Configure preproc-sess - Revision history

Chris: /* ERROR: 3dvolreg.afni & libxp.so.6 */

2022-05-11T17:30:54Z

ERROR: 3dvolreg.afni & libxp.so.6

← Older revision		Revision as of 13:30, 11 May 2022
Line 110:		Line 110:
	To fix this, we can either:		To fix this, we can either:
	# install an older version of the needed packages: [https://packages.debian.org/jessie/amd64/libxp6/download here]		# install an older version of the needed packages: [https://packages.debian.org/jessie/amd64/libxp6/download here]
	#* sudo dpkg --install <name of file>		#* sudo dpkg --install <name of file> (not recommended because library is deprecated and unsupported)
	# or symlink libXp.so.6 to libXpm4.so.11, which is included in the libXpm package		# or symlink libXp.so.6 to libXpm4.so.11, which is included in the libXpm package
			If you choose the latter option, you will find libXpm4 in <code>/usr/lib/x86_64-linux-gnu/</code>

	Note: if you're having this problem, you may also find yourself missing libpng12		Note: if you're having this problem, you may also find yourself missing libpng12

Chris at 15:00, 19 October 2020

2020-10-19T15:00:14Z

← Older revision		Revision as of 11:00, 19 October 2020
Line 1:		Line 1:
	You can preprocess multiple participants in a batch or individual participants, depending on how you invoke the preproc-sess command. This took ~30 min to run one participant on Brocasarea.		You can preprocess multiple participants in a batch or individual participants, depending on how you invoke the preproc-sess command. This took ~40 min to run one participant on Brocasarea.
	= Before you start =		= Before you start =
	Check down at the Problems section at the bottom of this page. In particular, there is an additional step you will have to do to work with data collected from the DENT Institute ('''Header Problems 1''').		Check down at the Problems section at the bottom of this page. In particular, there is an additional step you will have to do to work with data collected from the DENT Institute ('''Header Problems 1''').

Chris: /* Check Registration */

2020-10-19T14:32:25Z

Check Registration

← Older revision		Revision as of 10:32, 19 October 2020
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	=== Check Registration ===		=== Check Registration ===
	Before you proceed with any functional analyses, you should ensure that the bold data has been coregistered to the T1 anatomical data. You can use tkregister-sess to view a representative volume from each run, with the white matter surface contours mapped on to the volume:		Before you proceed with any functional analyses, you should ensure that the bold data has been coregistered to the T1 anatomical data. You can use tkregister-sess to view a representative volume from each run, with the white matter surface contours mapped on to the volume:
			cd $SUBJECTS_DIR
	SUBJECT_ID=FS_T1_501		SUBJECT_ID=FS_T1_501
	tkregister-sess -s ${SUBJECT_ID} -inorm -per-run		tkregister-sess -s ${SUBJECT_ID} -inorm -per-run
	If the contours are out of alignment with the functional data, you can use this interface to manually perform affine (i.e., rigid-body) transformations so that they line up. More information on this can be found [https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV4.5 here] and [https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration here].		If the contours are out of alignment with the functional data, you can use this interface to manually perform affine (i.e., rigid-body) transformations so that they line up. More information on this can be found [https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV4.5 here] and [https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/ManualRegistration here].

	Note: You must ~~cd to~~ your subjects directory for this to work.		Note: You must be in your subjects directory for this to work.

	=== Slice time correction ===		=== Slice time correction ===

Chris: /* Batch Subjectname Setup */

2020-10-14T15:59:41Z

Batch Subjectname Setup

← Older revision		Revision as of 11:59, 14 October 2020
Line 19:		Line 19:
	'''setsubjectnames.sh'''		'''setsubjectnames.sh'''

	!/bin/bash		#!/bin/bash
	#given a list of subject folders in $SUBJECTS_DIR, venture into each		#given a list of subject folders in $SUBJECTS_DIR, venture into each
	#folder and ensure that an initialized subjectname file exists		#folder and ensure that an initialized subjectname file exists

Chris: /* niiRead(): error opening file /tmp/mkbrainmask* */

2020-05-20T16:19:20Z

niiRead(): error opening file /tmp/mkbrainmask*

← Older revision		Revision as of 12:19, 20 May 2020
Line 118:		Line 118:
	You will need to get one of the End Bosses to run this as an admin.		You will need to get one of the End Bosses to run this as an admin.

	~~=== niiRead(): error opening file /tmp/mkbrainmask* ===~~
	~~You probably missed a step in matlab. Go back and make sure you dropped volumes, set TR, and extracted the parfiles. Make sure everything is in the right location and named properly.~~

	[[Category: FreeSurfer]]		[[Category: FreeSurfer]]

Chris: /* Ensure your BOLD file headers are correct! */

2020-05-20T16:18:08Z

Ensure your BOLD file headers are correct!

