26 Aug
2019
26 Aug
'19
2:02 p.m.
External Email - Use Caution
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.