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Dear all,
I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got nice results with a good delineation of all the nuclei.
Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to perform functional connectivity with cortical regions in SPM.
Therefore, I converted the outputs of the segmentation (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the command "mri_convert .mgz .nii".
However, the resulting labels of the thalamus have a different resolution and I cannot visualize anymore the different thalamic subnuclei but only the entire thalamus.
Do you have any suggestion to convert thalamic labels into nifti without losing the different subnuclei?
Do you think that the thalamic segmentation is accurate enough to be used to perform functional connectivity?
Thank you and best regards,
Valentina Mancini
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Dear Valentina Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? Cheers Eugenio
Sent from mobile, please excuse brevity and typos
________________________________ From: Valentina Mancini Valentina.Mancini@unige.ch Sent: Wednesday, March 27, 2019 5:56:34 AM To: freesurfer@nmr.mgh.harvard.edu Cc: Iglesias Gonzalez, Eugenio Subject: Conversion of thalamic nuclei labels
Dear all,
I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got nice results with a good delineation of all the nuclei.
Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to perform functional connectivity with cortical regions in SPM.
Therefore, I converted the outputs of the segmentation (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the command "mri_convert .mgz .nii".
However, the resulting labels of the thalamus have a different resolution and I cannot visualize anymore the different thalamic subnuclei but only the entire thalamus.
Do you have any suggestion to convert thalamic labels into nifti without losing the different subnuclei?
Do you think that the thalamic segmentation is accurate enough to be used to perform functional connectivity?
Thank you and best regards,
Valentina Mancini
and your full command line for conversion? On Wed, 27 Mar 2019, Iglesias Gonzalez, Eugenio wrote:
External Email - Use Caution
Dear Valentina Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? Cheers Eugenio
Sent from mobile, please excuse brevity and typos
From: Valentina Mancini Valentina.Mancini@unige.ch Sent: Wednesday, March 27, 2019 5:56:34 AM To: freesurfer@nmr.mgh.harvard.edu Cc: Iglesias Gonzalez, Eugenio Subject: Conversion of thalamic nuclei labels
Dear all,
I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got nice results with a good delineation of all the nuclei.
Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to perform functional connectivity with cortical regions in SPM.
Therefore, I converted the outputs of the segmentation (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the command "mri_convert .mgz .nii".
However, the resulting labels of the thalamus have a different resolution and I cannot visualize anymore the different thalamic subnuclei but only the entire thalamus.
Do you have any suggestion to convert thalamic labels into nifti without losing the different subnuclei?
Do you think that the thalamic segmentation is accurate enough to be used to perform functional connectivity?
Thank you and best regards,
Valentina Mancini
External Email - Use Caution
Hi Valentina, I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes? Cheers, /Eugenio
External Email - Use Caution
Hi Eugenio,
Yes, when I move the cursor I can see different pixel values corresponding to the different areas of the thalamus.
In FSLeyes you can select different lookup tables, and there is one called "Freeseurfer HSV", but it doesn't work anyway.
However, I used FSLeyes only because it was the default programm to open nifti files, but it was the same in SPM ad Conn.
Can you please suggest me any other way to open the nifti file with its lookup table?
As I was planning to use it in SPM, the ideal would be to manage to visualize the different subnuclei in SPM/Conn.