← Older revision		Revision as of 12:18, 20 May 2020
Line 2:		Line 2:
	= Before you start =		= Before you start =
	Check down at the Problems section at the bottom of this page. In particular, there is an additional step you will have to do to work with data collected from the DENT Institute ('''Header Problems 1''').		Check down at the Problems section at the bottom of this page. In particular, there is an additional step you will have to do to work with data collected from the DENT Institute ('''Header Problems 1''').
	==Ensure your BOLD ~~file headers are~~ correct!==		==Ensure your BOLD timing is correct!==
	There is a chance that the data collected at UB does not have the correct header information. In particular, the TR information may be inaccurately set to 1.0 (we have never run an experiment with a 1-second TR). Both the LDT and the Semantic Categories experiment used a 2.047 TR, and so you should consult the [[Freesurfer_BOLD_files]] page for information on how to correct these files -- if the timing is incorrect, then the slice timing calculations will be incorrect. Discover this too late (like I just did), and you'll have to run preprocessing all over again!		There is a chance that the data collected at UB does not have the correct header information. In particular, the TR information may be inaccurately set to 1.0 (we have never run an experiment with a 1-second TR). Both the LDT and the Semantic Categories experiment used a 2.047 TR, and so you should consult the [[Freesurfer_BOLD_files]] page for information on how to correct these files -- if the timing is incorrect, then the slice timing calculations will be incorrect. Discover this too late (like I just did), and you'll have to run preprocessing all over again!

Chris: /* Before you start */

2020-05-20T16:06:46Z

Before you start

← Older revision		Revision as of 12:06, 20 May 2020
Line 2:		Line 2:
	= Before you start =		= Before you start =
	Check down at the Problems section at the bottom of this page. In particular, there is an additional step you will have to do to work with data collected from the DENT Institute ('''Header Problems 1''').		Check down at the Problems section at the bottom of this page. In particular, there is an additional step you will have to do to work with data collected from the DENT Institute ('''Header Problems 1''').
			==Ensure your BOLD file headers are correct!==
			There is a chance that the data collected at UB does not have the correct header information. In particular, the TR information may be inaccurately set to 1.0 (we have never run an experiment with a 1-second TR). Both the LDT and the Semantic Categories experiment used a 2.047 TR, and so you should consult the [[Freesurfer_BOLD_files]] page for information on how to correct these files -- if the timing is incorrect, then the slice timing calculations will be incorrect. Discover this too late (like I just did), and you'll have to run preprocessing all over again!

	== Create a subjectname file ==		== Create a subjectname file ==

Chris: /* ERROR: 3dvolreg.afni & libxp.so.6 */

2020-03-22T16:24:14Z

ERROR: 3dvolreg.afni & libxp.so.6

← Older revision		Revision as of 12:24, 22 March 2020
Line 112:		Line 112:
	Note: if you're having this problem, you may also find yourself missing libpng12		Note: if you're having this problem, you may also find yourself missing libpng12
	wget http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb		wget http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
	OR
	~~wget https://launchpad.net/~ubuntu-security/+archive/ubuntu/ppa/+build/15108504/+files/libpng12-dev_1.2.54-1ubuntu1.1_amd64.deb~~

	sudo dpkg --install libpng12-0_1.2.54-1ubuntu1_amd64.deb		sudo dpkg --install libpng12-0_1.2.54-1ubuntu1_amd64.deb

Chris: /* ERROR: 3dvolreg.afni & libxp.so.6 */

2020-03-22T16:16:00Z

ERROR: 3dvolreg.afni & libxp.so.6

← Older revision		Revision as of 12:16, 22 March 2020
Line 112:		Line 112:
	Note: if you're having this problem, you may also find yourself missing libpng12		Note: if you're having this problem, you may also find yourself missing libpng12
	wget http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb		wget http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
			OR
			wget https://launchpad.net/~ubuntu-security/+archive/ubuntu/ppa/+build/15108504/+files/libpng12-dev_1.2.54-1ubuntu1.1_amd64.deb

	sudo dpkg --install libpng12-0_1.2.54-1ubuntu1_amd64.deb		sudo dpkg --install libpng12-0_1.2.54-1ubuntu1_amd64.deb

Chris: /* ERROR: 3dvolreg.afni & libxp.so.6 */

2020-03-22T15:31:35Z

ERROR: 3dvolreg.afni & libxp.so.6

← Older revision		Revision as of 11:31, 22 March 2020
Line 109:		Line 109:
	#* sudo dpkg --install <name of file>		#* sudo dpkg --install <name of file>
	# or symlink libXp.so.6 to libXpm4.so.11, which is included in the libXpm package		# or symlink libXp.so.6 to libXpm4.so.11, which is included in the libXpm package
	You ~~may~~ need to get one of the End Bosses to run this as an admin.
			Note: if you're having this problem, you may also find yourself missing libpng12
			wget http://se.archive.ubuntu.com/ubuntu/pool/main/libp/libpng/libpng12-0_1.2.54-1ubuntu1_amd64.deb
			sudo dpkg --install libpng12-0_1.2.54-1ubuntu1_amd64.deb

			You will need to get one of the End Bosses to run this as an admin.

	=== niiRead(): error opening file /tmp/mkbrainmask* ===		=== niiRead(): error opening file /tmp/mkbrainmask* ===