External Email - Use Caution
Hello experts,
As a sanity check in a pipeline I'm running I tried converting an atlas file containing visual ROIs from .mgz to .nii.gz and then immediately converting the resulting .nii.gz file back to .mgz:
mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1
mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1
Something is getting lost in this conversion and reconversion, because when I run the following two lines (to generate a label for V1) on the two different .mgz files, the original file correctly results in the identification of 1591 label voxels, while the converted/reconverted file incorrectly results in the identification of 111 label voxels, none of which overlap with the 1591 correct voxels:
mri_vol2surf --src mri/lh.atlas.mgz \
--src_type FLOAT \
--srcreg mri/register.dat \
--hemi lh \
--surf white \
--o mri/lh.atlas.mgh
mri_cor2label --c mri/lh.atlas.mgh \
--id 1 \
--surf SubID lh \
--l label/lh.V1_ventral.label
Any feedback on where I'm going wrong here would be greatly appreciated!
Thanks for your time, JD Knotts
1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OSX 10.11.6 3) Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64
Not sure what is going on here. What is lh.atlas.mgz? Is is a surface overlay? What is subject_t1.nii.gz? If it is not the same geometry of lh.atlas.mgz, then strange things will happen when you do it a second time.
On 3/31/2019 12:28 PM, JD Knotts wrote:
External Email - Use Caution
Hello experts,
As a sanity check in a pipeline I'm running I tried converting an atlas file containing visual ROIs from .mgz to .nii.gz and then immediately converting the resulting .nii.gz file back to .mgz:
mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1
mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 Something is getting lost in this conversion and reconversion, because when I run the following two lines (to generate a label for V1) on the two different .mgz files, the original file correctly results in the identification of 1591 label voxels, while the converted/reconverted file incorrectly results in the identification of 111 label voxels, none of which overlap with the 1591 correct voxels: mri_vol2surf --src mri/lh.atlas.mgz \
--src_type FLOAT \
--srcreg mri/register.dat \
--hemi lh \
--surf white \
--o mri/lh.atlas.mgh
mri_cor2label --c mri/lh.atlas.mgh \
--id 1 \
--surf SubID lh \
--l label/lh.V1_ventral.label
Any feedback on where I'm going wrong here would be greatly appreciated! Thanks for your time, JD Knotts 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OSX 10.11.6 3) Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64
-- Doctoral Candidate, Cognitive Neuroscience Department of Psychology University of California, Los Angeles
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Hi Dr. Greve,
Thanks very much for your reply! The lh.atlas.mgz file is a volumetric atlas (Kastner atlas https://www.ncbi.nlm.nih.gov/pubmed/25452571) generated for an individual subject as described here https://gizemaltan.com/get-rois-kastner-freesurfer-atlas/. And subject_t1.nii.gz is the subject's T1-weighted nifti file. Is there an easy way to check the respective geometries?
Thanks again, JD
On Mon, Apr 1, 2019 at 8:56 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Not sure what is going on here. What is lh.atlas.mgz? Is is a surface overlay? What is subject_t1.nii.gz? If it is not the same geometry of lh.atlas.mgz, then strange things will happen when you do it a second time.
On 3/31/2019 12:28 PM, JD Knotts wrote:
External Email - Use CautionHello experts,
As a sanity check in a pipeline I'm running I tried converting an atlas file containing visual ROIs from .mgz to .nii.gz and then immediately converting the resulting .nii.gz file back to .mgz:
mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1
mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 Something is getting lost in this conversion and reconversion, because when I run the following two lines (to generate a label for V1) on the two different .mgz files, the original file correctly results in the identification of 1591 label voxels, while the converted/reconverted file incorrectly results in the identification of 111 label voxels, none of which overlap with the 1591 correct voxels: mri_vol2surf --src mri/lh.atlas.mgz \
--src_type FLOAT \
--srcreg mri/register.dat \
--hemi lh \
--surf white \
--o mri/lh.atlas.mgh
mri_cor2label --c mri/lh.atlas.mgh \
--id 1 \
--surf SubID lh \
--l label/lh.V1_ventral.label Any feedback on where I'm going wrong here would be greatly appreciated! Thanks for your time, JD Knotts
- FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0
- Platform: Mac OSX 10.11.6
- Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0:
Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64
-- Doctoral Candidate, Cognitive Neuroscience Department of Psychology University of California, Los Angeles
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://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
mri_info will give you the voxel-to-RAS matrix and the number of cols, rows, slices. I don't think those commands are doing what you think. I don't understand where vol2surf or cor2label come in.
On 4/1/19 12:55 PM, JD Knotts wrote:
External Email - Use Caution
Hi Dr. Greve,
Thanks very much for your reply! The lh.atlas.mgz file is a volumetric atlas (Kastner atlas https://www.ncbi.nlm.nih.gov/pubmed/25452571) generated for an individual subject as described here https://gizemaltan.com/get-rois-kastner-freesurfer-atlas/. And subject_t1.nii.gz is the subject's T1-weighted nifti file. Is there an easy way to check the respective geometries?
Thanks again, JD
On Mon, Apr 1, 2019 at 8:56 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Not sure what is going on here. What is lh.atlas.mgz? Is is a surface overlay? What is subject_t1.nii.gz? If it is not the same geometry of lh.atlas.mgz, then strange things will happen when you do it a second time. On 3/31/2019 12:28 PM, JD Knotts wrote:External Email - Use Caution Hello experts, As a sanity check in a pipeline I'm running I tried converting an atlas file containing visual ROIs from .mgz to .nii.gz and then immediately converting the resulting .nii.gz file back to .mgz: mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like subject_t1.nii.gz--resample_type nearest --out_data_type int --no_scale 1 mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz --reslice_like subject_t1.nii.gz--resample_type nearest --out_data_type int --no_scale 1 Something is getting lost in this conversion and reconversion, because when I run the following two lines (to generate a label for V1) on the two different .mgz files, the original file correctly results in the identification of 1591 label voxels, while the converted/reconverted file incorrectly results in the identification of 111 label voxels, none of which overlap with the 1591 correct voxels: mri_vol2surf --src mri/lh.atlas.mgz \ --src_type FLOAT \ --srcreg mri/register.dat \ --hemi lh \ --surf white \ --o mri/lh.atlas.mgh mri_cor2label --c mri/lh.atlas.mgh \ --id 1 \ --surf SubID lh \ --l label/lh.V1_ventral.label Any feedback on where I'm going wrong here would be greatly appreciated! Thanks for your time, JD Knotts 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OSX 10.11.6 3) Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 -- Doctoral Candidate, Cognitive Neuroscience Department of Psychology University of California, Los Angeles _______________________________________________ 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-- JD Knotts Doctoral Candidate, Cognitive Neuroscience Department of Psychology University of California, Los Angeles
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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