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Dear FreeSurfer experts,
I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion?
Thank you Francesca
Use mri_label2vol to map the segmentation into the fMRI space, then use mri_segstats using the --avgwf option to get time courses. Run it with --help to get examples
On 11/26/2020 9:16 AM, Francesca Strappini wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion?
Thank you Francesca
-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.ilmailto:francesca.strappini@weizmann.ac.il
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thank you! I run mri_label2vol but I got this error.
mri_label2vol --label D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --temp /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz --reg registerNMT2toCassis.dat --fillthresh .3 --proj frac 0 1 .1 --subject MonkeyCassis --hemi lh --o D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz Number of labels: 1 D99_atlas_in_NMT_v2.0_asym_fh.nii.gz Annot File: (null) Template Volume: /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz Outut Volume: D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz Registration File: registerNMT2toCassis.dat Fill Threshold: 0.3 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 1 ProjDelta: 0.1 Subject: MonkeyCassis Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.49612 -0.00000 -0.00000 32.00000; -0.00000 -0.00000 -0.49612 32.00000; -0.00000 0.50000 -0.00000 10.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 8.12549 nHits Thresh: 2.43765 Loading registration from registerNMT2toCassis.dat RegMat: -------- -0.99904 -0.03839 0.02093 -1.00375; 0.02331 -0.06274 0.99776 -29.26276; 0.03699 -0.99729 -0.06358 -8.60775; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- 0.49565 0.01905 -0.01038 32.49799; -0.01835 0.49478 0.03154 36.27051; 0.01166 -0.03137 0.49888 -4.63138; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.white nvertices = 16975 Reading thickness /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.thickness nlabels = 1 Allocating Hit Volume (81920) voxels Loading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
�7��ա<�d�TGr��L�� �s�����L�����f�T�ot�9����eOԲ:|��L��� ���s/ ��,�' ��,3����~�铜��s�`�:�ǙG�] �I�Gu ��`�:�[g��>� <�\�٧S �N��L���<>�t��Mw��l���n�љ���ǢS �WM�K�4 f��Nu W3FfN�TGqt� �Nu �Nf6�V�����}�VG�?̄ޭ��x� �[ ꝣy�Ou��/� e:%�N�YܺՁ>�e�uu���3�k�:�����'O�:���w�[�%��v�Ou�w�����ث�t� �^u����L��pg �^2��ܱ��=�u���8wo�C}�[ {���M&� =<����G[�X�3]�㜙췪�|��tI掝�L�� w2g�Vu�;�\��(_Og_gN���P�'O3'�Vu�_M���, �̪ѯ�t�I8��q�z��ߓ����ONꗙ �_ �u �y�Wu��v�iݯ��x���d��a�'s�03���C��� �=ȣ�xϲ�� ��d5�;���Nf<Ձ���3
�s��9� �A�d��A��e��A/�;����:���Lr0�y��<��d�s�QѪ���^�Ou����̂]�� mri_label2vol: could not scan # of lines from label file ERROR reading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
Il giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
Use mri_label2vol to map the segmentation into the fMRI space, then use mri_segstats using the --avgwf option to get time courses. Run it with --help to get examples
On 11/26/2020 9:16 AM, Francesca Strappini wrote:
External Email - Use CautionDear FreeSurfer experts,
I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion?
Thank you Francesca
-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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The argument to the --label flag should be a freesurfer label file, this is a text file not an nii.gz file.
