[Freesurfer] can I apply freesurfer significant clusters as ROI in fMRI study?
Dear freesurfer experts, I searched on the wiki but can not figure out how to solve this problem: I found some significant clusters on graymatter thickness, how can I use it as a ROI in my functional MRI study? I have both structure and function data of the same subjects, so I can either do it in stardard space or native space one by one if possible. Any help is appriciated~ Best 2014-11-20 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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::ImageFileWriterTInputImage::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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@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-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edumailto:mreu...@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:part1.06060905.0900@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.iemailto:erikohan...@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: mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edumailto:reu...@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
Re: [Freesurfer] can I apply freesurfer significant clusters as ROI in fMRI study?
Hi Chunhui if you have the significant clusters as overlays in fsaverage you can load them in tksurfer and use the custom fill button to create ROIs from connected compontents that are above threshold, then go from there (e.g. mri_label2label to map them to individual subjects, etc...) cheers Bruce On Thu, 20 Nov 2014, chenchunhuichina wrote: Dear freesurfer experts, I searched on the wiki but can not figure out how to solve this problem: I found some significant clusters on graymatter thickness, how can I use it as a ROI in my functional MRI study? I have both structure and function data of the same subjects, so I can either do it in stardard space or native space one by one if possible. Any help is appriciated~ Best 2014-11-20 Chunhui Chen _ State Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China 100875 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@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::ImageFileWriterTInputImage::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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@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-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@nmr.mgh.harvard.edumailto:mreu...@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:part1.06060905.0900@nmr.mgh.harvard.edu] RCSI Psychiatry Royal College of Surgeons in Ireland Beaumont Road, Beaumont, D9, Ireland T: 8093740 E: erikohan...@rcsi.iemailto:erikohan...@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
Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
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 erikohan...@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::ImageFileWriterTInputImage::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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@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-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu ] on behalf of Martin Reuter [ mreu...@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: erikohan...@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 -- 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: mreu...@nmr.mgh.harvard.edu
Re: [Freesurfer] Longitudinal analysis and hippocampal subfields
Hi Eugenio, Should I send the files via dropbox, as it appears that the last one I sent is waiting approval due to size etc. Thanks and sorry for the hassle Erik From: Erik O'Hanlon Sent: 20 November 2014 15:51 To: Freesurfer support list Subject: RE: [Freesurfer] Longitudinal analysis and hippocampal subfields Hi Eugenio, Yes, it seems to have happened on a few cases, I've only started running it with the subfields and the jobs are running on a cluster so many have not run to end yet but al that have, exit with the error. I've attached the hippo_subfields-log you requested. As the other subfieldResults is quite large with subdirs, should I sent you a dropbox link? Thanks for help. Very much appreciated, Best regards Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu] Sent: 20 November 2014 14:47 To: Freesurfer support list Subject: Re: [Freesurfer] Longitudinal analysis and hippocampal subfields 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 erikohan...@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::ImageFileWriterTInputImage::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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Erik O'Hanlon [erikohan...@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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Martin Reuter [mreu...@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-boun...@nmr.mgh.harvard.edu [ freesurfer-boun...@nmr.mgh.harvard.edu ] on behalf of Martin Reuter [ mreu...@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
Re: [Freesurfer] Multiple comparision method
FDR doug On 11/20/2014 01:31 AM, wangzhiwei3233 wrote: Hi freesurfer experts, Is there other methods for multiple comparison correction apart from Monte carlo simulation in Freesurfer? Thanks! zhiwei ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Resample the surface mesh
