Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Great! Many thanks, Doug.
Best Wishes, Elijah
On 13 June 2017 at 07:05:13, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote: Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
_______________________________________________ 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Doug,
After resampling the aparc annotation into the functional native space, the LUT values no longer correspond to the correct regions. A screenshot is attached here: http://i.imgur.com/HNIgrKI.png
The values for the labels range from 1 - 35 only.
The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh --subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
The goal is to apply the annotation and extract the regional fMRI data (4D) using this 3D volume parcellation. Could we achieve that by using these steps?
Thanks.
Best Wishes, Elijah
On 13 June 2017 at 07:05:13, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote: Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
_______________________________________________ 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hmmm, not sure. can you send the full terminal output?
On 6/13/17 7:03 PM, Elijah Mak wrote:
Hi Doug,
After resampling the aparc annotation into the functional native space, the LUT values no longer correspond to the correct regions. A screenshot is attached here: http://i.imgur.com/HNIgrKI.png
The values for the labels range from 1 - 35 only.
The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh --subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
The goal is to apply the annotation and extract the regional fMRI data (4D) using this 3D volume parcellation. Could we achieve that by using these steps?
Thanks.
Best Wishes, Elijah
On 13 June 2017 at 07:05:13, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Hi Doug,
The full log for 1 subject is here:
dhcp-10-240-201-16:T1_Bd elijahmak_imac$ for i in `cat bd_list`; do mri_label2vol --annot $i/label/lh.aparc.annot --temp ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.lta --fillthresh 0.5 --hemi lh --subject $i --proj frac 0 .1 1 --o ${i}.lh.aparc.in.func.nii; done Number of labels: 0 Annot File: 23950/label/lh.aparc.annot Template Volume: 23950_medn.nii Outut Volume: 23950.lh.aparc.in.func.nii Registration File: 23950/fmri/fmri_t1_mricoreg.lta Fill Threshold: 0.5 Label Vox Vol: 1 ProjType: frac ProjTypeId: 2 ProjStart: 0 ProjStop: 0.1 ProjDelta: 1 Subject: 23950 Hemi: lh UseNewASeg2Vol: 0 DoLabelStatVol 0 LabelCodeOffset 0 setenv SUBJECTS_DIR /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd $Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $ Template RAS-to-Vox: -------- -0.42918 -0.00000 -0.00000 31.00000; -0.00000 -0.00000 -0.42918 39.00000; -0.00000 0.42918 -0.00000 33.50000; -0.00000 -0.00000 -0.00000 1.00000; Template Voxel Volume: 12.6493 nHits Thresh: 6.32467 Loading registration from 23950/fmri/fmri_t1_mricoreg.lta regio_read_register: loading lta RegMat: -------- -0.99901 -0.04205 -0.01419 -0.53889; -0.00761 -0.15273 0.98824 -0.11671; 0.04372 -0.98737 -0.15226 -9.41649; 0.00000 0.00000 0.00000 1.00000; Label RAS-to-Vox: -------- 0.42876 0.01805 0.00609 31.23128; -0.01877 0.42377 0.06535 43.04141; -0.00327 -0.06555 0.42414 33.44991; 0.00000 0.00000 0.00000 1.00000; INFO: loading surface /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.white
nvertices = 152772 Reading thickness /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.thickness Loading annotations from 23950/label/lh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) annotidmax = 36 nlabels = 36 Allocating Hit Volume (11664432) voxels
PVF (null) Thesholding hit volume. mri_label2vol done
Thanks. Appreciate your help.
Best Wishes, Elijah
On 14 June 2017 at 16:18:24, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:
Hmmm, not sure. can you send the full terminal output?
On 6/13/17 7:03 PM, Elijah Mak wrote: Hi Doug,
After resampling the aparc annotation into the functional native space, the LUT values no longer correspond to the correct regions. A screenshot is attached here: http://i.imgur.com/HNIgrKI.png
The values for the labels range from 1 - 35 only.
The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh --subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
The goal is to apply the annotation and extract the regional fMRI data (4D) using this 3D volume parcellation. Could we achieve that by using these steps?
Thanks.
