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Hi list,
I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce...). in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list,
I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce...).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Bruce,
my apologies, I have tried to do it with some errors. Could you suggest the command line, please?
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it wrote: > > >External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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
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Hi Doug,
my apologies, I have tried to do it with some errors. Could you suggest the command line, please?
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it wrote: > > >External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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
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Hi Stefano,
You can try the following
1) *Transform from fsaverage to subject's surface* mri_surf2surf --srcsubject fsaverage --trgsubject yoursubject --hemi lh --sval-annot path_to/lh.Yeo2011_17Networks_N1000.annot –tval $SUBJECTS_DIR/yoursubject/label/lh.Yeo_17Network_native.annot (repeat for rh)
2) *Transform from subject's surface into your subject's volume* mri_aparc2aseg --s yoursubject --annot Yeo_17Network_native --o $SUBJECTS_DIR/yoursubject/mri/outputfile.mgz
One thing to note: "mri_aparc2aseg" will automatically add 1000 for left cerebral cortex voxels and add 2000 for right cerebral cortex voxels. Therefore, for example, a left hemisphere voxel in network 5 will have a value of 1005 in your outputfile.mgz.
Thanks, Thomas
On Fri, Mar 8, 2019 at 7:29 PM stdp82@virgilio.it wrote:
External Email - Use CautionHi Doug,
my apologies, I have tried to do it with some errors. Could you suggest the command line, please?
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu> ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list,
I'd like to use the regions included in Yeo 17 networks ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it wrote: > > >External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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
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Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty?
Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM stdp82@virgilio.it wrote:
External Email - Use CautionI have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu> ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list,
I'd like to use the regions included in Yeo 17 networks ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu ha scritto:
External Email - Use Caution Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > >External Email - Use Caution I have run: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 to check the output tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot My concern is here: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz Yeo_17Net.mgz is empty. Stefano > > >Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > >External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:
External Email - Use Caution
Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas@csail.mit.edu> ha scritto: External Email - Use Caution Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty?Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:
External Email - Use Caution I have run: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 to check the output tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot My concern is here: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz Yeo_17Net.mgz is empty. Stefano Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it wrote: > External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks(https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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
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
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I will use freeview.
Have you any suggestion on the use of fcseed-config option?
Are you agree with the command line listed below?
fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite
My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
How can I select a specific seed (id) to be used in -segids?
Thanks
Stefano
Il 10 marzo 2019 alle 17.17 Bruce Fischl <fischl@nmr.mgh.harvard.edu> ha scritto: Hi Stefano is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote: > >External Email - Use Caution Thanks. My error is in tkmedit tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas@csail.mit.edu> ha scritto: External Email - Use Caution Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote: External Email - Use Caution I have run: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 to check the output tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot My concern is here: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz Yeo_17Net.mgz is empty. Stefano Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it wrote: > External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_cluste ring). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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 _______________________________________________ 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok.
On 3/10/19 4:05 PM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
External Email - Use Caution
I will use freeview.
Have you any suggestion on the use of fcseed-config option?
Are you agree with the command line listed below?
fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite
My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
How can I select a specific seed (id) to be used in -segids?
Thanks
Stefano
Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu ha scritto:
Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
External Email - Use Caution
Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edumailto:ythomas@csail.mit.edu ha scritto:
External Email - Use Caution
Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.itmailto:stdp82@virgilio.it> wrote:
External Email - Use Caution
I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list,
I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano
Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution I will use freeview. Have you any suggestion on the use of fcseed-config option? Are you agree with the command line listed below? fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? How can I select a specific seed (id) to be used in -segids? Thanks Stefano > > >Il 10 marzo 2019 alle 17.17 Bruce Fischl <fischl@nmr.mgh.harvard.edu> mailto:fischl@nmr.mgh.harvard.edu ha scritto: Hi Stefano is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution Thanks. My error is in tkmedit tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas@csail.mit.edu> mailto:ythomas@csail.mit.edu ha scritto: External Email - Use Caution Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: External Email - Use Caution I have run: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 to check the output tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot My concern is here: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz Yeo_17Net.mgz is empty. Stefano Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_cluste ring). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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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Hi Stefano,
Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.
If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parce...), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.
Regards, Thomas
On Sun, Mar 24, 2019 at 12:18 AM stdp82@virgilio.it wrote:
Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano
Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu> ha scritto:
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok.
