External Email - Use Caution 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." > <dgr...@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, std...@virgilio.it wrote: > > > > External Email - Use Caution > > > > 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 std...@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." > >>> <dgr...@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, std...@virgilio.it <mailto:std...@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." > >>>>> <dgr...@mgh.harvard.edu> <mailto:dgr...@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, std...@virgilio.it > >>>>> <mailto:std...@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." > >>>>>>> <dgr...@mgh.harvard.edu> <mailto:dgr...@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, std...@virgilio.it > >>>>>>> <mailto:std...@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. > >>> > >> > > > > > _______________________________________________ > 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