Best Wishes, Elijah
On 13 June 2017 at 07:05:13, Douglas Greve (greve@nmr.mgh.harvard.edu) wrote:
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote: Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
_______________________________________________ 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Add --offset 2000 to the command line (use 1000 for lh)
On 6/14/17 5:23 PM, Elijah Mak wrote:
Hi Doug,
The full log for 1 subject is here:
dhcp-10-240-201-16:T1_Bd elijahmak_imac$ for i in `cat bd_list`; do mri_label2vol --annot $i/label/lh.aparc.annot --temp ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.lta --fillthresh 0.5 --hemi lh --subject $i --proj frac 0 .1 1 --o ${i}.lh.aparc.in.func.nii; done
Number of labels: 0
Annot File: 23950/label/lh.aparc.annot
Template Volume: 23950_medn.nii
Outut Volume: 23950.lh.aparc.in.func.nii
Registration File: 23950/fmri/fmri_t1_mricoreg.lta
Fill Threshold: 0.5
Label Vox Vol: 1
ProjType: frac
ProjTypeId: 2
ProjStart: 0
ProjStop: 0.1
ProjDelta: 1
Subject: 23950
Hemi: lh
UseNewASeg2Vol: 0
DoLabelStatVol 0
LabelCodeOffset 0
setenv SUBJECTS_DIR /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd
$Id: mri_label2vol.c,v 1.46 2014/12/08 21:11:54 greve Exp $
Template RAS-to-Vox: --------
-0.42918 -0.00000 -0.00000 31.00000;
-0.00000 -0.00000 -0.42918 39.00000;
-0.00000 0.42918 -0.00000 33.50000;
-0.00000 -0.00000 -0.00000 1.00000;
Template Voxel Volume: 12.6493
nHits Thresh: 6.32467
Loading registration from 23950/fmri/fmri_t1_mricoreg.lta
regio_read_register: loading lta
RegMat: --------
-0.99901 -0.04205 -0.01419 -0.53889;
-0.00761 -0.15273 0.98824 -0.11671;
0.04372 -0.98737 -0.15226 -9.41649;
0.00000 0.00000 0.00000 1.00000;
Label RAS-to-Vox: --------
0.42876 0.01805 0.00609 31.23128;
-0.01877 0.42377 0.06535 43.04141;
-0.00327 -0.06555 0.42414 33.44991;
0.00000 0.00000 0.00000 1.00000;
INFO: loading surface /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.white
nvertices = 152772
Reading thickness /Users/elijahmak_imac/Documents/ValerieVoon_NODDI/Laurel/T1_Bd/23950/surf/lh.thickness
Loading annotations from 23950/label/lh.aparc.annot
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt)
annotidmax = 36
nlabels = 36
Allocating Hit Volume (11664432) voxels
PVF (null)
Thesholding hit volume.
mri_label2vol done
Thanks. Appreciate your help.
Best Wishes, Elijah
On 14 June 2017 at 16:18:24, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
Hmmm, not sure. can you send the full terminal output?
On 6/13/17 7:03 PM, Elijah Mak wrote:
Hi Doug,
After resampling the aparc annotation into the functional native space, the LUT values no longer correspond to the correct regions. A screenshot is attached here: http://i.imgur.com/HNIgrKI.png
The values for the labels range from 1 - 35 only.
The command is mri_label2vol --annot $i/label/rh.aparc.annot --temp ${i}_medn.nii --reg $i/fmri/fmri_t1_mricoreg.dat --fillthresh 0.5 --hemi rh --subject $i --proj frac 0 .1 1 --o ${i}.rh.aparc.in.func.nii
The goal is to apply the annotation and extract the regional fMRI data (4D) using this 3D volume parcellation. Could we achieve that by using these steps?
Thanks.
Best Wishes, Elijah
On 13 June 2017 at 07:05:13, Douglas Greve (greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu) wrote:
You can try mri_concat seg1.nii.gz seg2.nii.gz --sum --o seg.nii.gz
This will work if there are no overlapping voxels. If there are, you'll have to do something like
mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz
then use the masked in the mri_concat command
On 6/11/17 11:18 AM, Elijah Mak wrote:
Hi Freesurfer Team,
I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help.
Best Wishes, Elijah
_______________________________________________ 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
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Elijah Mak