On 3/10/19 4:05 PM, stdp82@virgilio.it wrote:
External Email - Use CautionI will use freeview.
Have you any suggestion on the use of fcseed-config option?
Are you agree with the command line listed below?
fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite
My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
How can I select a specific seed (id) to be used in -segids?
Thanks
Stefano
Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu ha scritto:
Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:
External Email - Use Caution
Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu ythomas@csail.mit.edu ha scritto:
External Email - Use Caution
Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:
External Email - Use Caution
I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000
--annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu DGREVE@mgh.harvard.edu ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list,
I'd like to use the regions included in Yeo 17 networks ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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Thanks.
Should I renumber for visualization purpose or for fs-fast?
How can I do it?
Il 26 marzo 2019 alle 4.01 Thomas Yeo ythomas@csail.mit.edu ha scritto:
Hi Stefano, Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while. If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057. Regards, Thomas On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > >Hi, my concern is the mri_aparc2aseg command line. In summary, I have done: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz The output is correct by the color label is those of aparc. Probably the error is the match between the annotations and annot-table. Could you check the command lines, please? Thanks Stefano > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto:Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution I will use freeview. Have you any suggestion on the use of fcseed-config option? Are you agree with the command line listed below? fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? How can I select a specific seed (id) to be used in -segids? Thanks Stefano > > > > >Il 10 marzo 2019 alle 17.17 Bruce Fischl <fischl@nmr.mgh.harvard.edu> mailto:fischl@nmr.mgh.harvard.edu ha scritto: Hi Stefano is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > >External Email - Use Caution Thanks. My error is in tkmedit tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas@csail.mit.edu> mailto:ythomas@csail.mit.edu ha scritto: External Email - Use Caution Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: External Email - Use Caution I have run: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 to check the output tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot My concern is here: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz Yeo_17Net.mgz is empty. Stefano Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_cluste ring). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>
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Renumber for visualization purpose.
Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit.
Thanks, Thomas
On Tue, Mar 26, 2019 at 6:44 PM stdp82@virgilio.it wrote:
Thanks.
Should I renumber for visualization purpose or for fs-fast?
How can I do it?
Il 26 marzo 2019 alle 4.01 Thomas Yeo ythomas@csail.mit.edu ha scritto:
Hi Stefano,
Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.
If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parce...), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.
Regards, Thomas
On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it> wrote:
Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano
Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu> ha scritto:
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok.
On 3/10/19 4:05 PM, stdp82@virgilio.it wrote:
External Email - Use CautionI will use freeview.
Have you any suggestion on the use of fcseed-config option?
Are you agree with the command line listed below?
fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite
My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
How can I select a specific seed (id) to be used in -segids?
Thanks
Stefano
Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu ha scritto:
Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:
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Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu ythomas@csail.mit.edu ha scritto:
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Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:
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I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000
--annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu DGREVE@mgh.harvard.edu ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
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Hi list,
I'd like to use the regions included in Yeo 17 networks ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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I have renumbered and run:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal.
What's happened?
Thanks
Best regards,
Stefano
Il 26 marzo 2019 alle 13.05 Thomas Yeo ythomas@csail.mit.edu ha scritto:
External Email - Use Caution Renumber for visualization purpose. Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit. Thanks, Thomas On Tue, Mar 26, 2019 at 6:44 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > >Thanks. Should I renumber for visualization purpose or for fs-fast? How can I do it? > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:Hi Stefano, Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while. If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057. Regards, Thomas On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > >Hi, my concern is the mri_aparc2aseg command line. In summary, I have done: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz The output is correct by the color label is those of aparc. Probably the error is the match between the annotations and annot-table. Could you check the command lines, please? Thanks Stefano > > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto:Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > >External Email - Use Caution I will use freeview. Have you any suggestion on the use of fcseed-config option? Are you agree with the command line listed below? fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? How can I select a specific seed (id) to be used in -segids? Thanks Stefano > > > > > > >> Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu ha scritto: > > Hi Stefano > > is there a reason you are using tkmedit and not freeview? We deprecated > tkmedit a long time ago now > > cheers > Bruce > On Sun, 10 Mar 2019, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > External Email - Use Caution > > > > Thanks. > > > > My error is in tkmedit > > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu ha scritto: > > > > External Email - Use Caution > > > > Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? > > Your tkmedit command seems to assume Yeo_17Net.mgz is in > > /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? > > > > On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > External Email - Use Caution > > > > I have run: > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 > > 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > > > to check the output > > > > tksurfer subj rh inflated -annot > > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot > > > > My concern is here: > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 > > --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU > > T_freeview.txt --sval-annot > > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot > > > > tkmeditfv fsaverage orig.mgz -ov > > /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz > > > > Yeo_17Net.mgz is empty. > > > > Stefano > > > > Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." > > DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha scritto: > > > > You have to convert the annotation to a volume using mri_aparc2aseg > > (look at recon-all.log for an example, but note that you'll need to > > specify the output so that it does not overwrite). You'll then need to > > look in the output segmentation and see what the segmentation ids are > > > > On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > External Email - Use Caution > > > > Hi list, > > > > I'd like to use the regions included in Yeo 17 networks > > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... > > ring). > > > > in FS-FAST. > > > > Which is the command line to be used to create a segmentation in > > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd > > like > > to use it to run fcseed-config, specify -seg yourseg.mgz > > -segid). > > > > Thanks > > > > Stefano > > > > _______________________________________________ > > 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 > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > 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 > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > 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 Freesurfer@nmr.mgh.harvard.edu mailto: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
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Hi Stefano,
Sorry. Can you confirm left hemisphere is ok?
