use --slabel, not --seg
doug
On 12/2/15 3:04 PM, Danielle Miller wrote:
Sure -- should be all here now!
The last email contained the following text:
"Hi Doug,
>
> Thanks for the response. I used the mri_label2label command:
> mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol
> --paint dmax --trglabel <output> --hemi lh
>
> When I input the output from this into mri_segstats as the --seg
> volume, I get the error:
> mri_read(): couldn't determine type of file
> fsaverage/label/lh_ACC_label_test.label
> ERROR loading fsaverage/label/lh_ACC_label_test.label
>
> Is there another step I am missing?"
Thanks,
Danielle
--
Ph.D. Program in Behavioral Neuroscience
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118
VA Boston Healthcare System Jamaica Plain
Memory Disorders Research Center
150 South Huntington Ave D11-103
Boston, MA 02130
OFFICE:(857) 364-2130
Hi Danielle, can you resubmit this email with the previous correspondence?
On 12/02/2015 01:14 PM, Danielle Miller wrote:
> Hi Doug,
>
> Thanks for the response. I used the mri_label2label command:
> mri_label2label --srclabel <labelfile> --s fsaverage --regmethod vol
> --paint dmax --trglabel <output> --hemi lh
>
> When I input the output from this into mri_segstats as the --seg
> volume, I get the error:
> mri_read(): couldn't determine type of file
> fsaverage/label/lh_ACC_label_test.label
> ERROR loading fsaverage/label/lh_ACC_label_test.label
>
> Is there another step I am missing?
>
> --
> Ph.D. Program in Behavioral Neuroscience
> Boston University School of Medicine L-815
> 72 E. Concord St
> Boston, MA 02118
>
>
> VA Boston Healthcare System Jamaica Plain
> Memory Disorders Research Center
> 150 South Huntington Ave D11-103
> Boston, MA 02130
> OFFICE:(857) 364-2130
It looks like the ces input is from a surface-based analysis. If
you're label is already on the surface, then no need to do the
label2vol step. If it is in the volume, then you'll need to transfer
it to the surface with mri_label2label with the --paint option
doug
On 11/24/15 12:14 PM, Danielle Miller wrote:
Hello freesurfer experts,
I am trying to extract an average percent signal change from a
functional roi label I created in tkmedit using fsaverage. I
followed previously discussed methods: 1) mri_label2vol --label
<name of label> --temp fsaverage/mri.2mm/orig.mgz --regheader
fsaverage/mri/orig.mgz --o <name of label mask> 2) I checked
(tkmedit fsaverage orig.mgz -overlay <label mask> -fminmax .5 1)
and the label looked fine 3) I ran mri_segstats --i ces.nii.gz
--seg <label mask from above> --id 1 --avgwf ces.label.dat
ces.nii.gz is the file from my group analysis (isxconcat-sess)
using the correct contrast
It returns with this error:
ERROR: dimension mismatch between input volume and seg
input 163842 1 1
seg 76 76 93
Is there something I am doing wrong here?
Also of note I tried using the following commands:
1) funcroi-config -label <label mask created from above
mri_label2vol> -analysis <analysis directory> -roi <name of roicfg
file>
2) funcroi-sess -sf sessid - roi <roicfg file from above>
But this returns with this error:
ERROR: cannot find
/Volumes/VA_Imaging/Projects/dmiller/COGCON/FSFAST/CC_001_recon/label/label_lh_ACC_correct_mask.mgz
Any suggestions would be extremely helpful.
Thanks,
Danielle
--
Ph.D. Program in Behavioral Neuroscience
Boston University School of Medicine L-815
72 E. Concord St
Boston, MA 02118
VA Boston Healthcare System Jamaica Plain
Memory Disorders Research Center
150 South Huntington Ave D11-103
Boston, MA 02130
OFFICE:(857) 364-2130
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