Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whatsdac@umich.edu wrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu
wrote:
No, it's not nifti, that should work.
Can you send me your log file and the command you issued.
Thanks, Martin
On 07/01/2013 03:13 PM, Jonathan Holt wrote:
Martin,
definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue?
jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
Hi Jon,
are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file.
Best, Martin
On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were created in the brief time this string was running
recon-all -all -s <tpNid> -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty.
upon further inspection the log file is complaining about my nifty.
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information
On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
can you cc the list so that others can answer?
On Mon, 1 Jul 2013, Jonathan Holt wrote:
I have not and I am not certain how to do so
On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:
Hi Jon
have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote:
Log file indicates manual talairach alignment may be necessary.
ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt whatsdac@umich.edu wrote:
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whatsdac@umich.edu wrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:
No, it's not nifti, that should work.
Can you send me your log file and the command you issued.
Thanks, Martin
On 07/01/2013 03:13 PM, Jonathan Holt wrote:
Martin,
definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue?
jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
Hi Jon,
are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file.
Best, Martin
On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were created in the brief time this string was running
recon-all -all -s <tpNid> -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty.
upon further inspection the log file is complaining about my nifty.
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information
On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
can you cc the list so that others can answer?
On Mon, 1 Jul 2013, Jonathan Holt wrote:
I have not and I am not certain how to do so
On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:
Hi Jon
have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote:
Log file indicates manual talairach alignment may be necessary. > ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm > ***FAILED*** (p=0.0079, > pval=0.0000 < threshold=0.0050) > Manual Talairach alignment may be necessary > Can anyone provide direction. Alternatively, the error indicates > talairach alignment can be skipped > with -notal-check flag. Is this step completely necessary? > jon > >
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
Hi Jonathan,
I changed the subject of the thread, to better reflect this problem, it (so far) has nothing to do with longitudinal processing.
Next time, can you send the log file, it is in /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log not the output on the screen.
But first lets check these:
- your command in the email below seems to be missing "-all"? Probably you passed it?
- and from your screen output it looks like there is a problem importing the nifit:
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume...
So you need to check the orientation of your /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz...
Not sure why your nifti files are incomplete. Can you point -i to the original dicom?
Best, Martin
On 07/02/2013 01:13 PM, Jonathan Holt wrote:
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt <whatsdac@umich.edu mailto:whatsdac@umich.edu> wrote:
Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt <whatsdac@umich.edu <mailto:whatsdac@umich.edu>> wrote: Here ya go. On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: No, it's not nifti, that should work. Can you send me your log file and the command you issued. Thanks, Martin On 07/01/2013 03:13 PM, Jonathan Holt wrote:Martin, definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue? jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:Hi Jon, are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file. Best, Martin On 07/01/2013 02:29 PM, Jonathan Holt wrote:I have tried to inspect the tal xfms that were created in the brief time this string was running recon-all -all -s <tpNid> -i path_to_tpN_dcm while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty. upon further inspection the log file is complaining about my nifty. WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: can you cc the list so that others can answer? On Mon, 1 Jul 2013, Jonathan Holt wrote: I have not and I am not certain how to do so On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote: Hi Jon have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote: Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu <http://reuter.mit.edu/>-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto: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
Thanks Martin,
I have attached recon-all.log. I tried to run the process several times, I clearly forgot to pass -all that time but I know for certain the first time I tried I passed -all and it provided the same issue. I can pass the dicom images but I'll have to wait for my PI to return in lab.
On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
Hi Jonathan,
I changed the subject of the thread, to better reflect this problem, it (so far) has nothing to do with longitudinal processing.
Next time, can you send the log file, it is in /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log not the output on the screen.
But first lets check these:
- your command in the email below seems to be missing "-all"? Probably you
passed it?
- and from your screen output it looks like there is a problem importing
the nifit:
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume...
So you need to check the orientation of your /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz...
Not sure why your nifti files are incomplete. Can you point -i to the original dicom?
Best, Martin
On 07/02/2013 01:13 PM, Jonathan Holt wrote:
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt whatsdac@umich.edu wrote:
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whatsdac@umich.eduwrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:
No, it's not nifti, that should work.
