Hi XJ,
I'm just starting to look at your log files. Just curious, did you decide to not do eddy current correction and b0 inhomogenity correction or accidentally left it out?
When I look at the configuration file, you've given all the parameters for b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the same is the case for eddy current correction too (set doeddy = 0). Just wanted to make sure you did not set that '0' accidentally. Eddy current correction is definitely one of the recommended preprocessing steps, so you might want to consider doing that.
Also looks like your original input dwi file (with NaNs) may be the root cause of the problem. If you do have the original dicoms, you can give that as an input. I'm not sure if you can give a series of 3D Nifti DWI files as an input in the configurations file...Anastasia (cc'd) might be able to answer that question.
Hope that helps, Priti
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] TRACULA dpath problem From: "XJ Kang" xkang@ucdavis.edu Date: Fri, June 15, 2012 2:22 pm To: "Priti Srinivasan" rspriti@nmr.mgh.harvard.edu
Hi Priti,
Attached are the tracula conf file and log files from two subjects.
I ran the two subjects. The results are almost the same. Here are what I found so far:
- There are NaN values in the 4D image. I created it from 3D images
using "fslmerge -a", and the 3G images have no NaNs. 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably this is the origin of all the problems?
Do you want me to send the email to you or to the mailing list? Probably many people are not interested in my email if I post on the whole list.
Thank you.
XJ
On 6/15/2012 11:02 AM, Priti Srinivasan wrote:
Can you send us your configuration file (mytracula.conf) and log file (it should be under scripts/trac-all.log). I can take a look.
Priti
Hi,
I am trying to run the last step of TRACULA. I used the command line:
% trac-all -path -c mytracula.conf
Here is all the info I got on the screen:
INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio INFO: Diffusion root is /home/xkang/DTI/ Actual FREESURFER_HOME /home/local/freesurfer-v510 trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log /home/xkang/DTI//S0006/scripts/trac-all.log -cmd /home/xkang/DTI//S0006/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 #------------------------------------- trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012
I didn't see "dpath" under the subject's directory. Seems nothing has been done. I already ran the "trac-all -prep" and "trac-all -bedp". I have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can any body help where the problems are?
I use DTI images in NIFTI format and the resolution is 2x2x2, which is not the same as that of the FreeSurfer orig.mgz. Probably this is fine.
Thanks.
XJ Kang _______________________________________________ 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
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contains patient information, please contact the Partners Compliance
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Hi Priti,
The 3D data are the averages of two or more sets of DWI data. All the DWIs were already perform the field map correction by "epidewarp.fsl", and they were also coregistered to T1 images in spm. So probably I don't need these two step. I may add the b0 inhomogenity correction.
For the NaNs in the merged 4D image, I found that I can use "fslmaths -nan" to remove them. I will try to run trac-all after that.
Thank you for your help.
XJ
On 6/15/2012 12:15 PM, Priti Srinivasan wrote:
Hi XJ,
I'm just starting to look at your log files. Just curious, did you decide to not do eddy current correction and b0 inhomogenity correction or accidentally left it out?
When I look at the configuration file, you've given all the parameters for b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the same is the case for eddy current correction too (set doeddy = 0). Just wanted to make sure you did not set that '0' accidentally. Eddy current correction is definitely one of the recommended preprocessing steps, so you might want to consider doing that.
Also looks like your original input dwi file (with NaNs) may be the root cause of the problem. If you do have the original dicoms, you can give that as an input. I'm not sure if you can give a series of 3D Nifti DWI files as an input in the configurations file...Anastasia (cc'd) might be able to answer that question.
Hope that helps, Priti
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] TRACULA dpath problem From: "XJ Kang"xkang@ucdavis.edu Date: Fri, June 15, 2012 2:22 pm To: "Priti Srinivasan"rspriti@nmr.mgh.harvard.edu
Hi Priti,
Attached are the tracula conf file and log files from two subjects.
I ran the two subjects. The results are almost the same. Here are what I found so far:
- There are NaN values in the 4D image. I created it from 3D images
using "fslmerge -a", and the 3G images have no NaNs. 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably this is the origin of all the problems?
Do you want me to send the email to you or to the mailing list? Probably many people are not interested in my email if I post on the whole list.
Thank you.
XJ
On 6/15/2012 11:02 AM, Priti Srinivasan wrote:
Can you send us your configuration file (mytracula.conf) and log file (it should be under scripts/trac-all.log). I can take a look.
Priti
Hi,
I am trying to run the last step of TRACULA. I used the command line:
% trac-all -path -c mytracula.conf
Here is all the info I got on the screen:
INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio INFO: Diffusion root is /home/xkang/DTI/ Actual FREESURFER_HOME /home/local/freesurfer-v510 trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log /home/xkang/DTI//S0006/scripts/trac-all.log -cmd /home/xkang/DTI//S0006/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 #------------------------------------- trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012
I didn't see "dpath" under the subject's directory. Seems nothing has been done. I already ran the "trac-all -prep" and "trac-all -bedp". I have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can any body help where the problems are?
I use DTI images in NIFTI format and the resolution is 2x2x2, which is not the same as that of the FreeSurfer orig.mgz. Probably this is fine.
Thanks.
XJ Kang _______________________________________________ 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
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 Priti,
I removed the NaNs in the 4D images and re-ran trac-all -prep. The warning message is gone (of course) but the error message of dlable/diff/White-Matter++.flt.nii.gz is still there since no "White-Matter++.flt.nii.gz" in the diff directory. Only one image in dlabel/diff/: lowb_brain_mask.nii.gz.
fslstats -t /home/xkang/DTI//S0001/dmri/dwi.nii.gz -k /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}' > /home/xkang/DTI//S0001/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt' ** ERROR: nifti_image_open(/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt): bad header info ERROR: failed to open file /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt ERROR: Could not open image /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt Image Exception : #22 :: Failed to read volume /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz
I am not sure if the error will affect the next steps of -bedp and -path. I want to make sure before run -bedp since that will take several hours.
Also there is no dpath directory yet. Probably it will be created during the -path processing?
Thanks.
XJ
On 6/15/2012 12:15 PM, Priti Srinivasan wrote:
Hi XJ,
I'm just starting to look at your log files. Just curious, did you decide to not do eddy current correction and b0 inhomogenity correction or accidentally left it out?
When I look at the configuration file, you've given all the parameters for b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the same is the case for eddy current correction too (set doeddy = 0). Just wanted to make sure you did not set that '0' accidentally. Eddy current correction is definitely one of the recommended preprocessing steps, so you might want to consider doing that.
Also looks like your original input dwi file (with NaNs) may be the root cause of the problem. If you do have the original dicoms, you can give that as an input. I'm not sure if you can give a series of 3D Nifti DWI files as an input in the configurations file...Anastasia (cc'd) might be able to answer that question.
Hope that helps, Priti
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] TRACULA dpath problem From: "XJ Kang"xkang@ucdavis.edu Date: Fri, June 15, 2012 2:22 pm To: "Priti Srinivasan"rspriti@nmr.mgh.harvard.edu
Hi Priti,
Attached are the tracula conf file and log files from two subjects.
I ran the two subjects. The results are almost the same. Here are what I found so far:
- There are NaN values in the 4D image. I created it from 3D images
using "fslmerge -a", and the 3G images have no NaNs. 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably this is the origin of all the problems?
Do you want me to send the email to you or to the mailing list? Probably many people are not interested in my email if I post on the whole list.
Thank you.
XJ
On 6/15/2012 11:02 AM, Priti Srinivasan wrote:
Can you send us your configuration file (mytracula.conf) and log file (it should be under scripts/trac-all.log). I can take a look.
Priti
Hi,
I am trying to run the last step of TRACULA. I used the command line:
% trac-all -path -c mytracula.conf
Here is all the info I got on the screen:
INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio INFO: Diffusion root is /home/xkang/DTI/ Actual FREESURFER_HOME /home/local/freesurfer-v510 trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log /home/xkang/DTI//S0006/scripts/trac-all.log -cmd /home/xkang/DTI//S0006/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 #------------------------------------- trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012
I didn't see "dpath" under the subject's directory. Seems nothing has been done. I already ran the "trac-all -prep" and "trac-all -bedp". I have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can any body help where the problems are?
I use DTI images in NIFTI format and the resolution is 2x2x2, which is not the same as that of the FreeSurfer orig.mgz. Probably this is fine.
Thanks.
