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Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS.
I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223
The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118
Please, I have other questions for you.
1) At starting, I have used the command line reported below:
preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd
The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added?
Thanks,
Stefano
You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 7:39 AM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
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Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS.
I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223
The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118
Please, I have other questions for you.
1) At starting, I have used the command line reported below:
preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd
The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added?
Thanks,
Stefano
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks!!
Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 7:39 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118 Please, I have other questions for you. 1) At starting, I have used the command line reported below: preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? Thanks, Stefano _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 1:46 PM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
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Thanks!!
Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu ha scritto:
You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 7:39 AM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
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Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS.
I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223
The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118
Please, I have other questions for you.
1) At starting, I have used the command line reported below:
preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd
The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added?
Thanks,
Stefano
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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converting the time series data into the conformed space
mri_vol2vol --reg /Applications/freesurfer/subjects/fMRI_ADNI/subj/rest/001/register.dof6.lta --mov /Applications/freesurfer/subjects/fMRI_ADNI/subj/rest/001/fmcpr.nii.gz --fstarg --o subj/rest/001/fmpr.conformed.mgz
mri_segstats --seg $SUBJECTS_DIR/subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmpr.conformed.mgz --avgwf /Users/Stefano/Desktop/FS_FAST_ADNI_Results/Thalami_nuclei/Time_Series/subj.MNI --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133
ERROR: dimension mismatch between input volume and seg
input 256 256 256
seg 169 105 118
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution Thanks!! Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto:You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 7:39 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118 Please, I have other questions for you. 1) At starting, I have used the command line reported below: preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? Thanks, Stefano _______________________________________________ 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>
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Hi,
If I interested to obtained the time course from a unique region expressing the merging of thalamic regions (i.e. 8121 plus 8122 plus 8123), which is the options that should I added to mri_segstats?
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution Thanks!! Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto:You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 7:39 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118 Please, I have other questions for you. 1) At starting, I have used the command line reported below: preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? Thanks, Stefano _______________________________________________ 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >>
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You should create a binary mask using mri_binarize with the --merge option, then run mri_segstats specifying --id 1 (since the mask will have a value of 1)
On 5/6/19 7:19 AM, stdp82@virgilio.it wrote:
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Hi,
If I interested to obtained the time course from a unique region expressing the merging of thalamic regions (i.e. 8121 plus 8122 plus 8123), which is the options that should I added to mri_segstats?
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
External Email - Use Caution
Thanks!!
Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha scritto:
You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 7:39 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS.
I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223
The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118
Please, I have other questions for you.
- At starting, I have used the command line reported below:
preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd
The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
- In the mri_segstats the input is
subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
- If I interested to obtained the time course from a unique
region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added?
Thanks,
Stefano
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi,
I have used:
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf time_course
The error occurs when the followed command is running: mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from f-in-anat.mgh... /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed
Thanks
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution Thanks!! Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto:You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 7:39 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118 Please, I have other questions for you. 1) At starting, I have used the command line reported below: preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? Thanks, Stefano _______________________________________________ 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 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
Is that all it prints out? BTW, you can just specify f-in-anat.nii as the output of mri_vol2vol, you never have to go into mgh format
On 8/23/2019 5:20 PM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
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Hi,
I have used:
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf time_course
The error occurs when the followed command is running: mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from f-in-anat.mgh... /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed
Thanks
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu ha scritto:
Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 1:46 PM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
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Thanks!!
Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu ha scritto:
You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 7:39 AM, stdp82@virgilio.itmailto:stdp82@virgilio.it wrote:
External Email - Use Caution
Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS.
I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223
The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118
Please, I have other questions for you.
1) At starting, I have used the command line reported below:
preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd
The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added?
Thanks,
Stefano
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command runs fine.
How can I convert into the functional space the ThalamicNuclei.v10.T1.mgz? Of note, to convert the orig.mgz I have already added to the line --inv.
Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Is that all it prints out? BTW, you can just specify f-in-anat.nii as the output of mri_vol2vol, you never have to go into mgh format On 8/23/2019 5:20 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution Hi, I have used: mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf time_course The error occurs when the followed command is running: mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from f-in-anat.mgh... /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed Thanks > > > Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto:Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution Thanks!! Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > > > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto:You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 7:39 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > >External Email - Use Caution Hi list, I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. I have run mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 The command produces this error: ERROR: dimension mismatch between input volume and seg input 76 76 93 seg 169 105 118 Please, I have other questions for you. 1) At starting, I have used the command line reported below: preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd The -mni305-1mm could be more useful? My raw-data are: data_type UINT16 dim1 64 dim2 64 dim3 48 dim4 140 datatype 512 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+ 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? Thanks, Stefano _______________________________________________ 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > >> > > _______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
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In addition,
a) to convert the time series data into the conformed space and viceversa, I have run the command line listed below:
SUBJECTS_DIR=/media/DATA_NAS/ADNI_USB/Dati/ mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.nii mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o anat-in-func.nii --inv Thus the command produce:
fslinfo f-in-anat.nii data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 140 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
I have also opt for --inv and obtained:
fslinfo anat-in-func.nii data_type FLOAT32 dim1 64 dim2 64 dim3 48 dim4 1 datatype 16 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 1.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
When I run mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133
the process crash: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133 sysname Linux hostname lab01 machine x86_64 UseRobust 0 Loading mri/ThalamicNuclei.v10.T1.mgz Loading f-in-anat.nii Killed
Moreover, when I use mri_vol2vol --reg register.dof6.lta --mov mri/ThalamicNuclei.v10.T1.nii.gz --fstarg --o ThalamicNuclei.v10.T1_struct2func.nii --interp nearest (with or without --inv) the output is not unusable.
Thanks
Stefano
Il 26 agosto 2019 alle 20.02 stdp82@virgilio.it ha scritto:
Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command runs fine. How can I convert into the functional space the ThalamicNuclei.v10.T1.mgz? Of note, to convert the orig.mgz I have already added to the line --inv. > > Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto:Is that all it prints out? BTW, you can just specify f-in-anat.nii as the output of mri_vol2vol, you never have to go into mgh format On 8/23/2019 5:20 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > >External Email - Use Caution Hi, I have used: mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf time_course The error occurs when the followed command is running: mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from f-in-anat.mgh... /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed Thanks > > > > Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto:Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > >External Email - Use Caution Thanks!! Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > > > > > > Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> mailto:DGREVE@mgh.harvard.edu ha scritto:You'll need to either convert the time series data into the conformed space or the segmentation into the functional space. The first is probably better (it will create a huge file but you can delete it when you are done). Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats On 4/12/2019 7:39 AM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > > > > > >> External Email - Use Caution > > Hi list, > I would like to extract fMRI time series from the thalamic subregions that I obtained by the recent tool implemented in FS. > > I have run > mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 > > The command produces this error: > ERROR: dimension mismatch between input volume and seg > input 76 76 93 > seg 169 105 118 > > Please, I have other questions for you. > > 1) At starting, I have used the command line reported below: > > preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 -fsd rest -per-run -sliceorder odd > > The -mni305-1mm could be more useful? > My raw-data are: > data_type UINT16 > dim1 64 > dim2 64 > dim3 48 > dim4 140 > datatype 512 > pixdim1 3.312500 > pixdim2 3.312500 > pixdim3 3.312500 > pixdim4 3.000000 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > > 2) In the mri_segstats the input is subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. > Do you agree? Conversely, should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? > > 3) If I interested to obtained the time course from a unique region expressing the merging of some thalamic regions (i.e. 8121plus 8122 plus 8123), which is the options that should I added? > > Thanks, > > Stefano > > > _______________________________________________ > 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > >> > > > _______________________________________________Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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. >
Is that all the output it prints to the terminal? It might be exceeding your available memory (it will need at least 10G). What does the limit command return?
On 8/28/19 6:27 PM, stdp82@virgilio.it wrote:
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In addition,
a) to convert the time series data into the conformed space and viceversa, I have run the command line listed below:
SUBJECTS_DIR=/media/DATA_NAS/ADNI_USB/Dati/ mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.nii mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o anat-in-func.nii --inv Thus the command produce:
fslinfo f-in-anat.nii data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 140 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
I have also opt for --inv and obtained:
fslinfo anat-in-func.nii data_type FLOAT32 dim1 64 dim2 64 dim3 48 dim4 1 datatype 16 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 1.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
When I run mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133
the process crash: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133 sysname Linux hostname lab01 machine x86_64 UseRobust 0 Loading mri/ThalamicNuclei.v10.T1.mgz Loading f-in-anat.nii Killed
Moreover, when I use mri_vol2vol --reg register.dof6.lta --mov mri/ThalamicNuclei.v10.T1.nii.gz --fstarg --o ThalamicNuclei.v10.T1_struct2func.nii --interp nearest (with or without --inv) the output is not unusable.
Thanks
Stefano
Il 26 agosto 2019 alle 20.02 stdp82@virgilio.it ha scritto:
Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command runs fine.