Can you send me your log file and the command you issued.
Thanks, Martin
On 07/01/2013 03:13 PM, Jonathan Holt wrote:
Martin,
definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue?
jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
Hi Jon,
are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file.
Best, Martin
On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were created in the brief time this string was running
recon-all -all -s <tpNid> -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty.
upon further inspection the log file is complaining about my nifty.
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information
On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
can you cc the list so that others can answer?
On Mon, 1 Jul 2013, Jonathan Holt wrote:
I have not and I am not certain how to do so
On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote:
Hi Jon > > have you visually inspected the results of the tal xform? > Bruce > On Mon, 1 Jul 2013, Jonathan Holt wrote: > > Log file indicates manual talairach alignment may be necessary. >> ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm >> ***FAILED*** (p=0.0079, >> pval=0.0000 < threshold=0.0050) >> Manual Talairach alignment may be necessary >> Can anyone provide direction. Alternatively, the error indicates >> talairach alignment can be skipped >> with -notal-check flag. Is this step completely necessary? >> jon >> >> > > 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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
In the meantime you can check how the mri/orig/001.mgz and the mri/orig.mgz and mri/orig_nu.mgz look.
Best, Martin
On 07/02/2013 02:16 PM, Jonathan Holt wrote:
Thanks Martin,
I have attached recon-all.log. I tried to run the process several times, I clearly forgot to pass -all that time but I know for certain the first time I tried I passed -all and it provided the same issue. I can pass the dicom images but I'll have to wait for my PI to return in lab.
On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu mailto:mreuter@nmr.mgh.harvard.edu> wrote:
Hi Jonathan, I changed the subject of the thread, to better reflect this problem, it (so far) has nothing to do with longitudinal processing. Next time, can you send the log file, it is in /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log not the output on the screen. But first lets check these: - your command in the email below seems to be missing "-all"? Probably you passed it? - and from your screen output it looks like there is a problem importing the nifit: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume... So you need to check the orientation of your /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz... Not sure why your nifti files are incomplete. Can you point -i to the original dicom? Best, Martin On 07/02/2013 01:13 PM, Jonathan Holt wrote:and the command nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt <whatsdac@umich.edu <mailto:whatsdac@umich.edu>> wrote: Here ya go (to list) On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt <whatsdac@umich.edu <mailto:whatsdac@umich.edu>> wrote: Here ya go. On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu>> wrote: No, it's not nifti, that should work. Can you send me your log file and the command you issued. Thanks, Martin On 07/01/2013 03:13 PM, Jonathan Holt wrote:Martin, definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue? jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:Hi Jon, are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file. Best, Martin On 07/01/2013 02:29 PM, Jonathan Holt wrote:I have tried to inspect the tal xfms that were created in the brief time this string was running recon-all -all -s <tpNid> -i path_to_tpN_dcm while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty. upon further inspection the log file is complaining about my nifty. WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: can you cc the list so that others can answer? On Mon, 1 Jul 2013, Jonathan Holt wrote: I have not and I am not certain how to do so On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote: Hi Jon have you visually inspected the results of the tal xform? Bruce On Mon, 1 Jul 2013, Jonathan Holt wrote: Log file indicates manual talairach alignment may be necessary. ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0079, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary Can anyone provide direction. Alternatively, the error indicates talairach alignment can be skipped with -notal-check flag. Is this step completely necessary? jon 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 <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu <http://reuter.mit.edu/>-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone:+1-617-724-5652 <tel:%2B1-617-724-5652> Email: mreuter@nmr.mgh.harvard.edu <mailto:mreuter@nmr.mgh.harvard.edu> reuter@mit.edu <mailto:reuter@mit.edu> Web :http://reuter.mit.edu
would it be possible to use volumes generated from recon-all -s <subjID> into the second and third steps of the longitudinal processing workflow?
On Tue, Jul 2, 2013 at 2:24 PM, Martin Reuter mreuter@nmr.mgh.harvard.eduwrote:
In the meantime you can check how the mri/orig/001.mgz and the mri/orig.mgz and mri/orig_nu.mgz look.
