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
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&a... 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-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@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.
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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/<subject_name>/label/?h.cortex.label \ <subject_name> lh $SUBJECTS_DIR/<subject_name>/surf/?h.sphere.reg \ <gcs_file_dir>/?h.parcellation_X.gcs \ $SUBJECTS_DIR/<subject_name>/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 <subjid> ?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 (glasserm@wustl.edu) escribió:
External Email - Use CautionI 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&a... 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-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@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 ofmy 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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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: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Álvaro Deleglise alvarodeleglise@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, July 14, 2020 at 9:49 AM To: Freesurfer support list 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/<subject_name>/label/?h.cortex.label \ <subject_name> lh $SUBJECTS_DIR/<subject_name>/surf/?h.sphere.reg \ <gcs_file_dir>/?h.parcellation_X.gcs \ $SUBJECTS_DIR/<subject_name>/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 <subjid> ?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 (<glasserm@wustl.edumailto:glasserm@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&a... 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@gmail.commailto:alinacolora@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.edumailto: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.edumailto: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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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 (glasserm@wustl.edu) escribió:
External Email - Use CautionSo 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: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Álvaro Deleglise alvarodeleglise@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, July 14, 2020 at 9:49 AM *To: *Freesurfer support list 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/<subject_name>/label/?h.cortex.label \ <subject_name> lh $SUBJECTS_DIR/<subject_name>/surf/?h.sphere.reg \ <gcs_file_dir>/?h.parcellation_X.gcs \ $SUBJECTS_DIR/<subject_name>/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 <subjid> ?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 (glasserm@wustl.edu) escribió:
External Email - Use CautionI 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&a... 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-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@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 ofmy 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
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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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: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Álvaro Deleglise alvarodeleglise@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, July 14, 2020 at 10:01 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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 (<glasserm@wustl.edumailto:glasserm@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: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Álvaro Deleglise <alvarodeleglise@gmail.commailto:alvarodeleglise@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, July 14, 2020 at 9:49 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto: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/<subject_name>/label/?h.cortex.label \ <subject_name> lh $SUBJECTS_DIR/<subject_name>/surf/?h.sphere.reg \ <gcs_file_dir>/?h.parcellation_X.gcs \ $SUBJECTS_DIR/<subject_name>/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 <subjid> ?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 (<glasserm@wustl.edumailto:glasserm@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&a... 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@gmail.commailto:alinacolora@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.edumailto: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.edumailto: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.edumailto: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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Thank you, the ciftify was run successfully! But now I have questions to the wb-command -cifti-parcellate: wb_command -cifti-parcellate <cifti-in> - the cifti file to parcellate <cifti-label> - a cifti label file to use for the parcellation <direction> - which mapping to parcellate (integer, ROW, or COLUMN) <cifti-out> - output - output cifti file I understand that <cifti-in> 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? 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 glasserm@wustl.edu:
External Email - Use CautionI 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&a... 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-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@gmail.com> wrote:
External Email - Caution *
External Email - Use CautionHello 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
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: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas alinacolora@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 20, 2020 at 4:32 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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
<cifti-in> - the cifti file to parcellate
<cifti-label> - a cifti label file to use for the parcellation
<direction> - which mapping to parcellate (integer, ROW, or COLUMN)
<cifti-out> - output - output cifti file I understand that <cifti-in> 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 <glasserm@wustl.edumailto:glasserm@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&a... 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@gmail.commailto:alinacolora@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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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 alinacolora@gmail.com:
Thank you, the ciftify was run successfully! But now I have questions to the wb-command -cifti-parcellate: wb_command -cifti-parcellate <cifti-in> - the cifti file to parcellate <cifti-label> - a cifti label file to use for the parcellation <direction> - which mapping to parcellate (integer, ROW, or COLUMN) <cifti-out> - output - output cifti file I understand that <cifti-in> 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? 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 <glasserm@wustl.edu mailto:glasserm@wustl.edu>:
External Email - Use CautionI would find using something like ciftify (https://github.com/edickie/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&a... 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-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@gmail.com mailto:alinacolora@gmail.com> wrote:
External Email - Caution *
External Email - Use CautionHello 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 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
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wb_command -file-information on the .dlabel.nii file should do the trick.
Matt.
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas alinacolora@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, July 20, 2020 at 6:13 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu 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 <alinacolora@gmail.commailto:alinacolora@gmail.com>:
Thank you, the ciftify was run successfully! But now I have questions to the wb-command -cifti-parcellate:
wb_command -cifti-parcellate
<cifti-in> - the cifti file to parcellate
<cifti-label> - a cifti label file to use for the parcellation
<direction> - which mapping to parcellate (integer, ROW, or COLUMN)
<cifti-out> - output - output cifti file I understand that <cifti-in> 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 <glasserm@wustl.edumailto:glasserm@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&a... 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Alina Rojas" <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of alinacolora@gmail.commailto:alinacolora@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.edumailto: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.edumailto: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@nmr.mgh.harvard.edu
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Alina Rojas -
Glasser, Matthew -
Álvaro Deleglise