[Freesurfer] Fsaverage stats
External Email - Use Caution Hello Freesurfer Developers, I'm attempting to compare the cortical thickness values from the stats (?h.aparc.stats) of a stack of subjects and compare them with fsaverage. With aparcstats2table I did it for my subjects without problem, but the fsaverage folder doesn’t have the ?.h.aparc.stats file. I need it to compare the cortical thickness values of the different regions of the brain from the stack of subjects with fsaverage to see if we have a relevant difference. Do you have a suggestion how I can do it? Thanks in advance, Alina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Lesioned hemisphere
External Email - Use Caution Hello Freesurfer experts, I’m analyzing subjects with a stroke in one hemisphere. Problem: recon-all breaks and gives an error at the white matter segmentation, what I understand. I don’t need the data from the lesioned hemisphere, I need the cortical thickness from the healthy one. Is there a possibility to only run one hemisphere through freesurfer? Or to project the healthy one on to the lesioned to have an intact brain and run recon-all succesfully? Thanks, Alina ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] HCP-MMP1 Parcellation to individual brain for stats
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
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? <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
___
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 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? <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 <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
>>
>> <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
>> <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
>
___
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Cortical thickness volume ROI to surface {Disarmed}
External Email - Use Caution Hello Freesurfer experts, I am attempting to register a ROI (.nii) to the surface of fsaverage to get the statistical output on the cortical thickness. I followed your instructions on https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5utz9wmCB_PLEjDtsOmyziziVBQRSmBgczrdyk56eX0vaBWBNP1iIevBdxOho3o-JJ64DuVK1J6XpzIFNVqqzBDHDrU6O2cYjWTNnglb4Ow4OIdXr5Qq28eboicyUSvLl2KmB0P0lQY9abQIfjX6hs_1Q1FvwX1Tx7YnGwsbJIgqcpDRG0dkvqZc0pgeiBQbnNjLadwozbHME2Ale8Kt0-V-I2Urmgq5zbEhzlAPvCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness <https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5utz9wmCB_PLEjDtsOmyziziVBQRSmBgczrdyk56eX0vaBWBNP1iIevBdxOho3o-JJ64DuVK1J6XpzIFNVqqzBDHDrU6O2cYjWTNnglb4Ow4OIdXr5Qq28eboicyUSvLl2KmB0P0lQY9abQIfjX6hs_1Q1FvwX1Tx7YnGwsbJIgqcpDRG0dkvqZc0pgeiBQbnNjLadwozbHME2Ale8Kt0-V-I2Urmgq5zbEhzlAPvCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness> but after mri_vol2surf I get this message, I can’t visualize the ROI on the surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, Alina Rojas. srcvol = M1_L.nii.gz srcreg = tmp.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjDist = 0.5 reshape = 0 interp = nearest float2int = round GetProjMax = 1 INFO: float2int code = 0 INFO: using NIfTI-1 qform Done loading volume INFO: This REGISTER_DAT transform is valid only for volumes between COR types with c_(r,a,s) = 0. Input reg is register.dat original matrix --- 1.0 0.0 0.0 2.49380; 0.0 0.0 1.0 -22.50500; 0.0 -1.0 0.0 -9.53872; 0.0 0.0 0.0 1.0; original matrix --- Reading surface /fsaverage/surf/lh.white Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 1 using old 2 0.1 0 1 using old 3 0.2 0 1 using old 4 0.3 0 1 using old 5 0.4 0 1 using old 6 0.5 0 1 using old 7 0.6 0 1 using old 8 0.7 0 1 using old 9 0.8 0 1 using old 10 0.9 0 1 using old Done mapping volume to surface Number of source voxels hit = 75073 Writing to lh.fsaverage.M1_L.mgh Dim: 163842 1 1 surfcolor: Subscript out of range. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cortical thickness volume ROI to surface {Disarmed}
External Email - Use Caution Thank you for your response! Here the commands: #register image to MNIspace flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat #Create a registration from the ROI-anatomical volume to a freesurfer template subject fslregister --s fsaverage --mov mydata_T1_MNI.nii.gz --reg tmp.dat #Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface overlay. mri_vol2surf --mov ROI_MNI.nii.gz --reg tmp.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh --out lh.fsaverage.ROI_MNI.mgh —noreshape tkmeditfv fsaverage lh inflated -overlay lh.fsaverage.M1_L.mgh -fthresh 0.5 I tried with another threshold, and to change it while in Freeview and it’s either the whole surface with the overlay or none. Thank you for your help! Alina Rojas > Am 16.11.2020 um 17:04 schrieb Douglas N. Greve : > > please send the command line > > On 11/16/2020 7:20 AM, Alina Rojas wrote: >> External Email - Use Caution >> >> Hello Freesurfer experts, >> >> I am attempting to register a ROI (.nii) to the surface of fsaverage to get >> the statistical output on the cortical thickness. I followed your >> instructions on MailScanner has detected a possible fraud attempt from >> "secure-web.cisco.com" claiming to >> behttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness >> <https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADoe1ai7ok5utz9wmCB_PLEjDtsOmyziziVBQRSmBgczrdyk56eX0vaBWBNP1iIevBdxOho3o-JJ64DuVK1J6XpzIFNVqqzBDHDrU6O2cYjWTNnglb4Ow4OIdXr5Qq28eboicyUSvLl2KmB0P0lQY9abQIfjX6hs_1Q1FvwX1Tx7YnGwsbJIgqcpDRG0dkvqZc0pgeiBQbnNjLadwozbHME2Ale8Kt0-V-I2Urmgq5zbEhzlAPvCA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVolumeRoiCorticalThickness> >> but after mri_vol2surf I get this message, I can’t visualize the ROI on the >> surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, >> Alina Rojas. >> >> srcvol = M1_L.nii.gz >> srcreg = tmp.dat >> srcregold = 0 >> srcwarp unspecified >> surf = white >> hemi = lh >> ProjDist = 0.5 >> reshape = 0 >> interp = nearest >> float2int = round >> GetProjMax = 1 >> INFO: float2int code = 0 >> INFO: using NIfTI-1 qform >> Done loading volume >> INFO: This REGISTER_DAT transform is valid only for volumes between COR >> types with c_(r,a,s) = 0. >> Input reg is register.dat >> original matrix --- >> 1.0 0.0 0.0 2.49380; >> 0.0 0.0 1.0 -22.50500; >> 0.0 -1.0 0.0 -9.53872; >> 0.0 0.0 0.0 1.0; >> original matrix --- >> Reading surface /fsaverage/surf/lh.white >> Done reading source surface >> Mapping Source Volume onto Source Subject Surface >> 1 0 0 1 >> using old >> 2 0.1 0 1 >> using old >> 3 0.2 0 1 >> using old >> 4 0.3 0 1 >> using old >> 5 0.4 0 1 >> using old >> 6 0.5 0 1 >> using old >> 7 0.6 0 1 >> using old >> 8 0.7 0 1 >> using old >> 9 0.8 0 1 >> using old >> 10 0.9 0 1 >> using old >> Done mapping volume to surface >> Number of source voxels hit = 75073 >> Writing to lh.fsaverage.M1_L.mgh >> Dim: 163842 1 1 >> surfcolor: Subscript out of range. >> >> >> >> >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer >> >> <https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT-xSV3Uin7CmBt_0BPg_0i1AWtJU1vZn2DKlHVGhyXp5WKXs1Q8ReIzK9xXEDa8NUDM3gsQVJpynhZD0gBj8FZlLEe9wNRv_4oDjFKtbqnX17Bqp5oWazA3LmrSeY0WMS-oVyt6_TjHFXCvvRLqx34lzCC8Be07NxJdDYc7K9_JaqoorFJc4KzIlIupp0UXZJiXV-VI33g3W95uw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer> > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://secure-web.cisco.com/182BqfOmZHFfN-HXG0WKcZl1t7mCNEi6craJT61YlVMJ8c1BoYM9RlZhjXTzA4TeZ05e3OGT
