That's almost right. Just specify the subject name and not the full path. Also, you will need to supply bvals and bvects dt_recon --i DTI_15.nii.gz --s NPI001 --o /usr/local/freesurfer/NPI001/DTI_15
Antonella Kis wrote:
Hi Doug,
Thanks again for helping. So my question is then: I will pass for --i (the input data) the .nii.gz file from the DTI data and the it is OK to use for the --s which defines the file of the structural recon a file called NPI001 where I have 10 files after recon-all (bem, label, mri, surf, stats, etc)? In other words if I will set-up:
setenv FREESURFER_HOME /usr/local/freesurfer setenv SUBJECTS_DIR $FREESURFER_HOME
and since my files are in /usr/local/freesurfer/NPI001 I am then doing:
cd /usr/local/freesurfer/NPI001
Here I have the pre-processed files after recon-all and a file called DTI_15 with my diffussion data and the DTI_15.nii.gz file so I can run:
dt_recon --i DTI_15.nii.gz --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/DTI_15
Is this right?
I will try by the time you answer but please let me know if you have any objection and/or advise.
Many thanks, AK
*From:* Douglas N Greve greve@nmr.mgh.harvard.edu *To:* Antonella Kis atorok9@yahoo.com; freesurfer freesurfer@nmr.mgh.harvard.edu *Sent:* Wednesday, August 31, 2011 1:49 PM *Subject:* Re: [Freesurfer]: Error with dt_recon
If you pass it dicom, it will try to extract the bvalues, which is where it is failing. doug
Antonella Kis wrote:
Dear Doug,
Sorry but I still have a question about this error: I understood that dt_recon it takes original dicom images as input
and it generates multiple NIFTI volumes that will be used in later steps.So why I need to use the NIFTI as input?
Thnak you. AK
*From:* Douglas N Greve <greve@nmr.mgh.harvard.edu
mailto:greve@nmr.mgh.harvard.edu>
*To:* Antonella Kis <atorok9@yahoo.com mailto:atorok9@yahoo.com> *Cc:* "fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu" <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>; "freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
*Sent:* Tuesday, August 30, 2011 3:51 PM *Subject:* Re: [Freesurfer] Fw: Error with dt_recon
It's looking for the values in the dicom file (which apparently does
not have them). Convert the dicom to nifit, then use the nifti as input, then pass files with bvals and bvects on the command line.
doug
Antonella Kis wrote:
Dear Bruce:
I am running the dt_recon: # setenv FREESURFER_HOME /usr/local/freesurfer # setenv
SUBJECTS_DIR $FREESURFER_HOME
# cd /usr/local/freesurfer/NPI001 # dt_recon --i
/usr/local/freesurfer/NPI001/dti/1.3.46.670589.11.17385.5.0.7524.2009112812454960001.dcm --s /usr/local/freesurfer/NPI001 --o /usr/local/freesurfer/NPI001/dti
and I am getting the following error:
ERROR: cannot extract sDiffusion.alBValue[1] from
/usr/local/freesurfer/NPI001/dti/dwi-infodump.dat
Can you please give me a hint?
Thank you. AK
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