Hi,
trying to do my first steps with tracula I got stuck early in the preprocessing step. The DICOM import and preparation for FSL seem to work (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does not exist. What did I wrong?
The command I used was
trac-all -prep -c dmrirc
The content of the configuration file "dmrirc" was the minimum as described in the tutorial:
setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer set dtroot = /dat/Hirnreifung/Auswertung/freesurfer set subjlist = (3001LT) set dcmroot = /dat/Hirnreifung/Daten/DICOM set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm)
dcminfo.dat and trac-all.log are in the attachments.
Peter
Hi all,
I am currently working on retinotopy data and I managed to get the maps but I don’t really understand the angle meanings in the polar case. Like is zero angle meaning horizontal or vertical stimulus.
The reason it is puzzling me is that I seem to get response over the whole 360 degrees from both hemispheres so I am thinking there is probably some error in the scale.
We use a double rotating wedge as our stimulus.
I would appreciate if some one would assist by giving an explanation of the output of the retinotopy analysis in FS.
Thank you, Mohamed
Hi Peter - Have you defined "bvecfile" in your configuration file? I suspect it doesn't know where to find the gradient table.
a.y
On Thu, 4 Feb 2016, Parzer, Peter wrote:
Hi,
trying to do my first steps with tracula I got stuck early in the preprocessing step. The DICOM import and preparation for FSL seem to work (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does not exist. What did I wrong?
The command I used was
trac-all -prep -c dmrircThe content of the configuration file "dmrirc" was the minimum as described in the tutorial:
setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer set dtroot = /dat/Hirnreifung/Auswertung/freesurfer set subjlist = (3001LT) set dcmroot = /dat/Hirnreifung/Daten/DICOM set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm)
dcminfo.dat and trac-all.log are in the attachments.
Peter
Hi Anastasia,
no, I did not define "bvecfile" and "bvalfile" in the configuration file, because the tutorial says, that these variables are not needed if the data is in Siemens DICOM format, and my data is in Siemens DICOM format. Do I need this additional step to extract bvec and bval from die DICOM images? And what is the best way to do it?
Peter ________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Gesendet: Donnerstag, 4. Februar 2016 16:29 An: Freesurfer support list Betreff: Re: [Freesurfer] tracula preproc complains about missing bvec-file
Hi Peter - Have you defined "bvecfile" in your configuration file? I suspect it doesn't know where to find the gradient table.
a.y
On Thu, 4 Feb 2016, Parzer, Peter wrote:
Hi,
trying to do my first steps with tracula I got stuck early in the preprocessing step. The DICOM import and preparation for FSL seem to work (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does not exist. What did I wrong?
The command I used was
trac-all -prep -c dmrircThe content of the configuration file "dmrirc" was the minimum as described in the tutorial:
setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer set dtroot = /dat/Hirnreifung/Auswertung/freesurfer set subjlist = (3001LT) set dcmroot = /dat/Hirnreifung/Daten/DICOM set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm)
dcminfo.dat and trac-all.log are in the attachments.
Peter
_______________________________________________ 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 Peter - From your dicom header, it looks like the fields that it's looking for to guess which standard Siemens gradient table to use are not there. So you'll have to pass the gradient table and the b-value table as separate text files using bvecfile and bvalfile.
Starting in 6.0 this'll all be more seemless, I promise!
a.y
On Fri, 5 Feb 2016, Parzer, Peter wrote:
Hi Anastasia,
no, I did not define "bvecfile" and "bvalfile" in the configuration file, because the tutorial says, that these variables are not needed if the data is in Siemens DICOM format, and my data is in Siemens DICOM format. Do I need this additional step to extract bvec and bval from die DICOM images? And what is the best way to do it?
Peter ________________________________________ Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu Gesendet: Donnerstag, 4. Februar 2016 16:29 An: Freesurfer support list Betreff: Re: [Freesurfer] tracula preproc complains about missing bvec-file
Hi Peter - Have you defined "bvecfile" in your configuration file? I suspect it doesn't know where to find the gradient table.
a.y
On Thu, 4 Feb 2016, Parzer, Peter wrote:
Hi,
trying to do my first steps with tracula I got stuck early in the preprocessing step. The DICOM import and preparation for FSL seem to work (mri_convert, mri_probedicom, flip4fsl, fslswapdim, fslorient). But then trac-preproc wants to move a file named dwi_orig_flip.mghdti.bvecs that does not exist. What did I wrong?
The command I used was
trac-all -prep -c dmrircThe content of the configuration file "dmrirc" was the minimum as described in the tutorial:
setenv SUBJECTS_DIR /dat/Hirnreifung/Auswertung/freesurfer set dtroot = /dat/Hirnreifung/Auswertung/freesurfer set subjlist = (3001LT) set dcmroot = /dat/Hirnreifung/Daten/DICOM set dcmlist = (3001LT/d_Diff_ax_64dir_1av_b0_1000_3000/IM-0001-0001.dcm)
dcminfo.dat and trac-all.log are in the attachments.
Peter
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
freesurfer@nmr.mgh.harvard.edu
-
Anastasia Yendiki -
m.abouelyazid＠gmail.com -
Parzer, Peter