Time Series Data in MNI Space - Revision history

Chris: /* Working with ROIs */

2020-09-20T19:55:47Z

Working with ROIs

← Older revision		Revision as of 15:55, 20 September 2020
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	=Working with ROIs=		=Working with ROIs=
	The above code extracts mean time series for all voxels in each labeled region in the aseg.mgz file. However, it is possible to use a masked subcortical segmentation file, which you can [[Working_with_Subcortical_ROIs_(Freesurfer) \| create]].		The above code extracts mean time series for all voxels in each labeled region in the aseg.mgz file. However, it is possible to use a masked subcortical segmentation file, which you can [[Working_with_Subcortical_ROIs_(Freesurfer) \| create]]. You would use the created mask file in place of the aseg.mgz file in the above example.

2020-09-20T19:53:49Z

← Older revision		Revision as of 15:53, 20 September 2020
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	fi		fi
	done		done

			=Working with ROIs=
			The above code extracts mean time series for all voxels in each labeled region in the aseg.mgz file. However, it is possible to use a masked subcortical segmentation file, which you can [[Working_with_Subcortical_ROIs_(Freesurfer) \| create]].

2019-06-13T23:45:05Z

← Older revision		Revision as of 19:45, 13 June 2019
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	This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).		This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).

	The following is a script which will automate ~~this~~ process.		The following is a script which will automate the process for just the MNI space files. The commands below have been incorporated into the more general gettimecourses.sh scripts, so the code below is appropriate for when surface space data have already been extracted and you wish to go back and get the subcortical data.

	'''getmnitimecourses.sh'''		'''getmnitimecourses.sh'''

2019-06-13T23:41:41Z

← Older revision		Revision as of 19:41, 13 June 2019
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	Thanks to Cary for sorting this out. It appears that the process for obtaining mean time series from the mni305 volumes generated by '''preproc-sess''' is very similar to that for [[Time_Series_Data_in_Surface_Space \| time series in surface space]]		Thanks to Cary for sorting this out. It appears that the process for obtaining mean time series from the mni305 volumes generated by '''preproc-sess''' is very similar to that for [[Time_Series_Data_in_Surface_Space \| time series in surface space]]

	After the data have been [[Detrending_FreeSurfer_Data \| detrended]], <code>mri_segstats</code> can be called on the detrended volume to extract the average waveform within each of the labeled segments~~. The next challenge would be to determine the identities of each segment so that you know which waveforms correspond to which subcortical or cortical region~~.		After the data have been [[Detrending_FreeSurfer_Data \| detrended]], <code>mri_segstats</code> can be called on the detrended volume to extract the average waveform within each of the labeled segments.

	#Assume ${sub} contains the subject ID		#Assume ${sub} contains the subject ID

2019-06-01T16:54:54Z

← Older revision		Revision as of 12:54, 1 June 2019
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	This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).		This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).

			The following is a script which will automate this process.

	'''getmnitimecourses.sh'''		'''getmnitimecourses.sh'''

2019-05-30T18:39:40Z

← Older revision		Revision as of 14:39, 30 May 2019
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	This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).		This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).

			'''getmnitimecourses.sh'''
			#!/bin/bash
			USAGE="Usage: getmnitimecourses.sh filepattern sub1 ... subN"

			if [ "$#" == "0" ]; then
			echo "$USAGE"
			exit 1
			fi

			#first two parameters are is the annot files and filepatterns for the \
			#.nii.gz time series to be detrended, up to the hemisphere indicator
			#e.g., fmcpr.sm6.self.?h.nii.gz would use fmcpr.sm6.self as the filepattern
			filepat="$1"
			shift