On 12/21/2020 10:52 AM, Francesca Strappini wrote:
External Email - Use Caution
Thank you! I run mri_label2vol but I got this error.
mri_label2vol --label D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --temp /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz --reg registerNMT2toCassis.dat --fillthresh .3 --proj frac 0 1 .1 --subject MonkeyCassis --hemi lh --o D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz Number of labels: 1 D99_atlas_in_NMT_v2.0_asym_fh.nii.gz Annot File: (null) Template Volume: /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz Outut Volume: D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz Registration File: registerNMT2toCassis.dat Fill Threshold: 0.3 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 1 ProjDelta: 0.1 Subject: MonkeyCassis Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.49612 -0.00000 -0.00000 32.00000; -0.00000 -0.00000 -0.49612 32.00000; -0.00000 0.50000 -0.00000 10.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 8.12549 nHits Thresh: 2.43765 Loading registration from registerNMT2toCassis.dat RegMat: -------- -0.99904 -0.03839 0.02093 -1.00375; 0.02331 -0.06274 0.99776 -29.26276; 0.03699 -0.99729 -0.06358 -8.60775; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- 0.49565 0.01905 -0.01038 32.49799; -0.01835 0.49478 0.03154 36.27051; 0.01166 -0.03137 0.49888 -4.63138; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.white nvertices = 16975 Reading thickness /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.thickness nlabels = 1 Allocating Hit Volume (81920) voxels Loading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
�7��ա<�d�TGr��L�� �s�����L�����f�T�ot�9����eOԲ:|��L��� ���s/ ��,�' ��,3����~�铜��s�`�:�ǙG�] �I�Gu ��`�:�[g��>� <�\�٧S �N��L���<>�t��Mw��l���n�љ���ǢS �WM�K�4 f��Nu W3FfN�TGqt� �Nu �Nf6�V�����}�VG�?̄ޭ��x� �[ ꝣy�Ou��/� e:%�N�YܺՁ>�e�uu���3�k�:�����'O�:���w�[�%��v�Ou�w�����ث�t� �^u����L��pg �^2��ܱ��=�u���8wo�C}�[ {���M&� =<����G[�X�3]�㜙췪�|��tI掝�L�� w2g�Vu�;�\��(_Og_gN���P�'O3'�Vu�_M���, �̪ѯ�t�I8��q�z��ߓ����ONꗙ �_ �u �y�Wu��v�iݯ��x���d��a�'s�03���C��� �=ȣ�xϲ�� ��d5�;���Nf<Ձ���3 �s��9� �A�d��A��e��A/�;����:���Lr0�y��<��d�s�QѪ���^�Ou����̂]�� mri_label2vol: could not scan # of lines from label file ERROR reading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
Il giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> ha scritto: Use mri_label2vol to map the segmentation into the fMRI space, then use mri_segstats using the --avgwf option to get time courses. Run it with --help to get examples
On 11/26/2020 9:16 AM, Francesca Strappini wrote:
External Email - Use Caution
Dear FreeSurfer experts,
I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion?
Thank you Francesca
-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.ilmailto:francesca.strappini@weizmann.ac.il
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-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.ilmailto:francesca.strappini@weizmann.ac.il
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Ok thanks. I need to extract the mean signal from the regions contained in this nifti file. I suppose I need first to resample it in functional space and then use mri_segstats, but I'm not sure which is the right way to do it. Any suggestion?
On Wed, Dec 23, 2020, 19:05 Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu wrote:
The argument to the --label flag should be a freesurfer label file, this is a text file not an nii.gz file.
On 12/21/2020 10:52 AM, Francesca Strappini wrote:
External Email - Use CautionThank you! I run mri_label2vol but I got this error.