I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114.
Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon.
Regards, Thomas
On Wed, Mar 27, 2019 at 6:14 PM stdp82@virgilio.it wrote:
I have renumbered and run:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal.
What's happened?
Thanks
Best regards,
Stefano
Il 26 marzo 2019 alle 13.05 Thomas Yeo ythomas@csail.mit.edu ha scritto:
External Email - Use CautionRenumber for visualization purpose.
Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit.
Thanks, Thomas
On Tue, Mar 26, 2019 at 6:44 PM < stdp82@virgilio.it> wrote:
Thanks.
Should I renumber for visualization purpose or for fs-fast?
How can I do it?
Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas@csail.mit.edu> ha scritto:
Hi Stefano,
Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.
If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parce...), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.
Regards, Thomas
On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it> wrote:
Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano
Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu> ha scritto:
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok.
On 3/10/19 4:05 PM, stdp82@virgilio.it wrote:
External Email - Use CautionI will use freeview.
Have you any suggestion on the use of fcseed-config option?
Are you agree with the command line listed below?
fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite
My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
How can I select a specific seed (id) to be used in -segids?
Thanks
Stefano
Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu ha scritto:
Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:
External Email - Use Caution
Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu ythomas@csail.mit.edu ha scritto:
External Email - Use Caution
Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:
External Email - Use Caution
I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000
--annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu DGREVE@mgh.harvard.edu ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list,
I'd like to use the regions included in Yeo 17 networks ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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Yes the left hemisphere is fine.
The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt.
Thanks
Stefano
Il 27 marzo 2019 alle 13.09 Thomas Yeo ythomas@csail.mit.edu ha scritto:
External Email - Use Caution Hi Stefano, Sorry. Can you confirm left hemisphere is ok? I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114. Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon. Regards, Thomas On Wed, Mar 27, 2019 at 6:14 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > >I have renumbered and run: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal. What's happened? Thanks Best regards, Stefano > > > Il 26 marzo 2019 alle 13.05 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:External Email - Use Caution Renumber for visualization purpose. Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit. Thanks, Thomas On Tue, Mar 26, 2019 at 6:44 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > >Thanks. Should I renumber for visualization purpose or for fs-fast? How can I do it? > > > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:Hi Stefano, Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while. If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057. Regards, Thomas On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > >Hi, my concern is the mri_aparc2aseg command line. In summary, I have done: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz The output is correct by the color label is those of aparc. Probably the error is the match between the annotations and annot-table. Could you check the command lines, please? Thanks Stefano > > > > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto:> > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. > > On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > External Email - Use Caution > > > > I will use freeview. > > > > Have you any suggestion on the use of fcseed-config option? > > > > Are you agree with the command line listed below? > > > > fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite > > > > My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? > > > > How can I select a specific seed (id) to be used in -segids? > > > > Thanks > > > > Stefano > > > > > > > > > > > > > > > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu ha scritto: > > > > > > Hi Stefano > > > > > > is there a reason you are using tkmedit and not freeview? We deprecated > > > tkmedit a long time ago now > > > > > > cheers > > > Bruce > > > On Sun, 10 Mar 2019, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > Thanks. > > > > > > > > My error is in tkmedit > > > > > > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > > > > > Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu ha scritto: > > > > > > > > External Email - Use Caution > > > > > > > > Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? > > > > Your tkmedit command seems to assume Yeo_17Net.mgz is in > > > > /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? > > > > > > > > On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > External Email - Use Caution > > > > > > > > I have run: > > > > > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 > > > > 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > > > > > > > to check the output > > > > > > > > tksurfer subj rh inflated -annot > > > > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot > > > > > > > > My concern is here: > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 > > > > --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU > > > > T_freeview.txt --sval-annot > > > > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot > > > > > > > > tkmeditfv fsaverage orig.mgz -ov > > > > /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz > > > > > > > > Yeo_17Net.mgz is empty. > > > > > > > > Stefano > > > > > > > > Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." > > > > DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha scritto: > > > > > > > > You have to convert the annotation to a volume using mri_aparc2aseg > > > > (look at recon-all.log for an example, but note that you'll need to > > > > specify the output so that it does not overwrite). You'll then need to > > > > look in the output segmentation and see what the segmentation ids are > > > > > > > > On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > Hi list, > > > > > > > > I'd like to use the regions included in Yeo 17 networks > > > > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... > > > > ring). > > > > > > > > in FS-FAST. > > > > > > > > Which is the command line to be used to create a segmentation in > > > > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd > > > > like > > > > to use it to run fcseed-config, specify -seg yourseg.mgz > > > > -segid). > > > > > > > > Thanks > > > > > > > > Stefano > > > > > > > > _______________________________________________ > > > > 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 > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > > > 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 > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > _______________________________________________ > > > > 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 > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > >
> > > > >> > > >> > > _______________________________________________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 Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Stefano,
Can you attach your updated colortable, so we can take a look?
Thanks, Thomas
On Wed, Mar 27, 2019 at 10:27 PM stdp82@virgilio.it wrote:
Yes the left hemisphere is fine.
The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt.
Thanks
Stefano
Il 27 marzo 2019 alle 13.09 Thomas Yeo ythomas@csail.mit.edu ha scritto:
External Email - Use CautionHi Stefano,
Sorry. Can you confirm left hemisphere is ok?
I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114.
Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon.
Regards, Thomas
On Wed, Mar 27, 2019 at 6:14 PM < stdp82@virgilio.it> wrote:
I have renumbered and run:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal.
What's happened?
Thanks
Best regards,
Stefano
Il 26 marzo 2019 alle 13.05 Thomas Yeo < ythomas@csail.mit.edu> ha scritto:
External Email - Use CautionRenumber for visualization purpose.
Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit.
Thanks, Thomas
On Tue, Mar 26, 2019 at 6:44 PM < stdp82@virgilio.it> wrote:
Thanks.
Should I renumber for visualization purpose or for fs-fast?
How can I do it?
Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas@csail.mit.edu> ha scritto:
Hi Stefano,
Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.
If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parce...), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.
Regards, Thomas
On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it> wrote:
Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano
Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu> ha scritto:
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok.
On 3/10/19 4:05 PM, stdp82@virgilio.it wrote:
External Email - Use CautionI will use freeview.
Have you any suggestion on the use of fcseed-config option?
Are you agree with the command line listed below?
fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite
My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
How can I select a specific seed (id) to be used in -segids?
Thanks
Stefano
Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu ha scritto:
Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:
External Email - Use Caution
Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu ythomas@csail.mit.edu ha scritto:
External Email - Use Caution
Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:
External Email - Use Caution
I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000
--annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu DGREVE@mgh.harvard.edu ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list,
I'd like to use the regions included in Yeo 17 networks ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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Please see the attached file.
