Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds?
Thanks in advance, Marcel
Hi Marcel, vlrmerge should handle multiple frames. what is your command line? Can you send the log file? doug
On 6/14/13 10:32 AM, Marcel Falkiewicz wrote:
Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds?
Thanks in advance, Marcel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello Doug, my command line is:
vlrmerge --o f_vol.nii.gz --v fmcpr.sm8.mni305.2mm.nii.gz --lh fmcpr.sm8.fsaverage.lh.nii.gz --rh fmcpr.sm8.fsaverage.rh.nii.gz --subcortmask masks/brain.mni305.2mm.nii.gz
I think it does work with multiple frames correctly, but has summing over the frames hardcoded :
Allocing output Done allocing nframes = 1702 Computing sum across frames Writing to f_vol.nii.gz sob, 15 cze 2013, 21:04:20 CEST vlrmerge done
Full log is attached.
Marcel
2013/6/15 Douglas Greve greve@nmr.mgh.harvard.edu
Hi Marcel, vlrmerge should handle multiple frames. what is your command line? Can you send the log file? doug
On 6/14/13 10:32 AM, Marcel Falkiewicz wrote:
Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds?
Thanks in advance, Marcel
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Oh, I see what the problem is. You can try replacing this line in the script:
set cmd = (mri_concat --sum $surfvol $involmasked --o $outvol)
with
set cmd = (fscalc $surfvol add $involmasked -o $outvol)
let me know if that works
doug
On 6/15/13 12:17 PM, Marcel Falkiewicz wrote:
Hello Doug, my command line is:
vlrmerge --o f_vol.nii.gz --v fmcpr.sm8.mni305.2mm.nii.gz --lh fmcpr.sm8.fsaverage.lh.nii.gz --rh fmcpr.sm8.fsaverage.rh.nii.gz --subcortmask masks/brain.mni305.2mm.nii.gz
I think it does work with multiple frames correctly, but has summing over the frames hardcoded :
Allocing output Done allocing nframes = 1702 Computing sum across frames Writing to f_vol.nii.gz sob, 15 cze 2013, 21:04:20 CEST vlrmerge done
Full log is attached.
Marcel
2013/6/15 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>
Hi Marcel, vlrmerge should handle multiple frames. what is your command line? Can you send the log file? doug On 6/14/13 10:32 AM, Marcel Falkiewicz wrote:Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds? Thanks in advance, Marcel _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.
Hello Doug, it worked perfectly, thanks !
Marcel
2013/6/16 Douglas Greve greve@nmr.mgh.harvard.edu
Oh, I see what the problem is. You can try replacing this line in the script:
set cmd = (mri_concat --sum $surfvol $involmasked --o $outvol)
with
set cmd = (fscalc $surfvol add $involmasked -o $outvol)
let me know if that works
doug
On 6/15/13 12:17 PM, Marcel Falkiewicz wrote:
Hello Doug, my command line is:
vlrmerge --o f_vol.nii.gz --v fmcpr.sm8.mni305.2mm.nii.gz --lh fmcpr.sm8.fsaverage.lh.nii.gz --rh fmcpr.sm8.fsaverage.rh.nii.gz --subcortmask masks/brain.mni305.2mm.nii.gz
I think it does work with multiple frames correctly, but has summing over the frames hardcoded :
Allocing output Done allocing nframes = 1702 Computing sum across frames Writing to f_vol.nii.gz sob, 15 cze 2013, 21:04:20 CEST vlrmerge done
Full log is attached.
Marcel
2013/6/15 Douglas Greve greve@nmr.mgh.harvard.edu
Hi Marcel, vlrmerge should handle multiple frames. what is your command line? Can you send the log file? doug
On 6/14/13 10:32 AM, Marcel Falkiewicz wrote:
Hello, I would like to perform some Bayesian analyses implemented in SPM, but with the data normalized with FreeSurfer. I would like to merge together surface and subcortal normalized timeseries into a single 4d timeseries in volumetric space, which could be used as an input to spm. I tried using vlrmerge, but it produces only a single volume. One method would be splitting the timeseries for each space into single volumes, using vlrmerge on each triplet and then merging the results. However, this would take enourmous ammout of time. Do you know any quicker workarounds?
Thanks in advance, Marcel
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects. I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your attention,Pablo Error:--------------------------------------------------------------------------------------------------------------------------------------------------#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013/Users/pablonajt/subjects/tr5713/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)Manual Talairach alignment may be necessary, orinclude the -notal-check flag to skip this test,making sure the -notal-check flag follows -allor -autorecon1 in the command string.See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TalairachDarwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8. I would greatly appreciate if you could advise me which step/s should I take to correct this.Thank you for your attention,Pablo Error:--------------------------------------------------------------------------------------------------------------------------------------------------#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013/Users/pablonajt/subjects/tr5713/mri\n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \nERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)Manual Talairach alignment may be necessary, orinclude the -notal-check flag to skip this test,making sure the -notal-check flag follows -allor -autorecon1 in the command string.See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TalairachDarwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:--------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct? Best,Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:--------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
_______________________________________________ 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.
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:-------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
_______________________________________________ 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.
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:-------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
_______________________________________________ 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 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.
