Hi,
I do the pre-processing with the following command:
trac-all -prep -c ./scripts/dmrirc_single_subject
THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow:
fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz
0 25
It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point?
Thank you.
Phoebe.
Hi Phoebe,
The fslroi part extracts all the low-b images from the 4D diffusion data and creates an average low-b mask.
fslroi <input> <output> <tmin> <tsize>
<tsize> is the number of 3D low-b volumes to be extracted from the 4D diffusion volume. For some reason tracula is unable to read the no. of low-b images from your dicom header (Is this an MGH acquisition?). If you know the number of low-b volumes you can specify that in the configuration file using the following command:
set nb0 = *No. of low-b images*
Once you set that value it should not throw that error. From what you ran in the commandline, I assume that in your dti acquisition 0 through 25 are low-b volumes.
Creating the low-b image mask is the last step in the first stepwise directive of tracula (-corr). You can go through the rest of the steps by specifying any or all of the stepwise directives:
Ex: trac-all -intra -inter -masks -tensor -prior -c ./scripts/dmrirc_single_subject
Please let us know if you have any questions or problems running the same.
Thanks, Priti
Hi,
I do the pre-processing with the following command:
trac-all -prep -c ./scripts/dmrirc_single_subject
THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow:
fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz
0 25
It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point?
Thank you.
Phoebe.
Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 phoebe@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Priti,
Thank you for your help. I get through the fslroi successfully by setting the nb0 variable. The lowb.nii.gz looks fine. However, when the process comes to bet, there's another error prompt for lowb.nii.gz.hdr.
fslmaths /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz -Tmean /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz bet /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz.hdr Linux guasha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
Kindly help.
Phoebe.
Hi Phoebe,
The fslroi part extracts all the low-b images from the 4D diffusion data and creates an average low-b mask.
fslroi <input> <output> <tmin> <tsize>
<tsize> is the number of 3D low-b volumes to be extracted from the 4D diffusion volume. For some reason tracula is unable to read the no. of low-b images from your dicom header (Is this an MGH acquisition?). If you know the number of low-b volumes you can specify that in the configuration file using the following command:
set nb0 = *No. of low-b images*
Once you set that value it should not throw that error. From what you ran in the commandline, I assume that in your dti acquisition 0 through 25 are low-b volumes.
Creating the low-b image mask is the last step in the first stepwise directive of tracula (-corr). You can go through the rest of the steps by specifying any or all of the stepwise directives:
Ex: trac-all -intra -inter -masks -tensor -prior -c ./scripts/dmrirc_single_subject
Please let us know if you have any questions or problems running the same.
Thanks, Priti
Hi,
I do the pre-processing with the following command:
trac-all -prep -c ./scripts/dmrirc_single_subject
THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow:
fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz
0 25
It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point?
Thank you.
Phoebe.
Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 phoebe@nmr.mgh.harvard.edu
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Phoebe - I don't have permission to access your files, but do you have FSLOUTPUTTYPE set to anything other than nifti by any chance?
a.y
On Thu, 14 Jul 2011, phoebe@nmr.mgh.harvard.edu wrote:
Hi Priti,
Thank you for your help. I get through the fslroi successfully by setting the nb0 variable. The lowb.nii.gz looks fine. However, when the process comes to bet, there's another error prompt for lowb.nii.gz.hdr.
fslmaths /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz -Tmean /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz bet /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb_brain.nii.gz -m -f 0.3 Can't open /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz.hdr Linux guasha 2.6.18-194.32.1.el5 #1 SMP Wed Jan 5 17:52:25 EST 2011 x86_64 x86_64 x86_64 GNU/Linux
Kindly help.
Phoebe.
Hi Phoebe,
The fslroi part extracts all the low-b images from the 4D diffusion data and creates an average low-b mask.
fslroi <input> <output> <tmin> <tsize>
<tsize> is the number of 3D low-b volumes to be extracted from the 4D diffusion volume. For some reason tracula is unable to read the no. of low-b images from your dicom header (Is this an MGH acquisition?). If you know the number of low-b volumes you can specify that in the configuration file using the following command:
set nb0 = *No. of low-b images*
Once you set that value it should not throw that error. From what you ran in the commandline, I assume that in your dti acquisition 0 through 25 are low-b volumes.
Creating the low-b image mask is the last step in the first stepwise directive of tracula (-corr). You can go through the rest of the steps by specifying any or all of the stepwise directives:
Ex: trac-all -intra -inter -masks -tensor -prior -c ./scripts/dmrirc_single_subject
Please let us know if you have any questions or problems running the same.
Thanks, Priti
Hi,
I do the pre-processing with the following command:
trac-all -prep -c ./scripts/dmrirc_single_subject
THe process exits with error when it comes to fslroi (attached pls find the log file). I try to re-run the fslroi command as follow:
fslroi /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/dwi.nii. gz /autofs/space/guasha_001/users/phoebe/strab_func_chan4/strab_func_chan_diffrecons/040826_cst/dmri/lowb.nii.gz
0 25
It works and the lowb.nii.gz looks normal. In case if I have the same problem with another dataset, how can I incorporate the number of frames (25) in the trac-all command for the fslroi? Can I continue the remaining procedures of trac-all from this point?
Thank you.
Phoebe.
Phoebe Suk-tak Chan, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Bldg. 149, 13th St., mailcode 149-2301 Charlestown, MA 02129 phoebe@nmr.mgh.harvard.edu
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 -
phoebe＠nmr.mgh.harvard.edu -
rspriti＠nmr.mgh.harvard.edu