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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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