Il 27 marzo 2019 alle 15.39 Thomas Yeo ythomas@csail.mit.edu ha scritto:
External Email - Use Caution Hi Stefano, Can you attach your updated colortable, so we can take a look? Thanks, Thomas On Wed, Mar 27, 2019 at 10:27 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > >Yes the left hemisphere is fine. The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt. Thanks Stefano > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:External Email - Use Caution Hi Stefano, Sorry. Can you confirm left hemisphere is ok? I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114. Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon. Regards, Thomas On Wed, Mar 27, 2019 at 6:14 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > >I have renumbered and run: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal. What's happened? Thanks Best regards, Stefano > > > > > Il 26 marzo 2019 alle 13.05 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:External Email - Use Caution Renumber for visualization purpose. Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit. Thanks, Thomas On Tue, Mar 26, 2019 at 6:44 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > >Thanks. Should I renumber for visualization purpose or for fs-fast? How can I do it? > > > > > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:> > Hi Stefano, > > Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? > > If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while. > > If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parce...), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057. > > Regards, > Thomas > > On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > Hi, my concern is the mri_aparc2aseg command line. > > > > In summary, I have done: > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > The output is correct by the color label is those of aparc. > > > > Probably the error is the match between the annotations and annot-table. > > > > Could you check the command lines, please? > > > > Thanks > > > > Stefano > > > > > > > > > > > > > > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto: > > > > > > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. > > > > > > On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > I will use freeview. > > > > > > > > Have you any suggestion on the use of fcseed-config option? > > > > > > > > Are you agree with the command line listed below? > > > > > > > > fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite > > > > > > > > My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? > > > > > > > > How can I select a specific seed (id) to be used in -segids? > > > > > > > > Thanks > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu ha scritto: > > > > > > > > > > Hi Stefano > > > > > > > > > > is there a reason you are using tkmedit and not freeview? We deprecated > > > > > tkmedit a long time ago now > > > > > > > > > > cheers > > > > > Bruce > > > > > On Sun, 10 Mar 2019, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > Thanks. > > > > > > > > > > > > My error is in tkmedit > > > > > > > > > > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > > > > > > > > > Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu ha scritto: > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? > > > > > > Your tkmedit command seems to assume Yeo_17Net.mgz is in > > > > > > /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? > > > > > > > > > > > > On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > I have run: > > > > > > > > > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 > > > > > > 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > > > > > > > > > > > to check the output > > > > > > > > > > > > tksurfer subj rh inflated -annot > > > > > > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot > > > > > > > > > > > > My concern is here: > > > > > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 > > > > > > --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU > > > > > > T_freeview.txt --sval-annot > > > > > > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot > > > > > > > > > > > > tkmeditfv fsaverage orig.mgz -ov > > > > > > /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz > > > > > > > > > > > > Yeo_17Net.mgz is empty. > > > > > > > > > > > > Stefano > > > > > > > > > > > > Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." > > > > > > DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha scritto: > > > > > > > > > > > > You have to convert the annotation to a volume using mri_aparc2aseg > > > > > > (look at recon-all.log for an example, but note that you'll need to > > > > > > specify the output so that it does not overwrite). You'll then need to > > > > > > look in the output segmentation and see what the segmentation ids are > > > > > > > > > > > > On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > Hi list, > > > > > > > > > > > > I'd like to use the regions included in Yeo 17 networks > > > > > > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... > > > > > > ring). > > > > > > > > > > > > in FS-FAST. > > > > > > > > > > > > Which is the command line to be used to create a segmentation in > > > > > > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd > > > > > > like > > > > > > to use it to run fcseed-config, specify -seg yourseg.mgz > > > > > > -segid). > > > > > > > > > > > > Thanks > > > > > > > > > > > > Stefano > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > _______________________________________________ > > > > > > 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 > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________
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 Freesurfer@nmr.mgh.harvard.edu mailto: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
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Hi Stefano,
Did you see the colortable that Aihuiping attached? Does it work for you?
Thanks, Thomas
On Wed, Mar 27, 2019 at 11:08 PM stdp82@virgilio.it wrote:
Please see the attached file.
Il 27 marzo 2019 alle 15.39 Thomas Yeo ythomas@csail.mit.edu ha scritto:
External Email - Use CautionHi Stefano,
Can you attach your updated colortable, so we can take a look?
Thanks, Thomas
On Wed, Mar 27, 2019 at 10:27 PM < stdp82@virgilio.it> wrote:
Yes the left hemisphere is fine.
The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt.
Thanks
Stefano
Il 27 marzo 2019 alle 13.09 Thomas Yeo < ythomas@csail.mit.edu> ha scritto:
External Email - Use CautionHi Stefano,
Sorry. Can you confirm left hemisphere is ok?
I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114.
Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon.
Regards, Thomas
On Wed, Mar 27, 2019 at 6:14 PM < stdp82@virgilio.it> wrote:
I have renumbered and run:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal.
What's happened?
Thanks
Best regards,
Stefano
Il 26 marzo 2019 alle 13.05 Thomas Yeo < ythomas@csail.mit.edu> ha scritto:
External Email - Use CautionRenumber for visualization purpose.
Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit.
