Sorry, forgot to say that I tried the -long option for two time points without the -hippo-subields option and it completed without errors.

Thanks again 

Erik
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohanlon@rcsi.ie]
Sent: 20 November 2014 13:04
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

Hi Martin,

I appear to have run into an issue when processing longitudinal data with the -hippo-subfields command. I get the following error. I have run the process in the cross (independent) mode and it ran okay at each time point (I have two).  

Wrote out aseg_thresholded.mgz

kvlMathematicalMorphology aseg_thresholded.mgz dilate 3

imageFileName: aseg_thresholded.mgz

radius: 3

Using dilating filter


itk::ExceptionObject (0x2ccf4d0)

Location: "void itk::ImageFileWriter<TInputImage>::Write() [with TInputImage = main(int, char**)::ImageType]"

File: /usr/pubsw/packages/itk/current/include/InsightToolkit/IO/itkImageFileWriter.txx

Line: 271

Description: itk::ERROR: ImageFileWriter(0x2cb8880): Largest possible region does not fully contain requested paste IO regionPaste$

  Dimension: 3

  Index: 0 0 0

  Size: 0 0 0

Largest possible region: ImageRegion (0x7fff9c9b02e0)

  Dimension: 3

  Index: [0, 0, 0]

  Size: [0, 0, 0]




failed to do kvlMathematicalMorphology aseg_thresholded.mgz dilate 3

Linux tcin-n08.cluster 2.6.18-274.18.1.el5 #1 SMP Thu Feb 9 12:20:03 EST 2012 x86_64 x86_64 x86_64 GNU/Linux


recon-all -s sub040_tp1.long.sub040_T1_baseimage exited with ERRORS at Wed Nov 19 20:34:12 GMT 2014


For more details, see the log file /projects/pi-frodlt/HPC_11_00383/Freesurfer_ABD/sub040_tp1.long.sub040_T1_baseimage$

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 

Any ideas very much appreciated.

Erik
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohanlon@rcsi.ie]
Sent: 18 November 2014 20:42
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

That's super!

Thanks again Martin

Best regards

Erik
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreuter@nmr.mgh.harvard.edu]
Sent: 18 November 2014 18:07
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

Hi Erik,

no need to re-run . no need even to do -all, just do the subfields.

Best, Martin

On 11/18/2014 12:57 PM, Erik O'Hanlon wrote:
Thanks Martin,

Could I also ask that if the -long command was run without the subfield option, is it best to delete the dir and rerun it or simply recur the command with the subfields option included (and that will continue on and run the remaining hippo camp things?).

Thanks again for your help, very much appreciated.

Best regards

Erik 
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreuter@nmr.mgh.harvard.edu]
Sent: 18 November 2014 17:04
To: Freesurfer support list
Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields

Hi Erik,

yes, you would do the subfields only in the -long. No need currently to include it in cross (independent) or base.

Best, Martin

On 11/18/2014 11:41 AM, Erik O'Hanlon wrote:
Dear FS Experts,

I'm running a longitudinal analysis and have run the individual time points using the hippocampal subfields. Do I also need to include the -hippo-subfields in the recon-all -long command too?

Thanks in advance for any input.

Kind regards

Erik 

Erik O'Hanlon
Postdoctoral researcher

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohanlon@rcsi.ie  W: www.rcsi.ie

RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE 




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-- 
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu 


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email: 
   mreuter@nmr.mgh.harvard.edu
   reuter@mit.edu
Web  : http://reuter.mit.edu