Best,
Valentina
________________________________ Da: Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Inviato: mercoledì 27 marzo 2019 14:55:00 A: Freesurfer support list Cc: Valentina Mancini Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Valentina, I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes? Cheers, /Eugenio
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
On 27/03/2019, 09:53, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
and your full command line for conversion? On Wed, 27 Mar 2019, Iglesias Gonzalez, Eugenio wrote:
> > External Email - Use Caution > > Dear Valentina > Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? > Cheers > Eugenio > > Sent from mobile, please excuse brevity and typos > > ____________________________________________________________________________________________________ > From: Valentina Mancini Valentina.Mancini@unige.ch > Sent: Wednesday, March 27, 2019 5:56:34 AM > To: freesurfer@nmr.mgh.harvard.edu > Cc: Iglesias Gonzalez, Eugenio > Subject: Conversion of thalamic nuclei labels > > Dear all, > > > I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got > nice results with a good delineation of all the nuclei. > > Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to > perform functional connectivity with cortical regions in SPM. > > Therefore, I converted the outputs of the segmentation > (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the > command "mri_convert .mgz .nii". > > However, the resulting labels of the thalamus have a different resolution and I cannot visualize > anymore the different thalamic subnuclei but only the entire thalamus. > > > > Do you have any suggestion to convert thalamic labels into nifti without losing the different > subnuclei? > > Do you think that the thalamic segmentation is accurate enough to be used to perform functional > connectivity? > > > > Thank you and best regards, > > > > Valentina Mancini > > >
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Thanks, Valentina. The thalamic nuclei were included in the FreeSurfer lookup table in the development version, so I doubt they’d be included in the FreeSurfer HSV. Is it possible to add them manually? Also: why don’t you use Freeview to visualize your niftis? Cheers, /E
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
From: Valentina Mancini Valentina.Mancini@unige.ch Date: Wednesday, 27 March 2019 at 10:08 To: "Iglesias Gonzalez, Eugenio" e.iglesias@ucl.ac.uk, Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Eugenio,
Yes, when I move the cursor I can see different pixel values corresponding to the different areas of the thalamus.
In FSLeyes you can select different lookup tables, and there is one called "Freeseurfer HSV", but it doesn't work anyway.
However, I used FSLeyes only because it was the default programm to open nifti files, but it was the same in SPM ad Conn.
Can you please suggest me any other way to open the nifti file with its lookup table?
As I was planning to use it in SPM, the ideal would be to manage to visualize the different subnuclei in SPM/Conn.
Best,
Valentina
________________________________ Da: Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Inviato: mercoledì 27 marzo 2019 14:55:00 A: Freesurfer support list Cc: Valentina Mancini Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Valentina, I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes? Cheers, /Eugenio
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
http://www.jeiglesias.comhttps://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com&data=02%7C01%7Ce.iglesias%40ucl.ac.uk%7Cfd1e3c21f6bb420769df08d6b2bdb777%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636892925227688578&sdata=QTSNSIU2i8dYs0sShmUrI7vitjOBg62WZSiQGKiQt9A%3D&reserved=0
On 27/03/2019, 09:53, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
and your full command line for conversion? On Wed, 27 Mar 2019, Iglesias Gonzalez, Eugenio wrote:
> > External Email - Use Caution > > Dear Valentina > Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? > Cheers > Eugenio > > Sent from mobile, please excuse brevity and typos > > ____________________________________________________________________________________________________ > From: Valentina Mancini Valentina.Mancini@unige.ch > Sent: Wednesday, March 27, 2019 5:56:34 AM > To: freesurfer@nmr.mgh.harvard.edu > Cc: Iglesias Gonzalez, Eugenio > Subject: Conversion of thalamic nuclei labels > > Dear all, > > > I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got > nice results with a good delineation of all the nuclei. > > Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to > perform functional connectivity with cortical regions in SPM. > > Therefore, I converted the outputs of the segmentation > (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the > command "mri_convert .mgz .nii". > > However, the resulting labels of the thalamus have a different resolution and I cannot visualize > anymore the different thalamic subnuclei but only the entire thalamus. > > > > Do you have any suggestion to convert thalamic labels into nifti without losing the different > subnuclei? > > Do you think that the thalamic segmentation is accurate enough to be used to perform functional > connectivity? > > > > Thank you and best regards, > > > > Valentina Mancini > > >
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We have run the thalamic and amyhip segmentation scripts on HCP data and were convert the segmented native nuclei into cifti space including the subcortial nifti
set thal = ${subjid}_ThalamicNuclei.v10.T1
mri_convert -rt nearest -rl $projdir/$subjid/T1w/T1w_acpc_dc_restore.nii.gz {$thal}.mgz {$thal}.nii.gz applywarp --rel --interp=nn -i {$thal}.nii.gz -r $projdir/$subjid/MNINonLinear/T1w_restore.nii.gz -w $projdir/$subjid/MNINonLinear/xfms/acpc_dc2standard -o {$thal}_native.nii.gz applywarp --interp=nn -i {$thal}_native.nii.gz -r $projdir/$subjid/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o {$thal}_Atlas_2mm.nii.gz
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Valentina Mancini Valentina.Mancini@unige.ch Sent: Wednesday, March 27, 2019 10:08:36 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
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Hi Eugenio,
Yes, when I move the cursor I can see different pixel values corresponding to the different areas of the thalamus.
