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