How can I convert into the functional space the ThalamicNuclei.v10.T1.mgz? Of note, to convert the orig.mgz I have already added to the line --inv.
Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Is that all it prints out? BTW, you can just specify f-in-anat.nii as the output of mri_vol2vol, you never have to go into mgh format
On 8/23/2019 5:20 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
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Hi,
I have used:
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf time_course
The error occurs when the followed command is running: mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from f-in-anat.mgh... /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed
Thanks
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha scritto:
Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
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Thanks!!
Using mri_segstats, is the input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz?
> Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." > DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha > scritto: > > You'll need to either convert the time series data into the > conformed space or the segmentation into the functional space. > The first is probably better (it will create a huge file but you > can delete it when you are done). Use mri_vol2vol --reg > register.dof6.lta --mov fmcpr.nii.gz --fstarg --o > fmpr.conformed.mgz > Then use the conformed thalamic nuclei volume when running > mri_segstats > > On 4/12/2019 7:39 AM, stdp82@virgilio.it > mailto:stdp82@virgilio.it wrote: >> >> External Email - Use Caution >> >> Hi list, >> I would like to extract fMRI time series from the thalamic >> subregions that I obtained by the recent tool implemented in FS. >> >> I have run >> mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab >> $FREESURFER_HOME/FreeSurferColorLUT.txt --i >> subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf >> Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 >> --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 >> >> The command produces this error: >> ERROR: dimension mismatch between input volume and seg >> input 76 76 93 >> seg 169 105 118 >> >> Please, I have other questions for you. >> >> 1) At starting, I have used the command line reported below: >> >> preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 >> -fsd rest -per-run -sliceorder odd >> >> The -mni305-1mm could be more useful? >> My raw-data are: >> data_type UINT16 >> dim1 64 >> dim2 64 >> dim3 48 >> dim4 140 >> datatype 512 >> pixdim1 3.312500 >> pixdim2 3.312500 >> pixdim3 3.312500 >> pixdim4 3.000000 >> cal_max 0.0000 >> cal_min 0.0000 >> file_type NIFTI-1+ >> >> 2) In the mri_segstats the input is >> subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. >> Do you agree? Conversely, should I use the .odd like >> fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? >> >> 3) If I interested to obtained the time course from a unique >> region expressing the merging of some thalamic regions (i.e. >> 8121plus 8122 plus 8123), which is the options that should I added? >> >> Thanks, >> >> Stefano >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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Yes, that's it. The memory should be ok, but I will do a check.
Anyway, is there a way to register the ThalamicNuclei.v10.T1 into EPI space? I would like to work in functional space.
Il 29 agosto 2019 alle 0.32 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Is that all the output it prints to the terminal? It might be exceeding your available memory (it will need at least 10G). What does the limit command return?
On 8/28/19 6:27 PM, stdp82@virgilio.it wrote:
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In addition,
a) to convert the time series data into the conformed space and viceversa, I have run the command line listed below:
SUBJECTS_DIR=/media/DATA_NAS/ADNI_USB/Dati/ mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.nii mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o anat-in-func.nii --inv Thus the command produce:
fslinfo f-in-anat.nii data_type FLOAT32 dim1 256 dim2 256 dim3 256 dim4 140 datatype 16 pixdim1 1.000000 pixdim2 1.000000 pixdim3 1.000000 pixdim4 3.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
I have also opt for --inv and obtained:
fslinfo anat-in-func.nii data_type FLOAT32 dim1 64 dim2 64 dim3 48 dim4 1 datatype 16 pixdim1 3.312500 pixdim2 3.312500 pixdim3 3.312500 pixdim4 1.000000 cal_max 0.0000 cal_min 0.0000 file_type NIFTI-1+
When I run mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133
the process crash: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ cwd cmdline mri_segstats --seg mri/ThalamicNuclei.v10.T1.mgz --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt --i f-in-anat.nii --avgwf prova --id 8103 --id 8104 --id 8105 --id 8106 --id 8108 --id 8109 --id 8110 --id 8111 --id 8112 --id 8113 --id 8115 --id 8116 --id 8117 --id 8118 --id 8119 --id 8120 --id 8121 --id 8122 --id 8123 --id 8125 --id 8126 --id 8127 --id 8128 --id 8129 --id 8130 --id 8133 sysname Linux hostname lab01 machine x86_64 UseRobust 0 Loading mri/ThalamicNuclei.v10.T1.mgz Loading f-in-anat.nii Killed
Moreover, when I use mri_vol2vol --reg register.dof6.lta --mov mri/ThalamicNuclei.v10.T1.nii.gz --fstarg --o ThalamicNuclei.v10.T1_struct2func.nii --interp nearest (with or without --inv) the output is not unusable.
