Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
; binvalnot 0 > > > > fstart = 0, fend = 0, nframes = 1 > > > > Found 0 values in range > > > > Counting number of voxels in first frame > > > > Found 0 voxels in final mask > > > > Count: 0 0.00 16777216 0.00 > > > > mri_binarize done > > > > mri_convert.bin > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii > > > > > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > > > reading from > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz... > > > > TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 > > > > i_ras = (-1, 0, 0) > > > > j_ras = (0, 0, -1) > > > > k_ras = (0, 1, 0) > > > > writing to > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii... > > > > Matrix from regfile: > > > > 1.0 -0.00055 0.00091 -0.38465; > > > > -0.00091 0.00095 1.0 0.38039; > > > > -0.00055 -1.0 0.00095 -0.14575; > > > > 0.0 0.0 0.0 1.0; > > > > movvol > > /data/project/vislab/raw/HCP_900sub/HCP_diff_data/211215/data.nii.gz > > > > targvol > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii > > > > outvol > > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_diffROI.nii > > > > regfile > > > /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/211215/register_edit.dat > > > > invert 1 > > > > tal0 > > > > talres 2 > > > > regheader 0 > > > > noresample 0 > > > > interp nearest (0) > > > > precision float (3) > > > > Gdiag_no -1 > > > > Synth 0 > > > > SynthSeed 1518108582 > > > > Invert! > > > > Inverting registration > > > > Final tkRAS-to-tkRAS Matrix is: > > > > 1.0 -0.00091 -0.00055 0.38491; > > > > -0.00055 0.00095 -1.0 -0.14632; > > > > 0.00091 1.0 0.00095 -0.37990; > > > > 0.0 0.0 0.0 1.0; > > > > Vox2Vox Matrix is: > > > > 1.25000 -0.00069 0.00114 36.96743; > > > > 0.00114 0.00118 -1.25000 218.81943; > > > > 0.00069 1.25000 0.00118 18.96824; > > > > 0.0 0.0 0.0 1.0; > > > > Resampling > > > > Output registration matrix is identity > > > > mri_vol2vol done > > > > Sara Sims > > > > Graduate Research Fellow > > > > University of Alabama at Birmingham > > > > Department of Psychology > > > > 205-975-4060 > > > > sno...@uab.edu > > > > *From: * on behalf of Douglas > > Greve > > *Reply-To: *Freesurfer support list > > *Date: *Saturday, February 3, 2018 at 1:12 PM > > *To: *"freesurfer@nmr.mgh.harvard.edu" > > *Subject: *Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm > > > > Can you send the terminal output of one of the runs that fails? > > > > On 1/31/18 4:10 PM, Sims, Sara A wrote: > > > > Freesurfers, > > > > I am trying to use a cortical label to label wm. I am using the > > following command line: > > > > mri_aparc2aseg --s $patient --annot 8V1 –labelwm > > > > And most of the time in most subjects this works, however > > sometimes the output file doesn’t label any wm with the 3000+N or > > 4000+N like it usually does. I have tried changing the > > -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I > > could find but it won’t budge even though doing other labels in > > the same
Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
>
> hostname c0039
>
> machine x86_64
>
> user snolin
>
> input
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz
>
> frame 0
>
> nErode3d 0
>
> nErode2d 0
>
> output
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz
>
> Binarizing based on matching values
>
> nMatch 2
>
> 0 4001
>
> 1 3001
>
> binval 1
>
> binvalnot 0
>
> fstart = 0, fend = 0, nframes = 1
>
> Found 0 values in range
>
> Counting number of voxels in first frame
>
> Found 0 voxels in final mask
>
> Count: 0 0.00 16777216 0.00
>
> mri_binarize done
>
> mri_convert.bin
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii
>
>
> $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $
>
> reading from
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz...
>
> TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00
>
> i_ras = (-1, 0, 0)
>
> j_ras = (0, 0, -1)
>
> k_ras = (0, 1, 0)
>
> writing to
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii...
>
> Matrix from regfile:
>
> 1.0 -0.00055 0.00091 -0.38465;
>
> -0.00091 0.00095 1.0 0.38039;
>
> -0.00055 -1.0 0.00095 -0.14575;
>
> 0.0 0.0 0.0 1.0;
>
> movvol
> /data/project/vislab/raw/HCP_900sub/HCP_diff_data/211215/data.nii.gz
>
> targvol
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii
>
> outvol
>
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_diffROI.nii
>
> regfile
>
/data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/211215/register_edit.dat
>
> invert 1
>
> tal0
>
> talres 2
>
> regheader 0
>
> noresample 0
>
> interp nearest (0)
>
> precision float (3)
>
> Gdiag_no -1
>
> Synth 0
>
> SynthSeed 1518108582
>
> Invert!