Thanks, Thomas
On Tue, Mar 26, 2019 at 6:44 PM < stdp82@virgilio.it> wrote:
Thanks.
Should I renumber for visualization purpose or for fs-fast?
How can I do it?
Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas@csail.mit.edu> ha scritto:
Hi Stefano,
Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057?
If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while.
If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parce...), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057.
Regards, Thomas
On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it> wrote:
Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano
Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu> ha scritto:
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok.
On 3/10/19 4:05 PM, stdp82@virgilio.it wrote:
External Email - Use CautionI will use freeview.
Have you any suggestion on the use of fcseed-config option?
Are you agree with the command line listed below?
fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite
My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt?
How can I select a specific seed (id) to be used in -segids?
Thanks
Stefano
Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu fischl@nmr.mgh.harvard.edu ha scritto:
Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:
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Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu ythomas@csail.mit.edu ha scritto:
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Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:
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I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000
--annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu DGREVE@mgh.harvard.edu ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.it wrote:
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Hi list,
I'd like to use the regions included in Yeo 17 networks ( https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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The problem persists.
We are sure that the command lines which I'm using are corrected?
Il 27 marzo 2019 alle 16.10 Thomas Yeo ythomas@csail.mit.edu ha scritto:
Hi Stefano, Did you see the colortable that Aihuiping attached? Does it work for you? Thanks, Thomas On Wed, Mar 27, 2019 at 11:08 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > >Please see the attached file. > > > Il 27 marzo 2019 alle 15.39 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:External Email - Use Caution Hi Stefano, Can you attach your updated colortable, so we can take a look? Thanks, Thomas On Wed, Mar 27, 2019 at 10:27 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > >Yes the left hemisphere is fine. The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt. Thanks Stefano > > > > > Il 27 marzo 2019 alle 13.09 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:External Email - Use Caution Hi Stefano, Sorry. Can you confirm left hemisphere is ok? I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114. Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon. Regards, Thomas On Wed, Mar 27, 2019 at 6:14 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > >I have renumbered and run: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN "2016 is visualized but labeled as rh_parahippocampal. What's happened? Thanks Best regards, Stefano > > > > > > > Il 26 marzo 2019 alle 13.05 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto:> > > External Email - Use Caution > > > > Renumber for visualization purpose. > > Do you mean how to re-number in the colortable? Just open the colortable in a text editing software and edit. > > Thanks, > Thomas > > On Tue, Mar 26, 2019 at 6:44 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > Thanks. > > > > Should I renumber for visualization purpose or for fs-fast? > > > > How can I do it? > > > > > > > > > > > > > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu > ha scritto: > > > > > > Hi Stefano, > > > > > > Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? > > > > > > If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while. > > > > > > If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parce...), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057. > > > > > > Regards, > > > Thomas > > > > > > On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > > > > > > > > > Hi, my concern is the mri_aparc2aseg command line. > > > > > > > > In summary, I have done: > > > > > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 > > > > > > > > > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot > > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > > > > > The output is correct by the color label is those of aparc. > > > > > > > > Probably the error is the match between the annotations and annot-table. > > > > > > > > Could you check the command lines, please? > > > > > > > > Thanks > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto: > > > > > > > > > > Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. > > > > > > > > > > On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > I will use freeview. > > > > > > > > > > > > Have you any suggestion on the use of fcseed-config option? > > > > > > > > > > > > Are you agree with the command line listed below? > > > > > > > > > > > > fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite > > > > > > > > > > > > My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? > > > > > > > > > > > > How can I select a specific seed (id) to be used in -segids? > > > > > > > > > > > > Thanks > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > Il 10 marzo 2019 alle 17.17 Bruce Fischl fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu ha scritto: > > > > > > > > > > > > > > Hi Stefano > > > > > > > > > > > > > > is there a reason you are using tkmedit and not freeview? We deprecated > > > > > > > tkmedit a long time ago now > > > > > > > > > > > > > > cheers > > > > > > > Bruce > > > > > > > On Sun, 10 Mar 2019, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > Thanks. > > > > > > > > > > > > > > > > My error is in tkmedit > > > > > > > > > > > > > > > > tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz > > > > > > > > > > > > > > > > Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edu mailto:ythomas@csail.mit.edu ha scritto: > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? > > > > > > > > Your tkmedit command seems to assume Yeo_17Net.mgz is in > > > > > > > > /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? > > > > > > > > > > > > > > > > On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > I have run: > > > > > > > > > > > > > > > > mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 > > > > > > > > 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 > > > > > > > > > > > > > > > > to check the output > > > > > > > > > > > > > > > > tksurfer subj rh