In FSLeyes you can select different lookup tables, and there is one called "Freeseurfer HSV", but it doesn't work anyway.
However, I used FSLeyes only because it was the default programm to open nifti files, but it was the same in SPM ad Conn.
Can you please suggest me any other way to open the nifti file with its lookup table?
As I was planning to use it in SPM, the ideal would be to manage to visualize the different subnuclei in SPM/Conn.
Best,
Valentina
________________________________ Da: Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Inviato: mercoledì 27 marzo 2019 14:55:00 A: Freesurfer support list Cc: Valentina Mancini Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Valentina, I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes? Cheers, /Eugenio
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
https://protect2.fireeye.com/url?k=c7ac8922-9b8f6ef9-c7ae7017-0cc47aa8c6e0-3...https://protect2.fireeye.com/url?k=1d91cfc4-41b2281f-1d9336f1-0cc47aa8c6e0-d9d69f6f3149b48e&u=http://www.jeiglesias.com/
On 27/03/2019, 09:53, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
and your full command line for conversion? On Wed, 27 Mar 2019, Iglesias Gonzalez, Eugenio wrote:
> > External Email - Use Caution > > Dear Valentina > Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? > Cheers > Eugenio > > Sent from mobile, please excuse brevity and typos > > ____________________________________________________________________________________________________ > From: Valentina Mancini Valentina.Mancini@unige.ch > Sent: Wednesday, March 27, 2019 5:56:34 AM > To: freesurfer@nmr.mgh.harvard.edu > Cc: Iglesias Gonzalez, Eugenio > Subject: Conversion of thalamic nuclei labels > > Dear all, > > > I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got > nice results with a good delineation of all the nuclei. > > Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to > perform functional connectivity with cortical regions in SPM. > > Therefore, I converted the outputs of the segmentation > (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the > command "mri_convert .mgz .nii". > > However, the resulting labels of the thalamus have a different resolution and I cannot visualize > anymore the different thalamic subnuclei but only the entire thalamus. > > > > Do you have any suggestion to convert thalamic labels into nifti without losing the different > subnuclei? > > Do you think that the thalamic segmentation is accurate enough to be used to perform functional > connectivity? > > > > Thank you and best regards, > > > > Valentina Mancini > > >
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wb_command -volume-label-import LR_amyhipthal.nii.gz $templatedir/SUBCORT_LR.txt LR_amyhipthal_labeled.nii.gz
this is with the amy and hip but can be done with just the thalamus
you just need to edit the label file
________________________________ From: Sanchez, Juan (NYSPI) Sent: Wednesday, March 27, 2019 10:15:18 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
We have run the thalamic and amyhip segmentation scripts on HCP data and were convert the segmented native nuclei into cifti space including the subcortial nifti
set thal = ${subjid}_ThalamicNuclei.v10.T1
mri_convert -rt nearest -rl $projdir/$subjid/T1w/T1w_acpc_dc_restore.nii.gz {$thal}.mgz {$thal}.nii.gz applywarp --rel --interp=nn -i {$thal}.nii.gz -r $projdir/$subjid/MNINonLinear/T1w_restore.nii.gz -w $projdir/$subjid/MNINonLinear/xfms/acpc_dc2standard -o {$thal}_native.nii.gz applywarp --interp=nn -i {$thal}_native.nii.gz -r $projdir/$subjid/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o {$thal}_Atlas_2mm.nii.gz
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Valentina Mancini Valentina.Mancini@unige.ch Sent: Wednesday, March 27, 2019 10:08:36 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
External Email - Use Caution
Hi Eugenio,
Yes, when I move the cursor I can see different pixel values corresponding to the different areas of the thalamus.
