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
[cid:rcsi-logob489c8]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.iemailto:erikohanlon@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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 mailto:erikohanlon@rcsi.ie *W: *www.rcsi.ie http://www.rcsi.ie
*RCSI* DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
[cid:part1.06080901.05020203@nmr.mgh.harvard.edu]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.iemailto:erikohanlon@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
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 mailto:erikohanlon@rcsi.ie *W: *www.rcsi.ie http://www.rcsi.ie
*RCSI* DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreuter@nmr.mgh.harvard.edumailto: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
[cid:part1.06060905.09000000@nmr.mgh.harvard.edu]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.iemailto:erikohanlon@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreuter@nmr.mgh.harvard.edumailto: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
[cid:part1.06060905.09000000@nmr.mgh.harvard.edu]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.iemailto:erikohanlon@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
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.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreuter@nmr.mgh.harvard.edumailto: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
[cid:part1.06060905.09000000@nmr.mgh.harvard.edu]
RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohanlon@rcsi.iemailto:erikohanlon@rcsi.ie W: www.rcsi.iehttp://www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS WHO MAKE A DIFFERENCE WORLDWIDE
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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.edumailto:mreuter@nmr.mgh.harvard.edu reuter@mit.edumailto:reuter@mit.edu Web : http://reuter.mit.edu
Hi Erik, did you experience the same problem with any other cases? Also, do you think you could send us the log file [subjectdir]/scripts/hippo-subfields.log, as well as the contents of [subjectdir]/tmp/subrieldResults? Cheers, /Eugenio
Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message ----- From: "Erik O'Hanlon" erikohanlon@rcsi.ie To: "Freesurfer support list" freesurfer@nmr.mgh.harvard.edu Sent: Thursday, November 20, 2014 2:04:15 PM 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu