ERROR "Could not determine file type" during mri_vol2surf AND opening a talairach.xfm in tkmedit
Hi all,
Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error:
mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii
Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file):
mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm
Has anyone seen such an error before and/or know how to fix it?
Please let me know! Thank you!!!
-Elise
***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona@mail.nih.gov
Hi Elise,
can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without the special character # and rerun mri_vol2surf. And regarding your second question, what was your command line. Were you trying to apply the transform talairach.xfm to a volume opened in tkmedit.
Sita.
On Thu, 10 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote:
Hi all,
Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error:
mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii
Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file):
mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm
Has anyone seen such an error before and/or know how to fix it?
Please let me know! Thank you!!!
-Elise
Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366
Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona@mail.nih.gov
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sita,
Thank you for your reply!!
I was wondering if that # character in the movable file name could be creating any problems; I will definitely try it without and keep you updated!
As for the second issue, I was trying to view Subject D10's talairach transformed brain in tkmedit. I followed the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to do so. My command line to open tkmedit was as follows:
tkmedit D10 brainmask.mgz
When the tkmedit GUI opened with the brainmask.mgz as the main volume, I went to File-->Transforms-->Load as Main volume and clicked OK
At this point, a dialog box popped up with the error "couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm" and the transform did not open.
***HOWEVER the really strange thing is that I had done the exact same order of operations about five minutes earlier to open and view the same subject's talairach transformed volume and everything worked perfectly. I then closed tkmedit and when I tried it again five minutes later the above occurred.***
I know that temporal proximity and similar error messages do not necessarily mean that the two problems are related, but since they are both happening in the same subject's data, it got me wondering.
Please let me know if you have any insights! Thanks so much again!
-Elise
________________________________________ From: Sita Kakunoori [sita@nmr.mgh.harvard.edu] Sent: Thursday, June 10, 2010 5:14 PM To: Dickinson, Annelise (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR "Could not determine file type" during mri_vol2surf AND opening a talairach.xfm in tkmedit
Hi Elise,
can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without the special character # and rerun mri_vol2surf. And regarding your second question, what was your command line. Were you trying to apply the transform talairach.xfm to a volume opened in tkmedit.
Sita.
On Thu, 10 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote:
Hi all,
Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error:
mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii
Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file):
mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm
Has anyone seen such an error before and/or know how to fix it?
Please let me know! Thank you!!!
-Elise
Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366
Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona@mail.nih.gov
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.
Quick update: Removing the # character from the filename cleared up Problem Number 1. Duh!
On 6/11/10 8:39 AM, "Annelise Dickinson" dickinsona@mail.nih.gov wrote:
Hi Sita,
Thank you for your reply!!
I was wondering if that # character in the movable file name could be creating any problems; I will definitely try it without and keep you updated!
As for the second issue, I was trying to view Subject D10's talairach transformed brain in tkmedit. I followed the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to do so. My command line to open tkmedit was as follows:
tkmedit D10 brainmask.mgz
When the tkmedit GUI opened with the brainmask.mgz as the main volume, I went to File-->Transforms-->Load as Main volume and clicked OK
At this point, a dialog box popped up with the error "couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm" and the transform did not open.
***HOWEVER the really strange thing is that I had done the exact same order of operations about five minutes earlier to open and view the same subject's talairach transformed volume and everything worked perfectly. I then closed tkmedit and when I tried it again five minutes later the above occurred.***
I know that temporal proximity and similar error messages do not necessarily mean that the two problems are related, but since they are both happening in the same subject's data, it got me wondering.
Please let me know if you have any insights! Thanks so much again!
-Elise
________________________________________ From: Sita Kakunoori [sita@nmr.mgh.harvard.edu] Sent: Thursday, June 10, 2010 5:14 PM To: Dickinson, Annelise (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR "Could not determine file type" during mri_vol2surf AND opening a talairach.xfm in tkmedit
Hi Elise,
can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without the special character # and rerun mri_vol2surf. And regarding your second question, what was your command line. Were you trying to apply the transform talairach.xfm to a volume opened in tkmedit.