In FSLeyes you can select different lookup tables, and there is one called "Freeseurfer HSV", but it doesn't work anyway.
However, I used FSLeyes only because it was the default programm to open nifti files, but it was the same in SPM ad Conn.
Can you please suggest me any other way to open the nifti file with its lookup table?
As I was planning to use it in SPM, the ideal would be to manage to visualize the different subnuclei in SPM/Conn.
Best,
Valentina
________________________________ Da: Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Inviato: mercoledì 27 marzo 2019 14:55:00 A: Freesurfer support list Cc: Valentina Mancini Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Valentina, I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes? Cheers, /Eugenio
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
https://protect2.fireeye.com/url?k=c7ac8922-9b8f6ef9-c7ae7017-0cc47aa8c6e0-3...https://protect2.fireeye.com/url?k=1d91cfc4-41b2281f-1d9336f1-0cc47aa8c6e0-d9d69f6f3149b48e&u=http://www.jeiglesias.com/
On 27/03/2019, 09:53, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
and your full command line for conversion? On Wed, 27 Mar 2019, Iglesias Gonzalez, Eugenio wrote:
> > External Email - Use Caution > > Dear Valentina > Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? > Cheers > Eugenio > > Sent from mobile, please excuse brevity and typos > > ____________________________________________________________________________________________________ > From: Valentina Mancini Valentina.Mancini@unige.ch > Sent: Wednesday, March 27, 2019 5:56:34 AM > To: freesurfer@nmr.mgh.harvard.edu > Cc: Iglesias Gonzalez, Eugenio > Subject: Conversion of thalamic nuclei labels > > Dear all, > > > I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got > nice results with a good delineation of all the nuclei. > > Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to > perform functional connectivity with cortical regions in SPM. > > Therefore, I converted the outputs of the segmentation > (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the > command "mri_convert .mgz .nii". > > However, the resulting labels of the thalamus have a different resolution and I cannot visualize > anymore the different thalamic subnuclei but only the entire thalamus. > > > > Do you have any suggestion to convert thalamic labels into nifti without losing the different > subnuclei? > > Do you think that the thalamic segmentation is accurate enough to be used to perform functional > connectivity? > > > > Thank you and best regards, > > > > Valentina Mancini > > >
External Email - Use Caution
First of all, I would like to thank you all for your help.
#Eugenio: yes probably there is a way to manually import the thalamic lookup table in FSLeyes. However, I don't have to use the thalamic segmentation in FSL, but in SPM and it would be much better if I could find a way to visualize the subnuclei in SPM.
#Juan: are you suggesting to convert the nifti files that I obtained from the mgz into cifti space or to directly convert from mgz to cifti space? Do you know if then it is possible to import the cifti files in SPM and to use them as ROIs?
________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Sanchez, Juan (NYSPI) Juan.Sanchez@nyspi.columbia.edu Inviato: mercoledì 27 marzo 2019 15:17:41 A: Iglesias Gonzalez, Eugenio; Freesurfer support list Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
External Email - Use Caution
wb_command -volume-label-import LR_amyhipthal.nii.gz $templatedir/SUBCORT_LR.txt LR_amyhipthal_labeled.nii.gz
this is with the amy and hip but can be done with just the thalamus
you just need to edit the label file
________________________________ From: Sanchez, Juan (NYSPI) Sent: Wednesday, March 27, 2019 10:15:18 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
We have run the thalamic and amyhip segmentation scripts on HCP data and were convert the segmented native nuclei into cifti space including the subcortial nifti
set thal = ${subjid}_ThalamicNuclei.v10.T1
mri_convert -rt nearest -rl $projdir/$subjid/T1w/T1w_acpc_dc_restore.nii.gz {$thal}.mgz {$thal}.nii.gz applywarp --rel --interp=nn -i {$thal}.nii.gz -r $projdir/$subjid/MNINonLinear/T1w_restore.nii.gz -w $projdir/$subjid/MNINonLinear/xfms/acpc_dc2standard -o {$thal}_native.nii.gz applywarp --interp=nn -i {$thal}_native.nii.gz -r $projdir/$subjid/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o {$thal}_Atlas_2mm.nii.gz
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Valentina Mancini Valentina.Mancini@unige.ch Sent: Wednesday, March 27, 2019 10:08:36 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
ATTENTION: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.