			#subjects
			subs=( "$@" );
			#hemispheres
			hemis=( lh rh )

			for sub in "${subs[@]}"; do
			source_dir=${SUBJECTS_DIR}/${sub}/bold

			if [ ! -d ${source_dir} ]; then
			#The subject_id does not exist
			echo "${source_dir} does not exist!"
			else
			cd ${source_dir}
			readarray -t runs < runs
			for hemi in "${hemis[@]}"; do
			for r in "${runs[@]}"; do
			if [ -n "${r}" ]; then
			mri_segstats \
			--seg /usr/local/freesurfer/5.3.0/subjects/fsaverage/mri.2mm/aseg.mgz \
			--i ${source_dir}/${r}/${filepat} \
			--sum ${sub}_${hemi}_${annot}_${r}.${filepat}.sum.txt \
			--ctab /usr/local/freesurfer/5.3.0/FreeSurferColorLUT.txt \
			--avgwf ${sub}_${hemi}_${annot}_${r}.${filepat}.wav.txt
			fi
			done
			done
			fi
			done

2019-05-30T18:29:20Z

← Older revision		Revision as of 14:29, 30 May 2019
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	FILEPAT=fmcpr.siemens.sm7.mni305.2mm.mgh		FILEPAT=fmcpr.siemens.sm7.mni305.2mm.mgh
	mri_segstats --seg /usr/local/freesurfer/5.3.0/subjects/fsaverage/mri.2mm/aseg.mgz --i ${sub}/bold/${r}/${FILEPAT} \		mri_segstats --seg /usr/local/freesurfer/5.3.0/subjects/fsaverage/mri.2mm/aseg.mgz --i ${sub}/bold/${r}/${FILEPAT} \
	--ctab /usr/local/freesurfer/5.3.0/FreeSurferColorLUT.txt \		--ctab /usr/local/freesurfer/5.3.0/FreeSurferColorLUT.txt \
	--sum ${sub}/bold/${r}/sum_subcort.txt \		--sum ${sub}/bold/${r}/sum_subcort.txt \
	--avgwf ${sub}_${r}.${FILEPAT}.wav.txt		--avgwf ${sub}_${r}.${FILEPAT}.wav.txt

	This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).		This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).

2019-05-30T18:29:11Z

← Older revision		Revision as of 14:29, 30 May 2019
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	FILEPAT=fmcpr.siemens.sm7.mni305.2mm.mgh		FILEPAT=fmcpr.siemens.sm7.mni305.2mm.mgh
	mri_segstats --seg /usr/local/freesurfer/5.3.0/subjects/fsaverage/mri.2mm/aseg.mgz --i ${sub}/bold/${r}/${FILEPAT} \		mri_segstats --seg /usr/local/freesurfer/5.3.0/subjects/fsaverage/mri.2mm/aseg.mgz --i ${sub}/bold/${r}/${FILEPAT} \
			--ctab /usr/local/freesurfer/5.3.0/FreeSurferColorLUT.txt \
	--sum ${sub}/bold/${r}/sum_subcort.txt \		--sum ${sub}/bold/${r}/sum_subcort.txt \
	--avgwf ${sub}_${r}.${FILEPAT}.wav.txt		--avgwf ${sub}_${r}.${FILEPAT}.wav.txt

	This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).		This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).

2019-05-29T02:47:22Z

← Older revision		Revision as of 22:47, 28 May 2019
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	--sum ${sub}/bold/${r}/sum_subcort.txt \		--sum ${sub}/bold/${r}/sum_subcort.txt \
	--avgwf ${sub}_${r}.${FILEPAT}.wav.txt		--avgwf ${sub}_${r}.${FILEPAT}.wav.txt

			This will generate a *.wav.txt file in the current working directory with t=timepoints rows and s=43 columns (1 per segment).

2019-05-29T02:44:12Z

← Older revision		Revision as of 22:44, 28 May 2019
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	mri_segstats --seg /usr/local/freesurfer/5.3.0/subjects/fsaverage/mri.2mm/aseg.mgz --i ${sub}/bold/${r}/${FILEPAT} \		mri_segstats --seg /usr/local/freesurfer/5.3.0/subjects/fsaverage/mri.2mm/aseg.mgz --i ${sub}/bold/${r}/${FILEPAT} \
	--sum ${sub}/bold/${r}/sum_subcort.txt \		--sum ${sub}/bold/${r}/sum_subcort.txt \
	--avgwf ${sub}_${r}.${~~filepat~~}.wav.txt		--avgwf ${sub}_${r}.${FILEPAT}.wav.txt