XJ Kang _______________________________________________ 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
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 XJ - In your configuration file, you've set both doregflt and doregbbr to 0. You have to set one of them to 1, otherwise no intra-subject registration will be done and every step that relies on it will fail.
a.y
On Fri, 15 Jun 2012, XJ Kang wrote:
Hi Priti,
I removed the NaNs in the 4D images and re-ran trac-all -prep. The warning message is gone (of course) but the error message of dlable/diff/White-Matter++.flt.nii.gz is still there since no "White-Matter++.flt.nii.gz" in the diff directory. Only one image in dlabel/diff/: lowb_brain_mask.nii.gz.
fslstats -t /home/xkang/DTI//S0001/dmri/dwi.nii.gz -k /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz -m -s | awk '{print $1/$2}' > /home/xkang/DTI//S0001/dmri/dwi_snr.txt ** ERROR (nifti_image_read): failed to find header file for '/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt' ** ERROR: nifti_image_open(/home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt): bad header info ERROR: failed to open file /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt ERROR: Could not open image /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt Image Exception : #22 :: Failed to read volume /home/xkang/DTI//S0001/dlabel/diff/White-Matter++.flt.nii.gz
I am not sure if the error will affect the next steps of -bedp and -path. I want to make sure before run -bedp since that will take several hours.
Also there is no dpath directory yet. Probably it will be created during the -path processing?
Thanks.
XJ
On 6/15/2012 12:15 PM, Priti Srinivasan wrote:
Hi XJ,
I'm just starting to look at your log files. Just curious, did you decide to not do eddy current correction and b0 inhomogenity correction or accidentally left it out?
When I look at the configuration file, you've given all the parameters for b0 inhomogenity correction, but it is set to '0' (set dob0 = 0) and the same is the case for eddy current correction too (set doeddy = 0). Just wanted to make sure you did not set that '0' accidentally. Eddy current correction is definitely one of the recommended preprocessing steps, so you might want to consider doing that.
Also looks like your original input dwi file (with NaNs) may be the root cause of the problem. If you do have the original dicoms, you can give that as an input. I'm not sure if you can give a series of 3D Nifti DWI files as an input in the configurations file...Anastasia (cc'd) might be able to answer that question.
Hope that helps, Priti
---------------------------- Original Message ---------------------------- Subject: Re: [Freesurfer] TRACULA dpath problem From: "XJ Kang"xkang@ucdavis.edu Date: Fri, June 15, 2012 2:22 pm To: "Priti Srinivasan"rspriti@nmr.mgh.harvard.edu
Hi Priti,
Attached are the tracula conf file and log files from two subjects.
I ran the two subjects. The results are almost the same. Here are what I found so far:
- There are NaN values in the 4D image. I created it from 3D images
using "fslmerge -a", and the 3G images have no NaNs. 2. The image "dlabel/diff/White-Matter++.flt" was not found. Probably this is the origin of all the problems?
Do you want me to send the email to you or to the mailing list? Probably many people are not interested in my email if I post on the whole list.
Thank you.
XJ
On 6/15/2012 11:02 AM, Priti Srinivasan wrote:
Can you send us your configuration file (mytracula.conf) and log file (it should be under scripts/trac-all.log). I can take a look.
Priti
Hi,
I am trying to run the last step of TRACULA. I used the command line:
% trac-all -path -c mytracula.conf
Here is all the info I got on the screen:
INFO: SUBJECTS_DIR is /home/sata2/FreeSurfer/Subjects.Verio INFO: Diffusion root is /home/xkang/DTI/ Actual FREESURFER_HOME /home/local/freesurfer-v510 trac-paths -c /home/xkang/DTI//S0006/scripts/dmrirc.local -log /home/xkang/DTI//S0006/scripts/trac-all.log -cmd /home/xkang/DTI//S0006/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/bin/trac-paths #------------------------------------- #@# Path reconstruction Fri Jun 15 10:47:44 PDT 2012 #------------------------------------- trac-paths finished without error at Fri Jun 15 10:47:44 PDT 2012
I didn't see "dpath" under the subject's directory. Seems nothing has been done. I already ran the "trac-all -prep" and "trac-all -bedp". I have the directories dlable, dmri and dmir.bedpostX, but not dpath. Can any body help where the problems are?
I use DTI images in NIFTI format and the resolution is 2x2x2, which is not the same as that of the FreeSurfer orig.mgz. Probably this is fine.
Thanks.
XJ Kang _______________________________________________ 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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Priti Srinivasan -
XJ Kang