Segmentation - Revision history

SRP Wiki: /* Creating Segmentation Files */

2014-10-13T18:34:43Z

Creating Segmentation Files

← Older revision		Revision as of 18:34, 13 October 2014
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	::4. In the window that appears, navigate to the subject's "nii" directory of NIfTI volume image files and select the "hhr_struct" file.		::4. In the window that appears, navigate to the subject's "nii" directory of NIfTI volume image files and select the "hhr_struct" file.
	::5. Another window with the image scan of the subject will appear. Begin drawing a rectangular box around the hippocampal region, covering both the left and right sides.		::5. Another window with the image scan of the subject will appear. Begin drawing a rectangular box around the hippocampal region, covering both the left and right sides.
	:::*Note: It is important to draw the rectangle with enough vertical space above and below the region to account for ~~height changes in~~ different slides.		:::*Note: It is important to draw the rectangle with enough vertical space above and below the region to account for positional differences of the hippocampal region across different slides.
	::6. Once the box has been drawn, double click inside the drawn region and Matlab will begin creating the file.		::6. Once the box has been drawn, double click inside the drawn region and Matlab will begin creating the file.

SRP Wiki: /* Creating Segmentation Files */

2014-10-13T18:33:40Z

Creating Segmentation Files

← Older revision		Revision as of 18:33, 13 October 2014
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	::2. cd /u/project/sbook/data/AD/subjects/AD_1XXXX/20######/analysis/structural/unfold		::2. cd /u/project/sbook/data/AD/subjects/AD_1XXXX/20######/analysis/structural/unfold
	:::*X's denote the subject number and # indicates scan date. Running this command will take you to the subject's unfold directory.		:::*X's denote the subject number and # indicates scan date. Running this command will take you to the subject's unfold directory.
	::3. ~~ls ../../../nii/~~		::3. NLF_InitVol
	:::*This command will ~~list~~ the ~~NIfTI~~ volume ~~image files for the particular subject while remaining in the subject's unfold directory~~.		:::*This command will begin initializing the volume anatomy file.
	::4. ~~Find~~ the ~~file~~ that ~~has~~ "~~hhr_struct~~" ~~in its name~~ and ~~copy~~ the ~~whole NAME~~		::4. In the window that appears, navigate to the subject's "nii" directory of NIfTI volume image files and select the "hhr_struct" file.
	::5. ~~NLF_InitVol("~~,~~'../../~~.~~./nii/NAME');~~		::5. Another window with the image scan of the subject will appear. Begin drawing a rectangular box around the hippocampal region, covering both the left and right sides.
	:::*~~The file name that you copied should be~~ in ~~place of NAME~~. ~~This command~~ will		:::*Note: It is important to draw the rectangle with enough vertical space above and below the region to account for height changes in different slides.
			::6. Once the box has been drawn, double click inside the drawn region and Matlab will begin creating the file.

SRP Wiki: /* Creating Segmentation Files */

2014-09-30T20:31:10Z

Creating Segmentation Files

← Older revision		Revision as of 20:31, 30 September 2014
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	:::*X's denote the subject number and # indicates scan date. Running this command will take you to the subject's unfold directory.		:::*X's denote the subject number and # indicates scan date. Running this command will take you to the subject's unfold directory.
	::3. ls ../../../nii/		::3. ls ../../../nii/
	:::*This command will list the NIfTI volume image files for the particular subject's while remaining in the unfold directory.		:::*This command will list the NIfTI volume image files for the particular subject while remaining in the subject's unfold directory.
	::4. Find the file that has "hhr_struct" in its name and copy the whole NAME		::4. Find the file that has "hhr_struct" in its name and copy the whole NAME
	::5. NLF_InitVol(",'../../../nii/NAME');		::5. NLF_InitVol(",'../../../nii/NAME');
	:::*The file name that you copied should be in place of NAME. This command will		:::*The file name that you copied should be in place of NAME. This command will

SRP Wiki: /* Creating Segmentation Files */

2014-09-30T20:29:58Z

Creating Segmentation Files

← Older revision		Revision as of 20:29, 30 September 2014
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	:::*This command will list the NIfTI volume image files for the particular subject's while remaining in the unfold directory.		:::*This command will list the NIfTI volume image files for the particular subject's while remaining in the unfold directory.
	::4. Find the file that has "hhr_struct" in its name and copy the whole NAME		::4. Find the file that has "hhr_struct" in its name and copy the whole NAME
	::5. NLF_InitVol('','../../../nii/NAME');		::5. NLF_InitVol(",'../../../nii/NAME');
	:::*The file name that you copied should be in place of NAME. This command will		:::*The file name that you copied should be in place of NAME. This command will

SRP Wiki: Created page with "===Creating Segmentation Files=== Segmentation files are created by first creating vAnatomy.dat files in Matlab. To open Matlab in Terminal you must be logged into hoffman. O..."

2014-09-30T20:29:28Z

Created page with "===Creating Segmentation Files=== Segmentation files are created by first creating vAnatomy.dat files in Matlab. To open Matlab in Terminal you must be logged into hoffman. O..."

New page

===Creating Segmentation Files===

Segmentation files are created by first creating vAnatomy.dat files in Matlab. To open Matlab in Terminal you must be logged into hoffman. Once you are logged on, you will run these commands in Terminal:

::1. qrsh -l i,h_rt=5:00:00,h_data=4G
:::*The "5:00:00" indicates that Matlab will run for 5 hours.
::2. module load matlab/7.14
::3. matlab

To create the vAnatomy.dat file and prepare the high resolution T2 images, you will run these following commands in Matlab:

::1. addpath(genpath('/u/home/FMRI/apps/unfolding/current/'));
:::*Note: The warning message can be ignored.
::2. cd /u/project/sbook/data/AD/subjects/AD_1XXXX/20######/analysis/structural/unfold
:::*X's denote the subject number and # indicates scan date. Running this command will take you to the subject's unfold directory.
::3. ls ../../../nii/
:::*This command will list the NIfTI volume image files for the particular subject's while remaining in the unfold directory.
::4. Find the file that has "hhr_struct" in its name and copy the whole NAME
::5. NLF_InitVol('','../../../nii/NAME');
:::*The file name that you copied should be in place of NAME. This command will