Dear freesurfer experts, Is there any way to down resample the native surface mesh and register the functional volume data to the down resampled surface in freesurfer? Many thanks, Ting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mri_convert : no output infinite loop
Dear FreeSurfer experts, I get a new message when I use mri_convert command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I get the new message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards Nooshin PhD Candidate Departments of Electrical Computer Engineering University of Miami Email: n.za...@miami.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FreeSurfer GUI tutorial
Hi Piotr, There are several tutorials that describe our standard data processing pipeline. You can start by looking at: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial with Introduction to Freesurfer and Analyzing the Individual Subject. If you have any further questions, please, send them to the freesurfer mailing list. Lilla On Thu, 20 Nov 2014, Piotr Konrad Chlebda wrote: Hello, I have downloaded and installed freesurfer(as VM for Windows), but I can not find any simple gui tutorial for it. I need to extract corpus callosum from DICOM pictures. I thought that freesurfer provide me with simple way to do that, but actually did not.Could you send me any easy step by step guide to perform what I need, please ? Best regards, Piotr ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Repost: estimating lesion size on surface
Hi Tim can you elaborate what the issue is? If you have binary lesion maps inthe volume, can't you just sample those onto the surface and measure surface area directly? I think I am missing something Bruce On Wed, 19 Nov 2014, Timothy Meier wrote: Hello, I just wanted to repost this to see if anyone had any thoughts on an appropriate 'lesion' size for a pothole analysis performed on the surface. We want to compare the average number of small surface lesions (estimated from cortical thickness) across single subjects for a control group relative to our patient group. We have done similar analyses in the volume for white matter, so one thought was to use that same lesion size. However, that requires estimating a surface area from our previously used volume. Any thoughts on how to approach this, or thoughts on an appropriate lesion size to use would be appreciated. Thanks, -Tim -- Message: 3 Date: Thu, 30 Oct 2014 15:03:53 -0500 From: Timothy Meier tme...@mrn.org Subject: [Freesurfer] Converting lesion volume to surface area To: freesurfer@nmr.mgh.harvard.edu Message-ID: CAGXOw+14YO4VBWUAA4YfzE7Gerxo-PG33FPCEmpm8PxpTpW=c...@mail.gmail.com Content-Type: text/plain; charset=utf-8 Hello, Previously we have used a lesion of 128 microliters and have filtered out anything smaller in volume than that for analyses (single subject pothole analysis). Now we want to do something similar on the surface. So we need to approximate the surface area of that 128 microliters when translated to group analysis surface (fsaverage). 128 microliters is 128 data points in 1x1x1 resolution. Let's say those data points only exist in the cortical ribbon volume. Question 1: How many of the 128 data points from cortical ribbon volume get translated into surface space? What is the volume to surface translation ratio? Question 2: Because we want to filter clusters with mri_surfcluster, we are interested in the resulting area of our original 128 lesion. Therefore, how much area is represented by each data point when translated onto the surface? Is this simply AvgVtxArea of the inflated surface multiplied by the number of data points that get translated from volume to surface? And what is the best way to answer these two questions from standard Freesurfer output: e.g. Should we calculate from the (NumVert SurfArea GrayVol) columns of the lh.aparc.stats file, get the mean of all SurfArea/GrayVol from aparc.stats, and then multiple by our 128? Any thoughts or suggestions would be appreciated. Thanks, Tim -- next part -- An HTML attachment was scrubbed... URL:http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141030/f e25ad38/attachment-0001.html -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Odd thing about mris_convert? Position changed from freesurfer format to .stl
Hi there, In my understanding, mris_convert does not change any information (vertices coordinates and triangles) during converting, right? However, I observed odd thing as bellow, Command I used:* mris_convert subjid/surf/lh.white subjid/surf/lh.white.stl* I convert the white surface to .stl format, then load original white surface and .stl file in freeview, with subjid/mri/brainmask.mgz as volume underlay. The shape of lh.white.stl mesh looks the same as original one, but the position of lh.white.stl was displaced. I attached a screenshot (yellow one is original white surface, red one is .stl format one). I also used freesurfer_read_surf function to read the coordinates and the faces in matlab, then compare it to .stl coordinate, they are the same. I need to use .stl format for my analysis outside freesurfer, then convert result back to freesurfer format. I am worried whether this would cause any problems? PS, if it is fsaverage template surface, no position shift after format transform. Many thanks if anyone help with this, Ting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