inflated -annot > > > > > > > > $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot > > > > > > > > > > > > > > > > My concern is here: > > > > > > > > > > > > > > > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 > > > > > > > > --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU > > > > > > > > T_freeview.txt --sval-annot > > > > > > > > yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot > > > > > > > > > > > > > > > > tkmeditfv fsaverage orig.mgz -ov > > > > > > > > /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz > > > > > > > > > > > > > > > > Yeo_17Net.mgz is empty. > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." > > > > > > > > DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha scritto: > > > > > > > > > > > > > > > > You have to convert the annotation to a volume using mri_aparc2aseg > > > > > > > > (look at recon-all.log for an example, but note that you'll need to > > > > > > > > specify the output so that it does not overwrite). You'll then need to > > > > > > > > look in the output segmentation and see what the segmentation ids are > > > > > > > > > > > > > > > > On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > > > > > > > > > > > > > > > > > > > > External Email - Use Caution > > > > > > > > > > > > > > > > Hi list, > > > > > > > > > > > > > > > > I'd like to use the regions included in Yeo 17 networks > > > > > > > > (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... > > > > > > > > ring). > > > > > > > > > > > > > > > > in FS-FAST. > > > > > > > > > > > > > > > > Which is the command line to be used to create a segmentation in > > > > > > > > $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd > > > > > > > > like > > > > > > > > to use it to run fcseed-config, specify -seg yourseg.mgz > > > > > > > > -segid). > > > > > > > > > > > > > > > > Thanks > > > > > > > > > > > > > > > > Stefano > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > 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 > > > > > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > 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 > > > > > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > > 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 > > > > > Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu > > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > 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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mri_aparc2aseg --s subj --o sub/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt freeview subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
I am not sure that the command line sound fine.
When I open the files in freeview, the name of labels is the same of aparc2009.
Il 26 marzo 2019 alle 4.01 Thomas Yeo ythomas@csail.mit.edu ha scritto:
Hi Stefano, Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? If so, you will just need the right colortable to view the Yeo_17Net.mgz. We are currently generating a new colortable that should work for you. This might take a while. If you are in a hurry, you can download the colortable here ( https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), but as you can see the range of values are not in the 1000-2000 range. So what you need to do is for the left hemisphere structures, you need to renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere structures, you need to renumber them from 58 to 114 to 2001 to 2057. Regards, Thomas On Sun, Mar 24, 2019 at 12:18 AM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: > >Hi, my concern is the mri_aparc2aseg command line. In summary, I have done: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj --hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000 mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz The output is correct by the color label is those of aparc. Probably the error is the match between the annotations and annot-table. Could you check the command lines, please? Thanks Stefano > > > Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." < DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu > ha scritto:Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution I will use freeview. Have you any suggestion on the use of fcseed-config option? Are you agree with the command line listed below? fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? How can I select a specific seed (id) to be used in -segids? Thanks Stefano > > > > >Il 10 marzo 2019 alle 17.17 Bruce Fischl <fischl@nmr.mgh.harvard.edu> mailto:fischl@nmr.mgh.harvard.edu ha scritto: Hi Stefano is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > >External Email - Use Caution Thanks. My error is in tkmedit tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas@csail.mit.edu> mailto:ythomas@csail.mit.edu ha scritto: External Email - Use Caution Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty? Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder? On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it mailto:stdp82@virgilio.it > wrote: External Email - Use Caution I have run: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 to check the output tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot My concern is here: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz Yeo_17Net.mgz is empty. Stefano Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_cluste ring). in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ 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 Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>
Load it as a segmentation, not an overlay (-seg Yeo_17Net.mgz)
On 3/10/19 4:46 AM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
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Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo ythomas@csail.mit.edumailto:ythomas@csail.mit.edu ha scritto:
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Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty?
Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.itmailto:stdp82@virgilio.it> wrote:
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I have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000
to check the output
tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot
My concern is here:
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot
tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz
Yeo_17Net.mgz is empty.
Stefano
Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto:
You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are
On 3/7/19 4:13 PM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
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Hi list,
I'd like to use the regions included in Yeo 17 networks (https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce...).
in FS-FAST.
Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid).
Thanks
Stefano
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