>
> Inverting registration
>
> Final tkRAS-to-tkRAS Matrix is:
>
> 1.0 -0.00091 -0.00055 0.38491;
>
> -0.00055 0.00095 -1.0 -0.14632;
>
> 0.00091 1.0 0.00095 -0.37990;
>
> 0.0 0.0 0.0 1.0;
>
> Vox2Vox Matrix is:
>
> 1.25000 -0.00069 0.00114 36.96743;
>
> 0.00114 0.00118 -1.25000 218.81943;
>
> 0.00069 1.25000 0.00118 18.96824;
>
> 0.0 0.0 0.0 1.0;
>
> Resampling
>
> Output registration matrix is identity
>
> mri_vol2vol done
>
> Sara Sims
>
> Graduate Research Fellow
>
> University of Alabama at Birmingham
>
> Department of Psychology
>
> 205-975-4060
>
> sno...@uab.edu
>
> *From: * on behalf of Douglas
> Greve
> *Reply-To: *Freesurfer support list
> *Date: *Saturday, February 3, 2018 at 1:12 PM
> *To: *"freesurfer@nmr.mgh.harvard.edu"
> *Subject: *Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
>
> Can you send the terminal output of one of the runs that fails?
>
> On 1/31/18 4:10 PM, Sims, Sara A wrote:
>
> Freesurfers,
>
> I am trying to use a cortical label to label wm. I am using the
> following command line:
>
> mri_aparc2aseg --s $patient --annot 8V1 –labelwm
Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
; > talres 2 > > regheader 0 > > noresample 0 > > interp nearest (0) > > precision float (3) > > Gdiag_no -1 > > Synth 0 > > SynthSeed 1518108582 > > Invert! > > Inverting registration > > Final tkRAS-to-tkRAS Matrix is: > > 1.0 -0.00091 -0.00055 0.38491; > > -0.00055 0.00095 -1.0 -0.14632; > > 0.00091 1.0 0.00095 -0.37990; > > 0.0 0.0 0.0 1.0; > > Vox2Vox Matrix is: > > 1.25000 -0.00069 0.00114 36.96743; > > 0.00114 0.00118 -1.25000 218.81943; > > 0.00069 1.25000 0.00118 18.96824; > > 0.0 0.0 0.0 1.0; > > Resampling > > Output registration matrix is identity > > mri_vol2vol done > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu > > *From: * on behalf of Douglas > Greve > *Reply-To: *Freesurfer support list > *Date: *Saturday, February 3, 2018 at 1:12 PM > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Subject: *Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm > > Can you send the terminal output of one of the runs that fails? > > On 1/31/18 4:10 PM, Sims, Sara A wrote: > > Freesurfers, > > I am trying to use a cortical label to label wm. I am using the > following command line: > > mri_aparc2aseg --s $patient --annot 8V1 –labelwm > > And most of the time in most subjects this works, however > sometimes the output file doesn’t label any wm with the 3000+N or > 4000+N like it usually does. I have tried changing the > -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I > could find but it won’t budge even though doing other labels in > the same person works fine. Fyi: The original cortical label is > also correctly place in the cortical ribbon. > > Any ideas? > > Please! > > Thanks, > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu<mailto:sno...@uab.edu> > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu<mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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
Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
165 166 167 168 169 170 171 172 173 174 175 176 > 177 178 179 > > 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 > 197 198 199 > > 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 > 217 218 219 > > 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 > 237 238 239 > > 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = > 1124316 > > Used brute-force search on 0 voxels > > Fixing Parahip LH WM > > Found 0 clusters > > Fixing Parahip RH WM > > Found 0 clusters > > Writing output aseg to > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz > > $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ > > cwd /data/user/snolin/Scripts/Labelmaker > > cmdline mri_binarize.bin --i > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz > > --o > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz > > --match 4001 3001 > > sysname Linux > > hostname c0039 > > machine x86_64 > > user snolin > > input > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz > > frame 0 > > nErode3d 0 > > nErode2d 0 > > output > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz > > Binarizing based on matching values > > nMatch 2 > > 0 4001 > > 1 3001 > > binval 1 > > binvalnot 0 > > fstart = 0, fend = 0, nframes = 1 > > Found 0 values in range > > Counting number of voxels in first frame > > Found 0 voxels in final mask > > Count: 0 0.00 16777216 0.00 > > mri_binarize done > > mri_convert.bin > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz > > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii > > > > $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ > > reading from > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz... > > TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 > > i_ras = (-1, 0, 0) > > j_ras = (0, 0, -1) > > k_ras = (0, 1, 0) > > writing to > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii... > > Matrix