on the native meshes and extract the stats.
>
> Matt.
>
> On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Alina Rojas" alinacol...@gmail.com> wrote:
>
> * External Email - Caution *
>
> External Email - Use Caution
>
> Hello Freesurfer support list,
>
> I’m attempting to map the HCP-MMP1-Atlas to the individual brains of
> my subjects to get the values of the parcellation, like aparc.stats but
> aparc being HCP-MMP1. The aim ist to compare the cortical thickness of the
> Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
> archive and didn’t find the solution. It would be so great if you could
> help me!
>
> Thank you and regards,
>
> Alina Rojas
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> Freesurfer mailing list
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>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> ___
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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
So how exactly did you make a .gcs without the individual subject parcellations
or the multi-modal features used for classifying cortical areas? Note that we
are working on a tool for folks to do this.
Matt.
From: on behalf of Álvaro Deleglise
Reply-To: Freesurfer support list
Date: Tuesday, July 14, 2020 at 9:49 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Hi Alina and Matthew,
I think there is a simple solution to the problem. You can use the .gcs files
of the parcellation you are interested in! You have to run the mris_ca_label
command to apply the parcellation in individual subject space and get de .annot
files of each hemisphere. Then, you can use mris_anatomical_stats to get the
.stats files from these annot files. Finally, you can use aparcstats2table to
get the metrics of your parcellation.
Here's and example:
mris_ca_label -l $SUBJECTS_DIR//label/?h.cortex.label \
lh $SUBJECTS_DIR//surf/?h.sphere.reg \
/?h.parcellation_X.gcs \
$SUBJECTS_DIR//label/?h.parcellation_X.annot
mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f
stats/?h.parcellation_X.stats -b -a label/?h.parcellation_X.annot -c
label/aparc.parcellation_X.ctab ?h
If you want to, I can provide you the .gcs files of the HCP-MMP1-Atlas.
El mar., 14 jul. 2020 a las 11:19, Glasser, Matthew
(mailto:glass...@wustl.edu>>) escribió:
External Email - Use Caution
I would find using something like ciftify (https://github.com/edickie/ciftify)
potentially more straightforward (and then you can just use wb_command
-cifti-parcellate on
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
It is possible to go the other direction too (e.g. using this link:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
and then perhaps someone on the list can explain how to go from GIFTI on
fsaverage to .annot on the native meshes and extract the stats.
Matt.
On 7/14/20, 8:54 AM,
"freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of Alina Rojas"
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
on behalf of alinacol...@gmail.com<mailto:alinacol...@gmail.com>> wrote:
* External Email - Caution *
External Email - Use Caution
Hello Freesurfer support list,
I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
subjects to get the values of the parcellation, like aparc.stats but aparc
being HCP-MMP1. The aim ist to compare the cortical thickness of the
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
archive and didn’t find the solution. It would be so great if you could help me!
Thank you and regards,
Alina Rojas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
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The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
Hi Alina and Matthew,
I think there is a simple solution to the problem. You can use the .gcs
files of the parcellation you are interested in! You have to run the
mris_ca_label command to apply the parcellation in individual subject space
and get de .annot files of each hemisphere. Then, you can use
mris_anatomical_stats to get the .stats files from these annot files.
Finally, you can use aparcstats2table to get the metrics of your
parcellation.
Here's and example:
mris_ca_label -l $SUBJECTS_DIR//label/?h.cortex.label \
lh $SUBJECTS_DIR//surf/?h.sphere.reg \
/?h.parcellation_X.gcs \
$SUBJECTS_DIR//label/?h.parcellation_X.annot
mris_anatomical_stats -th3 -mgz -cortex ../label/?h.cortex.label -f
stats/?h.parcellation_X.stats -b -a label/?h.parcellation_X.annot -c
label/aparc.parcellation_X.ctab ?h
If you want to, I can provide you the .gcs files of the HCP-MMP1-Atlas.
El mar., 14 jul. 2020 a las 11:19, Glasser, Matthew ()
escribió:
> External Email - Use Caution
>
> I would find using something like ciftify (
> https://github.com/edickie/ciftify) potentially more straightforward (and
> then you can just use wb_command -cifti-parcellate on
> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
> It is possible to go the other direction too (e.g. using this link:
> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
> and then perhaps someone on the list can explain how to go from GIFTI on
> fsaverage to .annot on the native meshes and extract the stats.
>
> Matt.
>
> On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
> of Alina Rojas" alinacol...@gmail.com> wrote:
>
> * External Email - Caution *
>
> External Email - Use Caution
>
> Hello Freesurfer support list,
>
> I’m attempting to map the HCP-MMP1-Atlas to the individual brains of
> my subjects to get the values of the parcellation, like aparc.stats but
> aparc being HCP-MMP1. The aim ist to compare the cortical thickness of the
> Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
> archive and didn’t find the solution. It would be so great if you could
> help me!
>
> Thank you and regards,
>
> Alina Rojas
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
External Email - Use Caution
I would find using something like ciftify (https://github.com/edickie/ciftify)
potentially more straightforward (and then you can just use wb_command
-cifti-parcellate on
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
It is possible to go the other direction too (e.g. using this link:
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
and then perhaps someone on the list can explain how to go from GIFTI on
fsaverage to .annot on the native meshes and extract the stats.
Matt.
On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Alina Rojas" wrote:
* External Email - Caution *
External Email - Use Caution
Hello Freesurfer support list,
I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my
subjects to get the values of the parcellation, like aparc.stats but aparc
being HCP-MMP1. The aim ist to compare the cortical thickness of the
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the
archive and didn’t find the solution. It would be so great if you could help me!
Thank you and regards,
Alina Rojas
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The materials in this message are private and may contain Protected Healthcare
Information or other information of a sensitive nature. If you are not the
intended recipient, be advised that any unauthorized use, disclosure, copying
or the taking of any action in reliance on the contents of this information is
strictly prohibited. If you have received this email in error, please
immediately notify the sender via telephone or return mail.
___
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