Hi again,I still have a doubt about how to proceed with the processing of my images. Correcting my original response to the format of my images: I ran recon -all -all with NIFTI images (but converted from analyze format). I have converted this by opening them with MRIron and saving as NIFTI.gz (compressed). Should this still produce a talairach failure? If yes, is there any way to convert my analyze images to a compatible format to FS? Sorry that I am going back to the original question, but I just found out from the technicians and our department automatically receives all scans in analyze format. Thank you for your support,Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 +0000 Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:-------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
_______________________________________________ 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 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 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.
Hi Pablo
once you go through analyze format the direction cosines are lost. Can you get the data before they were converted to analyze? If not, how will you ever tell left from right?
Bruce On Tue, 27 Aug 2013, pablo najt wrote:
Hi again,I still have a doubt about how to proceed with the processing of my images. Correcting my original response to the format of my images: I ran recon -all -all with NIFTI images (but converted from analyze format). I have converted this by opening them with MRIron and saving as NIFTI.gz (compressed). Should this still produce a talairach failure? If yes, is there any way to convert my analyze images to a compatible format to FS? Sorry that I am going back to the original question, but I just found out from the technicians and our department automatically receives all scans
in
analyze format. Thank you for your support, Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 +0000 Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks, Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format a
nd also I have visually inspected the images. Almost all my
scans consistently show an extended whole in the prefrontal area (with a f
ew exception of some scans showing this in posterior
locations). I am assuming the best is to start with either DICOM or NIFTI and avoid an
alyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching r
econ -all for one of my subjects (see below). I am using a
macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I
take to correct this.
Thank you for your attention, Pablo
Error:------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***F
AILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)
Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0
: Tue Jun 7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
_______________________________________________ Freesurfer mailing list Fr
eesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati
on 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 . I
f 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 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 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.
Dear FS,Following on my question about the initial format of my files for running recon -all, I finally managed to get the Dicom files for our images. However, as the imaging protocol includes several modalities, (resting state, functional, T1, DTI), we had to sort the dicom files. For my structural data, on which I intend to run FS. Now I get 163 files which I assume are the number of slices. They look like this:MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007879 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007961MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007880 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007962MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007881 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007963MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007882 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007964MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007883 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007965MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007884 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007966MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007885 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007967MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007886 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007968MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007887 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007969MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007888 MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007970 My question is, for running "recon-all -i john_time1.nii.gz -s john_time1" which file should I use in the place of "nii.gz" file? Can I use any of the MR.1.3.12.2 .... (listed above)? Many thanks,PabloFrom: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 +0000 Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks,Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:-------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
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_______________________________________________ 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 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.
Hi Pablo, each one of those files is a slice. Just pick one of them and recon-all will find all the slices that also belong with that series doug
On 08/30/2013 11:23 AM, pablo najt wrote:
Dear FS, Following on my question about the initial format of my files for running recon -all, I finally managed to get the Dicom files for our images. However, as the imaging protocol includes several modalities, (resting state, functional, T1, DTI), we had to sort the dicom files. For my structural data, on which I intend to run FS. Now I get 163 files which I assume are the number of slices. They look like this:
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007879MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007961
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007880MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007962
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007881MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007963
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007882MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007964
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007883MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007965
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007884MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007966
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007885MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007967
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007886MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007968
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007887MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007969
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007888MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007970
My question is, for running "recon-all -i john_time1.nii.gz -s john_time1" which file should I use in the place of "nii.gz" file? Can I use any of the MR.1.3.12.2 .... (listed above)? Many thanks, Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 +0000 Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI? Thanks, Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format and also I have visually inspected the images. Almost all my scans consistently show an extended whole in the prefrontal area (with a few exception of some scans showing this in posterior locations). I am assuming the best is to start with either DICOM or NIFTI and avoid analyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching recon -all for one of my subjects (see below). I am using a macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I take to correct this. Thank you for your attention, Pablo
Error:-------------------------------------------------------------------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0554, pval=0.0034 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. Seehttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
_______________________________________________ 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 athttp://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 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Pablo
yes, any single file that is in the correct series should be fine Bruce On Fri, 30 Aug 2013, pablo najt wrote:
Dear FS, Following on my question about the initial format of my files for running recon -all, I finally managed to get the Dicom files for our images. However, as the imaging protocol includes several modalities, (resting state, functional, T1, DTI), we had to sort the dicom files. For my structural data, on which I intend to run FS. Now I get 163 files which I assume are the number of slices. They look like this:
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007879 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007961
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007880 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007962
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007881 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007963
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007882 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007964
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007883 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007965
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007884 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007966
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007885 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007967
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007886 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007968
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007887 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007969
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007888 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007970
My question is, for running "recon-all -i john_time1.nii.gz -s john_time1" which file should I use in the place of "nii.gz" file? Can I use any of the MR.1.3.12.2 .... (listed above)? Many thanks, Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 +0000 Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks, Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format a
nd also I have visually inspected the images. Almost all my
scans consistently show an extended whole in the prefrontal area (with a f
ew exception of some scans showing this in posterior
locations). I am assuming the best is to start with either DICOM or NIFTI and avoid an
alyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching r
econ -all for one of my subjects (see below). I am using a
macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I
take to correct this.