from regfile: > > 1.0 -0.00055 0.00091 -0.38465; > > -0.00091 0.00095 1.0 0.38039; > > -0.00055 -1.0 0.00095 -0.14575; > > 0.0 0.0 0.0 1.0; > > movvol > /data/project/vislab/raw/HCP_900sub/HCP_diff_data/211215/data.nii.gz > > targvol > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii > > outvol > /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_diffROI.nii > > regfile > /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/211215/register_edit.dat > > invert 1 > > tal 0 > > talres 2 > > regheader 0 > > noresample 0 > > interp nearest (0) > > precision float (3) > > Gdiag_no -1 > > Synth 0 > > SynthSeed 1518108582 > > Invert! > > Inverting registration > > Final tkRAS-to-tkRAS Matrix is: > > 1.0 -0.00091 -0.00055 0.38491; > > -0.00055 0.00095 -1.0 -0.14632; > > 0.00091 1.0 0.00095 -0.37990; > > 0.0 0.0 0.0 1.0; > > Vox2Vox Matrix is: > > 1.25000 -0.00069 0.00114 36.96743; > > 0.00114 0.00118 -1.25000 218.81943; > > 0.00069 1.25000 0.00118 18.96824; > > 0.0 0.0 0.0 1.0; > > Resampling > > Output registration matrix is identity > > mri_vol2vol done > > Sara Sims > > Graduate Research Fellow > > University of Alabama at Birmingham > > Department of Psychology > > 205-975-4060 > > sno...@uab.edu > > *From: * on behalf of Douglas > Greve > *Reply-To: *Freesurfer support list > *Date: *Saturday, February 3, 2018 at 1:12 PM > *To: *"freesurfer@nmr.mgh.harvard.edu" > *Subject: *Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm > > Can you send the terminal output of one of the runs that fails? > > On 1/31/18 4:10 PM, Sims, Sara A wrote: > > Freesurfers, > > I am trying to use a cortical label to label wm. I am using the > following command line: > > mri_aparc2aseg --s $patient --annot 8V1 –labelwm > > And most of the time in most subjects this works, however > sometimes the output file doesn’t label any wm with the 3000+N or > 4000+N like it usually does. I have
Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz Binarizing based on matching values nMatch 2 0 4001 1 3001 binval1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.00 16777216 0.00 mri_binarize done mri_convert.bin /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii... Matrix from regfile: 1.0 -0.00055 0.00091 -0.38465; -0.00091 0.00095 1.0 0.38039; -0.00055 -1.0 0.00095 -0.14575; 0.0 0.0 0.0 1.0; movvol /data/project/vislab/raw/HCP_900sub/HCP_diff_data/211215/data.nii.gz targvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii outvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_diffROI.nii regfile /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/211215/register_edit.dat invert 1 tal0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1518108582 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 1.0 -0.00091 -0.00055 0.38491; -0.00055 0.00095 -1.0 -0.14632; 0.00091 1.0 0.00095 -0.37990; 0.0 0.0 0.0 1.0; Vox2Vox Matrix is: 1.25000 -0.00069 0.00114 36.96743; 0.00114 0.00118 -1.25000 218.81943; 0.00069 1.25000 0.00118 18.96824; 0.0 0.0 0.0 1.0; Resampling Output registration matrix is identity mri_vol2vol done Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu From: on behalf of Douglas Greve Reply-To: Freesurfer support list Date: Saturday, February 3, 2018 at 1:12 PM To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm Can you send the terminal output of one of the runs that fails? On 1/31/18 4:10 PM, Sims, Sara A wrote: Freesurfers, I am trying to use a cortical label to label wm. I am using the following command line: mri_aparc2aseg --s $patient --annot 8V1 –labelwm And most of the time in most subjects this works, however sometimes the output file doesn’t label any wm with the 3000+N or 4000+N like it usually does. I have tried changing the -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I could find but it won’t budge even though doing other labels in the same person works fine. Fyi: The original cortical label is also correctly place in the cortical ribbon. Any ideas? Please! Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu<mailto:sno...@uab.edu> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
Re: [Freesurfer] mri_aparc2aseg labelwm not labelling wm
Can you send the terminal output of one of the runs that fails? On 1/31/18 4:10 PM, Sims, Sara A wrote: Freesurfers, I am trying to use a cortical label to label wm. I am using the following command line: mri_aparc2aseg --s $patient --annot 8V1 –labelwm And most of the time in most subjects this works, however sometimes the output file doesn’t label any wm with the 3000+N or 4000+N like it usually does. I have tried changing the -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I could find but it won’t budge even though doing other labels in the same person works fine. Fyi: The original cortical label is also correctly place in the cortical ribbon. Any ideas? Please! Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu ___ 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.