Best, Martin
On 07/02/2013 02:16 PM, Jonathan Holt wrote:
Thanks Martin,
I have attached recon-all.log. I tried to run the process several times, I clearly forgot to pass -all that time but I know for certain the first time I tried I passed -all and it provided the same issue. I can pass the dicom images but I'll have to wait for my PI to return in lab.
On Tue, Jul 2, 2013 at 2:05 PM, Martin Reuter <mreuter@nmr.mgh.harvard.edu
wrote:
Hi Jonathan,
I changed the subject of the thread, to better reflect this problem, it (so far) has nothing to do with longitudinal processing.
Next time, can you send the log file, it is in /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/scripts/recon-all.log not the output on the screen.
But first lets check these:
- your command in the email below seems to be missing "-all"? Probably
you passed it?
- and from your screen output it looks like there is a problem importing
the nifit:
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information in the input to assign orientation to the volume...
So you need to check the orientation of your /net/data4/ALSSCI/FreeSurfer201211/FreeSurfer/tpNdt/mri/orig/001.mgz...
Not sure why your nifti files are incomplete. Can you point -i to the original dicom?
Best, Martin
On 07/02/2013 01:13 PM, Jonathan Holt wrote:
and the command
nohup recon-all -s 100922dt_01 -i 100922dt_nifti_revised.nii
On Tue, Jul 2, 2013 at 12:40 PM, Jonathan Holt whatsdac@umich.eduwrote:
Here ya go (to list)
On Tue, Jul 2, 2013 at 12:38 PM, Jonathan Holt whatsdac@umich.eduwrote:
Here ya go.
On Mon, Jul 1, 2013 at 3:31 PM, Martin Reuter < mreuter@nmr.mgh.harvard.edu> wrote:
No, it's not nifti, that should work.
Can you send me your log file and the command you issued.
Thanks, Martin
On 07/01/2013 03:13 PM, Jonathan Holt wrote:
Martin,
definitely passing my images and naming time points appropriately. I have been passing nifti as opposed to dicom and it's entirely possible that may be the issue?
jon On Jul 1, 2013, at 2:32 PM, Martin Reuter wrote:
Hi Jon,
are you passing your images? <tpNid> is a placeholder for the id of your subject+time point, for example it could be jon_01 the "path_to_tpN_dcm" needs to specify the path to the dicom files, point it to the first file in the MPRAGE series (or multi echo mprage or what you are using). This is the full path on your file system to that file.
Best, Martin
On 07/01/2013 02:29 PM, Jonathan Holt wrote:
I have tried to inspect the tal xfms that were created in the brief time this string was running
recon-all -all -s <tpNid> -i path_to_tpN_dcm
while viewing orig.mgz in tkmedit. they were talairach.xfm and talairach.auto.xfm, both were empty and the tkmedit window was empty.
upon further inspection the log file is complaining about my nifty.
WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /net/data4/ALSSCI/FreeSurfer201211/Subjects/DT/100922dt/anatomy/ht1spgr.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 WARNING: it does not appear that there was sufficient information
On Mon, Jul 1, 2013 at 1:46 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote:
can you cc the list so that others can answer?
On Mon, 1 Jul 2013, Jonathan Holt wrote:
I have not and I am not certain how to do so > > > > On Jul 1, 2013, at 1:03 PM, Bruce Fischl wrote: > > Hi Jon >> >> have you visually inspected the results of the tal xform? >> Bruce >> On Mon, 1 Jul 2013, Jonathan Holt wrote: >> >> Log file indicates manual talairach alignment may be necessary. >>> ERROR: talairach_afd: Talairach Transform: >>> transforms/talairach.xfm ***FAILED*** (p=0.0079, >>> pval=0.0000 < threshold=0.0050) >>> Manual Talairach alignment may be necessary >>> Can anyone provide direction. Alternatively, the error indicates >>> talairach alignment can be skipped >>> with -notal-check flag. Is this step completely necessary? >>> jon >>> >>> >> >> 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. >> > > > > >
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-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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 listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
-- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT
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
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