Hello -
I am a new graduate student working with Dr. Russ Poldrack at UCLA and I am trying to learn how to use Freesurfer. I downloaded all of the sample data from the page FSTutorial/Data, but many of the tutorials seem to refer to data that is not included in the sample data.
The first tutorial I tried was FSTutorial/MorphAndRecon. - Exercise B in this tutorial is the page FSTutorial/Talairach. This page refers to the files tal_before and tal_after which are not in the sample data. - Exercise C in this tutorial is the page FSTutorial/ControlPoints. This page refers to the file cp_before which is not in the sample data. - Exercise D in this tutorial is the page FSTutorial/SkullStripFix. This page refers to the files skullstrip1_before, skullstrip2_before, skullstrip2_after and skullstrip3_before which are not in the sample data - Exercise F in this tutorial is the page FSTutorial/WhiteMatterEdits. This page refers to the files wm1_edits_before, wm2_edits_before and wm3_edits_before whic are not in the sample data - Exercise G in this tutorial is the page FSTutorial/PialEdits. This page refers to the file pial_edits_before which is not in the sample data.
The second tutorial I tried was FSFastTutorial. This tutorial seems to refer to data from the FsFastTutorialData page (from files fsfast-tutorial.tar.gz and fsfast-tutorial.subjects.tar.gz). However, I am unable to download these files from this page.
Please either let me know where I can find these files so I can complete the tutorials, or if there are different tutorials that correspond with the data I downloaded from FSTutorial/Data.
Thank you very much. Sincerely, Jennifer Brace
Hi Jennifer
When did you download the data? We overhauled the tutorials and I believe Nick updated the wiki with the new data couple of days back. Please download the new one and try.
Krish
On Jan 21, 2009, at 3:56 PM, jbrace@ucla.edu wrote:
Hello -
I am a new graduate student working with Dr. Russ Poldrack at UCLA and I am trying to learn how to use Freesurfer. I downloaded all of the sample data from the page FSTutorial/Data, but many of the tutorials seem to refer to data that is not included in the sample data.
The first tutorial I tried was FSTutorial/MorphAndRecon.
- Exercise B in this tutorial is the page FSTutorial/Talairach.
This page refers to the files tal_before and tal_after which are not in the sample data.
- Exercise C in this tutorial is the page FSTutorial/ControlPoints.
This page refers to the file cp_before which is not in the sample data.
- Exercise D in this tutorial is the page FSTutorial/SkullStripFix.
This page refers to the files skullstrip1_before, skullstrip2_before, skullstrip2_after and skullstrip3_before which are not in the sample data
- Exercise F in this tutorial is the page FSTutorial/
WhiteMatterEdits. This page refers to the files wm1_edits_before, wm2_edits_before and wm3_edits_before whic are not in the sample data
- Exercise G in this tutorial is the page FSTutorial/PialEdits.
This page refers to the file pial_edits_before which is not in the sample data.
The second tutorial I tried was FSFastTutorial. This tutorial seems to refer to data from the FsFastTutorialData page (from files fsfast-tutorial.tar.gz and fsfast-tutorial.subjects.tar.gz). However, I am unable to download these files from this page.
Please either let me know where I can find these files so I can complete the tutorials, or if there are different tutorials that correspond with the data I downloaded from FSTutorial/Data.
Thank you very much. Sincerely, Jennifer Brace
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Jennifer,
The tutorials matching the newly available data are found here:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial
You will need to get v4.2.0, which will be released in a couple days (actually, you can do the tutorial with what you have, but will bump into a couple unrecognized flags here and there).
The MorphAndRecon page is an old tutorial (although the information is still relevant).
Nick
On Wed, 2009-01-21 at 12:56 -0800, jbrace@ucla.edu wrote:
Hello -
I am a new graduate student working with Dr. Russ Poldrack at UCLA and I am trying to learn how to use Freesurfer. I downloaded all of the sample data from the page FSTutorial/Data, but many of the tutorials seem to refer to data that is not included in the sample data.
The first tutorial I tried was FSTutorial/MorphAndRecon.
- Exercise B in this tutorial is the page FSTutorial/Talairach.
This page refers to the files tal_before and tal_after which are not in the sample data.
- Exercise C in this tutorial is the page FSTutorial/ControlPoints.
This page refers to the file cp_before which is not in the sample data.
- Exercise D in this tutorial is the page FSTutorial/SkullStripFix.
This page refers to the files skullstrip1_before, skullstrip2_before, skullstrip2_after and skullstrip3_before which are not in the sample data
- Exercise F in this tutorial is the page
FSTutorial/WhiteMatterEdits. This page refers to the files wm1_edits_before, wm2_edits_before and wm3_edits_before whic are not in the sample data
- Exercise G in this tutorial is the page FSTutorial/PialEdits.
This page refers to the file pial_edits_before which is not in the sample data.
The second tutorial I tried was FSFastTutorial. This tutorial seems to refer to data from the FsFastTutorialData page (from files fsfast-tutorial.tar.gz and fsfast-tutorial.subjects.tar.gz). However, I am unable to download these files from this page.
Please either let me know where I can find these files so I can complete the tutorials, or if there are different tutorials that correspond with the data I downloaded from FSTutorial/Data.
Thank you very much. Sincerely, Jennifer Brace
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
jbrace＠ucla.edu -
Krish Subramaniam -
Nick Schmansky