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 (gr...@nmr.mgh.harvard.edu
<mailto:gr...@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 (gr...@nmr.mgh.harvard.edu
<mailto:gr...@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
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