Freesurfer BOLD files - Revision history

Chris: /* File Organization */

2022-02-16T21:30:38Z

File Organization

← Older revision		Revision as of 17:30, 16 February 2022
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	***<span style="color:red">bold</span>		***<span style="color:red">bold</span>
	****<span style="color:red">001</span>		****<span style="color:red">001</span>
	*****<span style="color:red">f.nii</span>		*****<span style="color:red">f.nii.gz</span>
	****<span style="color:red">002</span>		****<span style="color:red">002</span>
	*****<span style="color:red">f.nii</span>		*****<span style="color:red">f.nii.gz</span>
	****<span style="color:red">006</span>		****<span style="color:red">006</span>
	*****<span style="color:red">f.nii</span>		*****<span style="color:red">f.nii.gz</span>
	***label		***label
	***mri		***mri

Chris: /* Coregister.sh */

2020-10-07T14:50:50Z

Coregister.sh

← Older revision		Revision as of 10:50, 7 October 2020
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	http://dx.doi.org/10.1016/j.neuroimage.2010.07.020		http://dx.doi.org/10.1016/j.neuroimage.2010.07.020
	==== Coregister.sh ====		==== Coregister.sh ====
	I've written a shell script that coregisters multisession BOLD data to a reference functional file. ~~You will find~~ coregister.sh in the ubfs Scripts/Shell/ folder. It requires that your bold/ directory contains a file called '''runs''' that contains the BOLD subdirectories you wish to coregister. The script will coregister the f.nii.gz files in each of the directories with the f.nii.gz file it find in the first listed directory. For example:		I've written a shell script that coregisters multisession BOLD data to a reference functional file. A copy of coregister.sh can be found in the ubfs Scripts/Shell/ folder if it is not already in your path (/opt/scripts). It requires that your bold/ directory contains a file called '''runs''' that contains the BOLD subdirectories you wish to coregister. The script will coregister the f.nii.gz files in each of the directories with the f.nii.gz file it find in the first listed directory. For example:
	'''Sample runs file'''		'''Sample runs file'''
	001		001

Chris: /* Dropping Volumes Using dropvols.sh */

2020-10-07T13:49:37Z

Dropping Volumes Using dropvols.sh

← Older revision		Revision as of 09:49, 7 October 2020
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	'''Egads!''' The new file and the original data both have 220 volumes, meaning that the new file has not yet had the first 4 volumes dropped, and so you're going to need to check out the procedures below.		'''Egads!''' The new file and the original data both have 220 volumes, meaning that the new file has not yet had the first 4 volumes dropped, and so you're going to need to check out the procedures below.
	====Dropping Volumes Using dropvols.sh====		====Dropping Volumes Using dropvols.sh====
	Upon learning that fslroi can be used to easily drop volumes in a single step, I wrote a script found in /ubfs/Scripts/Shell/dropvols.sh. You should also find that it's on your path (/opt/scripts). If not, let someone know. The script will drop the first n volumes from the named file.		Upon learning that fslroi can be used to easily drop volumes in a single step, I wrote a shell script found in /ubfs/Scripts/Shell/dropvols.sh. You should also find that it's on your path (/opt/scripts). If not, let someone know. You can find out whether it's in your path by running the following command in the shell terminal:
			which dropvols.sh
			If the command is in your path, it will tell you the location of the script.

			The script will drop the first n volumes from the named file.
	'''dropvols.sh'''		'''dropvols.sh'''
	Usage: dropvols.sh <filename> <vols>		Usage: dropvols.sh <filename> <vols>

Chris: /* Fixing Files in the Terminal */

2020-10-07T13:46:52Z

Fixing Files in the Terminal

@@ Line 112: / Line 112: @@
 '''Egads!''' The new file and the original data both have 220 volumes, meaning that the new file has not yet had the first 4 volumes dropped, and so you're going to need to check out the procedures below.
 ===Setting the TR in the Terminal using fsledithd===
 Having seen the output from fslhd, the fsl utility, fsledithd, is similar. It uses the linux tool <code>nano</code> as a backend text editor to modify the header information:
@@ Line 182: / Line 222: @@
    + loading and re-writing dataset f.nii (./f.nii in NIFTI storage)
   ++ 3drefit processed 1 datasets
 == File Organization==