Thanks
Stefano
Il 26 agosto 2019 alle 20.02 stdp82@virgilio.it ha scritto:
Thanks. By specifying f-in-anat.nii as output the mri_vol2vol command runs fine.
How can I convert into the functional space the ThalamicNuclei.v10.T1.mgz? Of note, to convert the orig.mgz I have already added to the line --inv.
Il 26 agosto 2019 alle 15.35 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Is that all it prints out? BTW, you can just specify f-in-anat.nii as the output of mri_vol2vol, you never have to go into mgh format
On 8/23/2019 5:20 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote:
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Hi,
I have used:
mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o f-in-anat.mgh mri_binarize --i mri/ThalamicNuclei.v10.T1.mgz --min 8112 --max 8114 --o merged_ROIs.nii.gz mri_segstats --seg merged_ROIs.nii.gz --id 1 --i f-in-anat.mgh --avgwf time_course
The error occurs when the followed command is running: mri_convert.bin f-in-anat.mgh f-in-anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from f-in-anat.mgh... /usr/local/freesurfer/bin/mri_convert: line 3: 29749 Killed
Thanks
Il 12 aprile 2019 alle 20.42 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha scritto:
Use mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg --o fmpr.conformed.mgz Then use the conformed thalamic nuclei volume when running mri_segstats
On 4/12/2019 1:46 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > > External Email - Use Caution > > Thanks!! > > Using mri_segstats, is the > input subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz? > Or should I use the .odd like fmcpr.odd.sm6.mni305.1mm.nii.gz or > fmcpr.odd.sm6.mni305.2mm.nii.gz? > > >> Il 12 aprile 2019 alle 16.59 "Greve, Douglas N.,Ph.D." >> DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu ha >> scritto: >> >> You'll need to either convert the time series data into the >> conformed space or the segmentation into the functional space. >> The first is probably better (it will create a huge file but you >> can delete it when you are done). Use mri_vol2vol --reg >> register.dof6.lta --mov fmcpr.nii.gz --fstarg --o >> fmpr.conformed.mgz >> Then use the conformed thalamic nuclei volume when running >> mri_segstats >> >> On 4/12/2019 7:39 AM, stdp82@virgilio.it >> mailto:stdp82@virgilio.it wrote: >>> >>> External Email - Use Caution >>> >>> Hi list, >>> I would like to extract fMRI time series from the thalamic >>> subregions that I obtained by the recent tool implemented in FS. >>> >>> I have run >>> mri_segstats --seg subj/mri/ThalamicNuclei.v10.T1.mgz --ctab >>> $FREESURFER_HOME/FreeSurferColorLUT.txt --i >>> subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz --avgwf >>> Time_Seriesfolder/ADNI011_HC.MNI --id 8120 --id 8121 --id 8122 >>> --id 8123 --id 8220 --id 8221 --id 8222 --id 8223 >>> >>> The command produces this error: >>> ERROR: dimension mismatch between input volume and seg >>> input 76 76 93 >>> seg 169 105 118 >>> >>> Please, I have other questions for you. >>> >>> 1) At starting, I have used the command line reported below: >>> >>> preproc-sess -sf sessid -fwhm 6 -surface fsaverage lhrh -mni305 >>> -fsd rest -per-run -sliceorder odd >>> >>> The -mni305-1mm could be more useful? >>> My raw-data are: >>> data_type UINT16 >>> dim1 64 >>> dim2 64 >>> dim3 48 >>> dim4 140 >>> datatype 512 >>> pixdim1 3.312500 >>> pixdim2 3.312500 >>> pixdim3 3.312500 >>> pixdim4 3.000000 >>> cal_max 0.0000 >>> cal_min 0.0000 >>> file_type NIFTI-1+ >>> >>> 2) In the mri_segstats the input is >>> subj/rest/001/fmcpr.sm6.mni305.2mm.nii.gz. >>> Do you agree? Conversely, should I use the .odd like >>> fmcpr.odd.sm6.mni305.1mm.nii.gz or fmcpr.odd.sm6.mni305.2mm.nii.gz? >>> >>> 3) If I interested to obtained the time course from a unique >>> region expressing the merging of some thalamic regions (i.e. >>> 8121plus 8122 plus 8123), which is the options that should I added? >>> >>> Thanks, >>> >>> Stefano >>> >>> >>> _______________________________________________ >>> 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 >> mailto:Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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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.
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