mri_label2vol --label D99_atlas_in_NMT_v2.0_asym_fh.nii.gz --temp /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz --reg registerNMT2toCassis.dat --fillthresh .3 --proj frac 0 1 .1 --subject MonkeyCassis --hemi lh --o D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz Number of labels: 1 D99_atlas_in_NMT_v2.0_asym_fh.nii.gz Annot File: (null) Template Volume: /usr/local/freesurfer/fsfast/Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz Outut Volume: D99_atlas_in_NMT_v2.0_asym_fh_Cassis_lh.nii.gz Registration File: registerNMT2toCassis.dat Fill Threshold: 0.3 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 1 ProjDelta: 0.1 Subject: MonkeyCassis Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /usr/local/freesurfer/subjects $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.49612 -0.00000 -0.00000 32.00000; -0.00000 -0.00000 -0.49612 32.00000; -0.00000 0.50000 -0.00000 10.00000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 8.12549 nHits Thresh: 2.43765 Loading registration from registerNMT2toCassis.dat RegMat: -------- -0.99904 -0.03839 0.02093 -1.00375; 0.02331 -0.06274 0.99776 -29.26276; 0.03699 -0.99729 -0.06358 -8.60775; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- 0.49565 0.01905 -0.01038 32.49799; -0.01835 0.49478 0.03154 36.27051; 0.01166 -0.03137 0.49888 -4.63138; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.white nvertices = 16975 Reading thickness /usr/local/freesurfer/subjects/MonkeyCassis/surf/lh.thickness nlabels = 1 Allocating Hit Volume (81920) voxels Loading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
�7��ա<�d�TGr��L�� �s�����L�����f�T�ot�9����eOԲ:|��L��� ���s/ ��,�' ��,3����~�铜��s�`�:�ǙG�] �I�Gu ��`�:�[g��>� <�\�٧S �N��L���<>�t��Mw��l���n�љ���ǢS �WM�K�4 f��Nu W3FfN�TGqt� �Nu �Nf6�V�����}�VG�?̄ޭ��x� �[ ꝣy�Ou��/� e:%�N�YܺՁ>�e�uu���3�k�:�����'O�:���w�[�%��v�Ou�w�����ث�t� �^u����L��pg �^2��ܱ��=�u���8wo�C}�[ {���M&� =<����G[�X�3]�㜙췪�|��tI掝�L�� w2g�Vu�;�\��(_Og_gN���P�'O3'�Vu�_M���, �̪ѯ�t�I8��q�z��ߓ����ONꗙ �_ �u �y�Wu��v�iݯ��x���d��a�'s�03���C��� �=ȣ�xϲ�� ��d5�;���Nf<Ձ���3
�s��9� �A�d��A��e��A/�;����:���Lr0�y��<��d�s�QѪ���^�Ou����̂]��mri_label2vol: could not scan # of lines from label file ERROR reading D99_atlas_in_NMT_v2.0_asym_fh.nii.gz
Il giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> ha scritto:
Use mri_label2vol to map the segmentation into the fMRI space, then use mri_segstats using the --avgwf option to get time courses. Run it with --help to get examples
On 11/26/2020 9:16 AM, Francesca Strappini wrote:
External Email - Use CautionDear FreeSurfer experts,
I'm trying to use the monkey atlas D99. First, I registered the segmentation atlas to the monkey anatomy through bbregister. Now, I need to resample the segmentation to the functional data and extract the mean value from each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion?
Thank you Francesca
-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.edu*MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be* https://secure-web.cisco.com/1Ho8qJ8mxsN0AX49O_6zs9_eJ06UHQqVRcEGI9EiMM8L4sU... https://secure-web.cisco.com/1OSQzH25ch8h2koY-2WgW3vl2N5u_7AcNIyzIWDo69jLql0pA2DXIIaahni8EcIy68SNACHeoWD7dNzPDAR1J0vFU-LJTNAWTU38-LHnMIuz3DAt-DvC5T9XdBs_xRmsniCTrNd6q69Mb1bHR4VqRYgspTedJxTSI2dHHcAA4YFZF-7gwZHLBsd1cPxnBy281dCCtn2Xa-K3-4DhAL_FDGdAKRRcx6qutksc9N8xS8uMDBOqN0b37yC3-Fi3QwlK7M2Z3A-6AT9tdzZ-RfXEQ9w/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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-- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini@weizmann.ac.il
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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freesurfer@nmr.mgh.harvard.edu
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Francesca Strappini -
Greve, Douglas N.,Ph.D.