Dear freesurfer experts,
I am having a problem in extracting ROI data using func2roi-sess, and any help would be most appreciated. I wish to evaluate functional data in two ROIs that I created using mri_cor2label (left and right amygdala). Here is the command line:
func2roi-sess -roidef 54 -analysis autreg_analysis_vol -anatlabel 54 -s 20110519_12925 -maskthresh 1.3
Below, I pasted the relevant portion of the logfile produced by func2roi-sess. To the best of my understanding, at least part of the problem seems to be due to the fact that a file called COR-.info can't be found, nor can a file called "bold/001//../transforms/talairach.xfm". I've also tried it with the flag -labelspace tal (and native), but no luck.
Should these have been produced by selxavg3-sess , or perhaps I am missing a step somewhere along the way?
Many thanks, J Richey
... INFO: label2mask_linear: there were 2141 label hits voxsize = 60.8, rszthresh = 1e-07, thresh = 6.08e-06 INFO: label2mask_linear: there were 75 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 75 Done averging over ROI (nhits = 75) ------------------------------------------- /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt ------------------------------------------- corRead(): can't open file bold/001/COR-.info -------------------------------------------------------- /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt version $Id: mri_vol2roi.c,v 1.32 2011/03/02 00:04:25 nicks Exp $ -------------------------------------------------------- roifile = bold/autreg_analysis_vol/54/-001 roitxtfile = bold/autreg_analysis_vol/54/-001.txt oldtxtstyle = 0 srcvol = bold/001/ srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/001/ ...can't find talairach file 'bold/001//../transforms/talairach.xfm'
Hi John, I'm not sure what is going on there. Try running it with -noraw. doug
John Richey wrote:
Dear freesurfer experts,
I am having a problem in extracting ROI data using func2roi-sess, and any help would be most appreciated. I wish to evaluate functional data in two ROIs that I created using mri_cor2label (left and right amygdala). Here is the command line:
func2roi-sess -roidef 54 -analysis autreg_analysis_vol -anatlabel 54 -s 20110519_12925 -maskthresh 1.3
Below, I pasted the relevant portion of the logfile produced by func2roi-sess. To the best of my understanding, at least part of the problem seems to be due to the fact that a file called COR-.info can't be found, nor can a file called "bold/001//../transforms/talairach.xfm". I've also tried it with the flag -labelspace tal (and native), but no luck.
Should these have been produced by selxavg3-sess , or perhaps I am missing a step somewhere along the way?
Many thanks, J Richey
... INFO: label2mask_linear: there were 2141 label hits voxsize = 60.8, rszthresh = 1e-07, thresh = 6.08e-06 INFO: label2mask_linear: there were 75 hits in final mask label2mask_linear: done Averging over ROI INFO: vol2maskavg: nhits = 75 Done averging over ROI (nhits = 75)
/mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt
corRead(): can't open file bold/001/COR-.info
/mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925 mri_vol2roi --srcvol bold/001/ --roiavg bold/autreg_analysis_vol/54/-001 --srcreg bold/register.dat --label /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label --talxfm talairach.xfm --finalmskvol bold/autreg_analysis_vol/54/mask --roiavgtxt bold/autreg_analysis_vol/54/-001.txt version $Id: mri_vol2roi.c,v 1.32 2011/03/02 00:04:25 nicks Exp $
roifile = bold/autreg_analysis_vol/54/-001 roitxtfile = bold/autreg_analysis_vol/54/-001.txt oldtxtstyle = 0 srcvol = bold/001/ srcfmt = bvolume srcreg = bold/register.dat srcregold = 0 srcwarp unspecified label file = /mnt/users/jar62/hill/data/Dichter/AutReg.01/Data/ANALYSIS/freesurfer/201105 19_12925/label/54.label labelreg unspecified label fill thresh = 1e-07 mskvol unspecified Loading volume bold/001/ ...can't find talairach file 'bold/001//../transforms/talairach.xfm' _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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John Richey