Differences between revisions 10 and 13 (spanning 3 versions)

Unpack the data from bourget:

Find your subject...

To find your data, run the findsession command, passing it the "patient name", which is the name that you registered the subject under when scanning:

["findsession patientname"]

This will give you a list of all matching data sets, including paths to where each one can be found. Eg,

/space/chartres/6/siemens/TRIO-20501-20020416-124756-468000

All the runs/series for your subject's visit will be in this directory.

Unpack the data

Unpacking is the processes through which you convert the data from DICOM format (which is not very useful) to a format that can be used by an analysis programe (eg, bhdr, nifti, analyze, mgh, mgz). The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). mri_convert can also be used to convert individual runs, whereas unpacksdcmdir can be used to unpack any or all data from a directory.

The first step in unpacking is to decide where you want your data to be stored. Usually, you choose a "parent" directory underwhich all of the visits for a study will be stored. Eg, /space/data/1/users/you/data-parent. The the actual target data for a given visit from a subject would be stored under something like /space/data/1/users/you/data-parent/yoursubject.

Next, you need to find out exactly what data are in the dicom directory. Specificially you need to know which run/series number corresponds to which acquisition. To do this run:

["unpacksdcmdir"] -src dicomdir -targ targetdir -scanonly targetdir/scan.info

where dicomdir is the directory where the dicom data reside (as found above by findsession), targetdir is where you want the individual's data to go, and the scan.info file will contain a list of run/series numbers along with the scanning protocol that was used to acquire the data, and will look something like this:

1 circle_localizer ok 256 256 3 1 74407231BR 2 ge_functionals ok 64 64 10 146 74407258BR 3 ge_functionals ok 64 64 10 146 74406408BR 4 ge_functionals ok 64 64 10 146 74405551BR 5 ge_functionals ok 64 64 10 146 74401663BR 6 ge_functionals ok 64 64 25 3 74400790BR 7 ep2d_T1w ok 64 64 10 1 74400835BR 8 tfl3d1_ns T1_MPRAGE_sag ok 256 256 128 1 74401012BR

To actually do the unpacking, you will need to run unpacksdcmdir again with a slightly different set of arguments:

["unpacksdcmdir"] -src dicomdir -targ targetdir -fsfast \BR

-run 2 bold bshort f\BR -run 3 bold bshort f\BR -run 4 bold bshort f\BR -run 5 bold bshort f\BR -run 6 bold bshort f\BR -run 8 3danat mgz 001.mgz\BR

If it is .ima format data...

Note: I have come across old data which was *.ima format. This can be unpacked using

["unpackimadir2"]

which works just like unpacksdcmdir.

Check for TR bug

*** There is always a problem after unpacking that the TR is not set correctly. Please fix it.

pico $SUBJECTS_DIR/$SUBJECT/bold/seq.info

Copy the 3danat

Goto the 3danat/ dir

cd $SUBJECTS_DIR/$SUBJECT/

Copy contents to mri/orig. For example...

cp 3danat/* mri/orig

-  ⇤ ← Revision 10 as of 2006-04-11 14:21:25 → 
  Size: 2339
  Editor: icebox
  Comment:
+   ← Revision 13 as of 2006-04-11 14:45:59 → ⇥
  Size: 3277
  Editor: icebox
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 12:
+All the runs/series for your subject's visit will be in this directory.
-Line 14:
+Line 16:
-Unpacking is the processes through which you convert the data from DICOM format (which is not very useful) to a format that can be used by an analysis programe (eg, bhdr, nifti, analyze, mgh, mgz). The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). mri_convert can also be used to convert individual runs.
+Unpacking is the processes through which you convert the data from DICOM format (which is not very useful) to a format that can be used by an analysis programe (eg, bhdr, nifti, analyze, mgh, mgz). The program that does this is unpacksdcmdir (this is only used to unpack Siemens DICOM files). mri_convert can also be used to convert individual runs, whereas unpacksdcmdir can be used to unpack any or all data from a directory.
-Line 16:
+Line 18:
-Ask it to start, and you will find that instead it will tell you the path for unpacking.
+The first step in unpacking is to decide where you want your data to be stored. Usually, you choose a "parent" directory underwhich all of the visits for a study will be stored. Eg, /space/data/1/users/you/data-parent. The the actual target data for a given visit from a subject would be stored under something like /space/data/1/users/you/data-parent/yoursubject.
-Line 18:
+Line 20:
- ["unpacksdcmdir"] -src <source> -targ <target> -scanonly file
+Next, you need to find out exactly what data are in the dicom directory. Specificially you need to know which run/series number corresponds to which acquisition. To do this run:
-Line 20:
+Line 22:
-NOTE: you must be in the targ dir for that command to work.
This outputs the type of scans used. Now use a file at 
 $FREESURFER_HOME/numaris4-protocols.unpackcfg
+ ["unpacksdcmdir"] -src dicomdir -targ  targetdir -scanonly targetdir/scan.info
 Line 24:
-to correctly make a config file. If you cannot find the file, check here
 [http://www.nmr.mgh.harvard.edu/~daniel/links/how/numaris4-protocols.unpackcfg]
+where dicomdir is the directory where the dicom data reside (as found above by findsession), targetdir is where you want the individual's data to go, and the scan.info file will contain a list of run/series numbers along with the scanning protocol that was used to acquire the data, and will look something like this:
-Line 27:
+Line 26:
-The format is:
num folder format fileprefix
Here is an example config file.
||1 scout bshort f||
||3 bold bshort f||
||4 bold bshort f||
||5 bold bshort f||
||6 bold bshort f||
||7 bold bshort f||
||8 bold bshort f||
The number is acquisition number.
The folder is where that acquisition is stored (bold directory, scout directory etc)
The format is the form of the data files.
The fileprefix is how the filenames start.
+circle_localizer  ok  256 256   3   1 74407231[[BR]]
  2       ge_functionals  ok   64  64  10 146 74407258[[BR]]
  3       ge_functionals  ok   64  64  10 146 74406408[[BR]]
  4       ge_functionals  ok   64  64  10 146 74405551[[BR]]
  5       ge_functionals  ok   64  64  10 146 74401663[[BR]]
  6       ge_functionals  ok   64  64  25   3 74400790[[BR]]
  7             ep2d_T1w  ok   64  64  10   1 74400835[[BR]]
  8 tfl3d1_ns T1_MPRAGE_sag ok 256 256 128  1 74401012[[BR]]
-Line 42:
+Line 35:
-== Next run it again with your config file. ==
 ["unpacksdcmdir"] -src <source> -targ <target> -cfg<configfile> -fsfast
+To actually do the unpacking, you will need to run unpacksdcmdir again with a slightly different set of arguments:

["unpacksdcmdir"] -src dicomdir -targ  targetdir -fsfast \[[BR]]
  -run 2 bold bshort f\[[BR]]
  -run 3 bold bshort f\[[BR]]
  -run 4 bold bshort f\[[BR]]
  -run 5 bold bshort f\[[BR]]
  -run 6 bold bshort f\[[BR]]
  -run 8 3danat mgz  001.mgz\[[BR]]