Thank you for your attention, Pablo
Error:------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***F
AILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)
Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0
: Tue Jun 7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
_______________________________________________ Freesurfer mailing list Fr
eesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati
on 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 . I
f 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 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 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.
Thanks a lot!,Pablo
Date: Fri, 30 Aug 2013 11:38:26 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
yes, any single file that is in the correct series should be fine Bruce On Fri, 30 Aug 2013, pablo najt wrote:
Dear FS, Following on my question about the initial format of my files for running recon -all, I finally managed to get the Dicom files for our images. However, as the imaging protocol includes several modalities, (resting state, functional, T1, DTI), we had to sort the dicom files. For my structural data, on which I intend to run FS. Now I get 163 files which I assume are the number of slices. They look like this:
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007879 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007961
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007880 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007962
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007881 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007963
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007882 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007964
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007883 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007965
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007884 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007966
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007885 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007967
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007886 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007968
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007887 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007969
MR.1.3.12.2.1107.5.2.13.20520.30000006050913395956200007888 MR.1.3.12.2.11 07.5.2.13.20520.30000006050913395956200007970
My question is, for running "recon-all -i john_time1.nii.gz -s john_time1" which file should I use in the place of "nii.gz" file? Can I use any of the MR.1.3.12.2 .... (listed above)? Many thanks, Pablo
From: pablonajt@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Tue, 27 Aug 2013 17:14:04 +0000 Subject: Re: [Freesurfer] Talairach Failure Detection
Hi I have one last question. I just noticed that my images are in Philips format. Would you recommend to convert to DICOM anyway? Or should I used NIFTI?Thanks, Pablo
Date: Tue, 27 Aug 2013 12:31:09 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
yes, definitely. The dicoms are best On Tue, 27 Aug 2013, pablo najt wrote:
Thank you very much for your input. Yes, I did start with analyze format a
nd also I have visually inspected the images. Almost all my
scans consistently show an extended whole in the prefrontal area (with a f
ew exception of some scans showing this in posterior
locations). I am assuming the best is to start with either DICOM or NIFTI and avoid an
alyze format. Is this correct?
Best, Pablo
Date: Tue, 27 Aug 2013 12:08:22 -0400 From: fischl@nmr.mgh.harvard.edu To: pablonajt@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach Failure Detection
Hi Pablo
have you visually inspected the talairach xform to see if it is indeed incorrect? What input format did you start with? Most of these occur because people start with analyze, which doesn't have the direction cosines, and so the data is oriented incorrectly
cheers Bruce
On Tue, 27 Aug 2013, pablo najt wrote:
Dear FS experts,I am contacting you to report an error after launching r
econ -all for one of my subjects (see below). I am using a
macbook pro with snow leopard version 10.6.8.
I would greatly appreciate if you could advise me which step/s should I
take to correct this.
Thank you for your attention, Pablo
Error:------------------------------------------------------------------
#@# Talairach Failure Detection Mon Aug 19 23:01:43 EDT 2013 /Users/pablonajt/subjects/tr5713/mri \n talairach_afd -T 0.005 -xfm transforms/talairach.xfm \n ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***F
AILED*** (p=0.0554, pval=0.0034 < threshold=0.0050)
Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Darwin Pablo-Najts-MacBook-Pro.local 10.8.0 Darwin Kernel Version 10.8.0
: Tue Jun 7 16:33:36 PDT 2011;
root:xnu-1504.15.3~1/RELEASE_I386 i386
recon-all -s tr5713 exited with ERRORS at Mon Aug 19 23:01:43 EDT 2013
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Dear FS experts,I have a doubt about a potential registration problem after running recon-all -all. I noticed that one of the image outcome when opened with tkmedit shows no-brain tissue (perhaps eye tracts) ventral to orbitofrontal areas. I have attached snapshots to illustrate the image.I would greatly appreciate your output on this since I have no experience with FS and I am not sure what to expect. I would like to enquire whether I should be concerned about this image or if this is not a problem. Many thanks,Pablo
Hi Pablo, this is a skull stripped image. In the human brain there is no brain tissue ventral to the orbital frontal areaso any tissue there has been stripped away. doug
On 09/02/2013 12:49 AM, pablo najt wrote:
Dear FS experts, I have a doubt about a potential registration problem after running recon-all -all. I noticed that one of the image outcome when opened with tkmedit shows no-brain tissue (perhaps eye tracts) ventral to orbitofrontal areas. I have attached snapshots to illustrate the image. I would greatly appreciate your output on this since I have no experience with FS and I am not sure what to expect. I would like to enquire whether I should be concerned about this image or if this is not a problem.
Many thanks, Pablo
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pablo najt