Chris: /* Setting the TR in the Terminal using fsledithd */

2020-10-05T14:56:19Z

Setting the TR in the Terminal using fsledithd

← Older revision		Revision as of 10:56, 5 October 2020
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	fsledithd f.nii		fsledithd f.nii
	The <code>nano</code> program will open, displaying each of the fields on a line. Pay attention to the dt field in red:		The <code>nano</code> program will open, displaying each of the fields on a line. Pay attention to the dt field in red:
	# FSLEDITHD		# FSLEDITHD
	# This text file contains the header information for an Analyze or Nifti file		# This text file contains the header information for an Analyze or Nifti file
	# Simply edit this file then save it and the header will be regenerated		# Simply edit this file then save it and the header will be regenerated
	# All lines starting with the hash (#) character, like this line, will be ignored		# All lines starting with the hash (#) character, like this line, will be ignored
	# Ensure that all lines intended to set values take the form: name = 'value'		# Ensure that all lines intended to set values take the form: name = 'value'
	# Note that if the file is Analyze then many settings will be ignored		# Note that if the file is Analyze then many settings will be ignored
	# Further note that the filetype cannot be changed by this program		# Further note that the filetype cannot be changed by this program
	# i.e. changing the nifti_type has no effect		# i.e. changing the nifti_type has no effect

	<nifti_image		<nifti_image
	nifti_type = 'NIFTI-1+'		nifti_type = 'NIFTI-1+'

Chris at 14:55, 5 October 2020

2020-10-05T14:55:41Z

@@ Line 71: / Line 71: @@
 Now we're good to go: we have a series of files named ''f.nii.gz'' that all have the first 4 volumes dropped, have the correct number of time points in the header, and have the correct TR.
-===Fixing Files in the Terminal===
+==Fixing Files in the Terminal==
 It turns out there are several useful utilities associated with AFNI and FSL that can let us do everything we need to do in the terminal, without running MATLAB. This is helpful if you want to automate the process with a script, but note also that the method described below doesn't handle 4D volumes where early stopping affects motion correction. Automation would require computing when the last TR of real data was acquired so that padded volumes could automatically be dropped.
-===== Do I need to drop any volumes? =====
+=== Do I need to drop any volumes? ===
 Run the following command to examine the .nii header for one of your BOLD files:
   fslhd <filename.nii>
@@ Line 112: / Line 112: @@
 '''Egads!''' The new file and the original data both have 220 volumes, meaning that the new file has not yet had the first 4 volumes dropped, and so you're going to need to check out the procedures below.
-====Setting the TR in the Terminal Using the AFNI tool <span style="color:blue">3drefit</span>====
+ <nifti_image
 The AFNI utility, <code>3drefit</code> can do all sorts of things, including the trivial task of modifying the TR field in your BOLD data when you use the <code>-TR</code> switch:
   BASEFILENAME=f.nii.gz #the name of the file to modify

Chris: /* Setting the TR in the Terminal Using 3drefit */

2020-10-05T14:45:40Z

Setting the TR in the Terminal Using 3drefit

← Older revision		Revision as of 10:45, 5 October 2020
Line 113:		Line 113:
	'''Egads!''' The new file and the original data both have 220 volumes, meaning that the new file has not yet had the first 4 volumes dropped, and so you're going to need to check out the procedures below.		'''Egads!''' The new file and the original data both have 220 volumes, meaning that the new file has not yet had the first 4 volumes dropped, and so you're going to need to check out the procedures below.

	====Setting the TR in the Terminal Using 3drefit====		====Setting the TR in the Terminal Using the AFNI tool <span style="color:blue">3drefit</span>====
	The AFNI utility, <code>3drefit</code> can do all sorts of things, including the trivial task of modifying the TR field in your BOLD data when you use the <code>-TR</code> switch:		The AFNI utility, <code>3drefit</code> can do all sorts of things, including the trivial task of modifying the TR field in your BOLD data when you use the <code>-TR</code> switch:
	BASEFILENAME=f.nii.gz #the name of the file to modify		BASEFILENAME=f.nii.gz #the name of the file to modify
Line 125:		Line 125:
	+ loading and re-writing dataset f.nii (./f.nii in NIFTI storage)		+ loading and re-writing dataset f.nii (./f.nii in NIFTI storage)
	++ 3drefit processed 1 datasets		++ 3drefit processed 1 datasets