Sita.
On Thu, 10 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote:
Hi all,
Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error:
mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii
Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file):
mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm
Has anyone seen such an error before and/or know how to fix it?
Please let me know! Thank you!!!
-Elise
Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366
Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona@mail.nih.gov
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
***************************************************** Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366 ***************************************************** Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona@mail.nih.gov
Hi Elise,
After loading brainmask.mgz in tkmedit, apply the transform as 'File -> Transforms -> Load Transform for Main Volume' and select talairach.xfm.
Sita.
On Fri, 11 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote:
Hi Sita,
Thank you for your reply!!
I was wondering if that # character in the movable file name could be creating any problems; I will definitely try it without and keep you updated!
As for the second issue, I was trying to view Subject D10's talairach transformed brain in tkmedit. I followed the instructions on http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach to do so. My command line to open tkmedit was as follows:
tkmedit D10 brainmask.mgz
When the tkmedit GUI opened with the brainmask.mgz as the main volume, I went to File-->Transforms-->Load as Main volume and clicked OK
At this point, a dialog box popped up with the error "couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm" and the transform did not open.
***HOWEVER the really strange thing is that I had done the exact same order of operations about five minutes earlier to open and view the same subject's talairach transformed volume and everything worked perfectly. I then closed tkmedit and when I tried it again five minutes later the above occurred.***
I know that temporal proximity and similar error messages do not necessarily mean that the two problems are related, but since they are both happening in the same subject's data, it got me wondering.
Please let me know if you have any insights! Thanks so much again!
-Elise
From: Sita Kakunoori [sita@nmr.mgh.harvard.edu] Sent: Thursday, June 10, 2010 5:14 PM To: Dickinson, Annelise (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ERROR "Could not determine file type" during mri_vol2surf AND opening a talairach.xfm in tkmedit
Hi Elise,
can you try renaming the file Wedges6_r1_D10_0_pi3_1#0_Coef.nii without the special character # and rerun mri_vol2surf. And regarding your second question, what was your command line. Were you trying to apply the transform talairach.xfm to a volume opened in tkmedit.
Sita.
On Thu, 10 Jun 2010, Dickinson, Annelise (NIH/NIMH) [F] wrote:
Hi all,
Hopefully this is not too stupid of a question. Something seems to have happened to one of our subjects' surface data, such that when I try to resample the volume Wedges6_r1_D10_0_pi3_1#0_Coef.nii onto subject D10's surface, I get the following error:
mri_vol2surf --mov Wedges6_r1_D10_0_pi3_1#0_Coef.nii --noreshape --reg register.Wedges6_raw_D10.dat --projfrac 0.5 --interp nearest --hemi rh --o Wedges6_r1_D10_0_pi3_1#0_Coef.mgh ERROR: could not determine type of Wedges6_r1_D10_0_pi3_1#0_Coef.nii
Not sure if it is related, but I recently tried opening the same subject's talairach.xfm brain in tkmedit and got a similar error (from the error.log file):
mri_read(): couldn't determine type of file /nfs/data17/hansenka/ntopy/surf/D/D10/mri/transforms/talairach.xfm
Has anyone seen such an error before and/or know how to fix it?
Please let me know! Thank you!!!
-Elise
Annelise Dickinson Post-Bac IRTA Laboratory of Brain and Cognition, NIMH/NIH/DHHS Building 10, Room 4C212 10 CENTER DR MSC 1366 BETHESDA MD 20892-1366
Phone: (301) 435-4941 FAX: (301) 402-0921 E-Mail : dickinsona@mail.nih.gov
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@nmr.mgh.harvard.edu
-
Dickinson, Annelise (NIH/NIMH) [F] -
Sita Kakunoori