External Email - Use Caution
Hi Eugenio,
Yes, when I move the cursor I can see different pixel values corresponding to the different areas of the thalamus.
In FSLeyes you can select different lookup tables, and there is one called "Freeseurfer HSV", but it doesn't work anyway.
However, I used FSLeyes only because it was the default programm to open nifti files, but it was the same in SPM ad Conn.
Can you please suggest me any other way to open the nifti file with its lookup table?
As I was planning to use it in SPM, the ideal would be to manage to visualize the different subnuclei in SPM/Conn.
Best,
Valentina
________________________________ Da: Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Inviato: mercoledì 27 marzo 2019 14:55:00 A: Freesurfer support list Cc: Valentina Mancini Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Valentina, I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes? Cheers, /Eugenio
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
https://protect2.fireeye.com/url?k=c7ac8922-9b8f6ef9-c7ae7017-0cc47aa8c6e0-3...https://protect2.fireeye.com/url?k=1d91cfc4-41b2281f-1d9336f1-0cc47aa8c6e0-d9d69f6f3149b48e&u=http://www.jeiglesias.com/
On 27/03/2019, 09:53, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
and your full command line for conversion? On Wed, 27 Mar 2019, Iglesias Gonzalez, Eugenio wrote:
> > External Email - Use Caution > > Dear Valentina > Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? > Cheers > Eugenio > > Sent from mobile, please excuse brevity and typos > > ____________________________________________________________________________________________________ > From: Valentina Mancini Valentina.Mancini@unige.ch > Sent: Wednesday, March 27, 2019 5:56:34 AM > To: freesurfer@nmr.mgh.harvard.edu > Cc: Iglesias Gonzalez, Eugenio > Subject: Conversion of thalamic nuclei labels > > Dear all, > > > I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got > nice results with a good delineation of all the nuclei. > > Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to > perform functional connectivity with cortical regions in SPM. > > Therefore, I converted the outputs of the segmentation > (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the > command "mri_convert .mgz .nii". > > However, the resulting labels of the thalamus have a different resolution and I cannot visualize > anymore the different thalamic subnuclei but only the entire thalamus. > > > > Do you have any suggestion to convert thalamic labels into nifti without losing the different > subnuclei? > > Do you think that the thalamic segmentation is accurate enough to be used to perform functional > connectivity? > > > > Thank you and best regards, > > > > Valentina Mancini > > >
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You dont have to go all the way into a cifti space dlabel you could use the steps I sent to create a labeled nifti
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Valentina Mancini Valentina.Mancini@unige.ch Sent: Wednesday, March 27, 2019 10:34:28 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
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First of all, I would like to thank you all for your help.
#Eugenio: yes probably there is a way to manually import the thalamic lookup table in FSLeyes. However, I don't have to use the thalamic segmentation in FSL, but in SPM and it would be much better if I could find a way to visualize the subnuclei in SPM.
#Juan: are you suggesting to convert the nifti files that I obtained from the mgz into cifti space or to directly convert from mgz to cifti space? Do you know if then it is possible to import the cifti files in SPM and to use them as ROIs?
________________________________ Da: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu per conto di Sanchez, Juan (NYSPI) Juan.Sanchez@nyspi.columbia.edu Inviato: mercoledì 27 marzo 2019 15:17:41 A: Iglesias Gonzalez, Eugenio; Freesurfer support list Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
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wb_command -volume-label-import LR_amyhipthal.nii.gz $templatedir/SUBCORT_LR.txt LR_amyhipthal_labeled.nii.gz
this is with the amy and hip but can be done with just the thalamus
you just need to edit the label file
________________________________ From: Sanchez, Juan (NYSPI) Sent: Wednesday, March 27, 2019 10:15:18 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
We have run the thalamic and amyhip segmentation scripts on HCP data and were convert the segmented native nuclei into cifti space including the subcortial nifti
set thal = ${subjid}_ThalamicNuclei.v10.T1
mri_convert -rt nearest -rl $projdir/$subjid/T1w/T1w_acpc_dc_restore.nii.gz {$thal}.mgz {$thal}.nii.gz applywarp --rel --interp=nn -i {$thal}.nii.gz -r $projdir/$subjid/MNINonLinear/T1w_restore.nii.gz -w $projdir/$subjid/MNINonLinear/xfms/acpc_dc2standard -o {$thal}_native.nii.gz applywarp --interp=nn -i {$thal}_native.nii.gz -r $projdir/$subjid/MNINonLinear/ROIs/Atlas_ROIs.2.nii.gz -o {$thal}_Atlas_2mm.nii.gz
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Valentina Mancini Valentina.Mancini@unige.ch Sent: Wednesday, March 27, 2019 10:08:36 AM To: Iglesias Gonzalez, Eugenio; Freesurfer support list Subject: Re: [Freesurfer] Conversion of thalamic nuclei labels
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Hi Eugenio,
Yes, when I move the cursor I can see different pixel values corresponding to the different areas of the thalamus.
In FSLeyes you can select different lookup tables, and there is one called "Freeseurfer HSV", but it doesn't work anyway.
However, I used FSLeyes only because it was the default programm to open nifti files, but it was the same in SPM ad Conn.
Can you please suggest me any other way to open the nifti file with its lookup table?
As I was planning to use it in SPM, the ideal would be to manage to visualize the different subnuclei in SPM/Conn.
Best,
Valentina
________________________________ Da: Iglesias Gonzalez, Eugenio e.iglesias@ucl.ac.uk Inviato: mercoledì 27 marzo 2019 14:55:00 A: Freesurfer support list Cc: Valentina Mancini Oggetto: Re: [Freesurfer] Conversion of thalamic nuclei labels
Hi Valentina, I've never used FSLeyes but I suspect you'd need a lookup table to visualize the nuclei properly. Do you see different pixel values when you move your cursor over the different areas of the thalamus in FSLeyes? Cheers, /Eugenio
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
https://protect2.fireeye.com/url?k=d5d7bf7e-89ef19c3-d5d5464b-000babd9fa3f-4...https://protect2.fireeye.com/url?k=8956ac67-d56e0ada-89545552-000babd9fa3f-4737edc8d012f7a6&u=https://protect2.fireeye.com/url?k=1d91cfc4-41b2281f-1d9336f1-0cc47aa8c6e0-d9d69f6f3149b48e&u=http://www.jeiglesias.com/
On 27/03/2019, 09:53, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of fischl@nmr.mgh.harvard.edu> wrote:
and your full command line for conversion? On Wed, 27 Mar 2019, Iglesias Gonzalez, Eugenio wrote:
> > External Email - Use Caution > > Dear Valentina > Resolution should not be affected by MRI_convert. Can you please send us an example/screen capture? > Cheers > Eugenio > > Sent from mobile, please excuse brevity and typos > > ____________________________________________________________________________________________________ > From: Valentina Mancini Valentina.Mancini@unige.ch > Sent: Wednesday, March 27, 2019 5:56:34 AM > To: freesurfer@nmr.mgh.harvard.edu > Cc: Iglesias Gonzalez, Eugenio > Subject: Conversion of thalamic nuclei labels > > Dear all, > > > I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got > nice results with a good delineation of all the nuclei. > > Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to > perform functional connectivity with cortical regions in SPM. > > Therefore, I converted the outputs of the segmentation > (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the > command "mri_convert .mgz .nii". > > However, the resulting labels of the thalamus have a different resolution and I cannot visualize > anymore the different thalamic subnuclei but only the entire thalamus. > > > > Do you have any suggestion to convert thalamic labels into nifti without losing the different > subnuclei? > > Do you think that the thalamic segmentation is accurate enough to be used to perform functional > connectivity? > > > > Thank you and best regards, > > > > Valentina Mancini > > >
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Iglesias Gonzalez, Eugenio -
Sanchez, Juan (NYSPI) -
Valentina Mancini