	====Dropping Volumes Using dropvols.sh====		====Dropping Volumes Using dropvols.sh====
	Upon learning that fslroi can be used to easily drop volumes in a single step, I wrote a script found in /ubfs/Scripts/Shell/dropvols.sh. You should also find that it's on your path (/opt/scripts). If not, let someone know. The script will drop the first n volumes from the named file.		Upon learning that fslroi can be used to easily drop volumes in a single step, I wrote a script found in /ubfs/Scripts/Shell/dropvols.sh. You should also find that it's on your path (/opt/scripts). If not, let someone know. The script will drop the first n volumes from the named file.

Chris: /* Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge */

2020-10-05T14:43:16Z

Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge

← Older revision		Revision as of 10:43, 5 October 2020
Line 134:		Line 134:

	====<span style="color:gray">Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge</span>====		====<span style="color:gray">Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge</span>====
	'''These steps are deprecated as of May, 2020 when I accidentally discovered that a single FSL utility, fslroi, can do this all in one shot. I leave these instructions for posterity.'''		'''These steps are deprecated as of May, 2020 when I accidentally discovered that a single FSL utility, fslroi, can do this all in one shot. dropvols.sh now uses fslroi for this task. I leave these instructions for posterity.'''

	<span style="color:blue">Dropping the volumes with fslsplit</span>		<span style="color:blue">Dropping the volumes with fslsplit</span>

Chris: /* Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge */

2020-10-05T14:42:25Z

Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge

← Older revision		Revision as of 10:42, 5 October 2020
Line 134:		Line 134:

	====<span style="color:gray">Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge</span>====		====<span style="color:gray">Deprecated: Dropping Volumes in the Terminal Using fslsplit and fslmerge</span>====
	These steps are deprecated as of May, 2020 when I accidentally discovered that a single FSL utility, fslroi, can do this all in one shot. I leave these instructions for posterity.		'''These steps are deprecated as of May, 2020 when I accidentally discovered that a single FSL utility, fslroi, can do this all in one shot. I leave these instructions for posterity.'''

	<span style="color:blue">Dropping the volumes with fslsplit</span>		<span style="color:blue">Dropping the volumes with fslsplit</span>

Chris: /* Fixing Files Using Drag and Drop with MRICron */

2020-10-05T14:35:06Z

Fixing Files Using Drag and Drop with MRICron

← Older revision		Revision as of 10:35, 5 October 2020
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	This would tell us that nothing happened during volumes 1:4 and during the volumes from 242:end. You will almost certainly want to drop the first 4 volumes. Depending on your requirements, you may wish to drop the volumes at the end as well, but consult with a knowledgeable lab member first, if you have any question (it is essential that all data sets are treated the same way within a single study).		This would tell us that nothing happened during volumes 1:4 and during the volumes from 242:end. You will almost certainly want to drop the first 4 volumes. Depending on your requirements, you may wish to drop the volumes at the end as well, but consult with a knowledgeable lab member first, if you have any question (it is essential that all data sets are treated the same way within a single study).

	===Fixing Files Using Drag and Drop with MRICron ===		===DENT Data: Fixing Files Using Drag and Drop with MRICron ===
	NIfTI (.nii) files collected from DENT may have the incorrect number of volumes listed in the file header. Though the run often terminates before the 256 volume maximum has been reached, their system nonetheless indicates that the 4D volumes have 256 frames. If you open up the headers using fsledithd, you will receive a warning, and fsl will automatically pad the end of the 4D volumes with empty data frames (volumes containing only zeroes) until they reach the requisite file size. It turns out that the files with partial data frames are problematic for the motion correction for reasons that you will appreciate when you follow these directions.		NIfTI (.nii) files collected from DENT may have the incorrect number of volumes listed in the file header. Though the run often terminates before the 256 volume maximum has been reached, their system nonetheless indicates that the 4D volumes have 256 frames. If you open up the headers using fsledithd, you will receive a warning, and fsl will automatically pad the end of the 4D volumes with empty data frames (volumes containing only zeroes) until they reach the requisite file size. It turns out that the files with partial data frames are problematic for the motion correction for reasons that you will appreciate when you follow these directions.