Hi,
I have a basic question, but the answer can be useful for others as well.
I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So:
My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan)
My EPI data: fmc.nii.gz files in run folders
Now I have three questions:
1) How can I unpack the fieldmap data? An example command ...
2) How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an example command would be very useful.
3) How will the undistorted volumes be used later on in the FS-FAST analysis stream?
Your help would be very much appreciated.
Thanks, Reza
I forgot to mention that I want to use undistorted EPI volumes for the functional-anatomical registration.
Hi,
I have a basic question, but the answer can be useful for others as well.
I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So:
My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan)
My EPI data: fmc.nii.gz files in run folders
Now I have three questions:
How can I unpack the fieldmap data? An example command ...
How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
example command would be very useful.
- How will the undistorted volumes be used later on in the FS-FAST
analysis stream?
Your help would be very much appreciated.
Thanks, Reza
Hi Reza,
On Sep 6, 2014, at 13:47 , Reza Rajimehr reza@nmr.mgh.harvard.edu wrote:
I forgot to mention that I want to use undistorted EPI volumes for the functional-anatomical registration.
Well that is simple then, just undistorted the 3D EPI image you used as template for motion correction and register this tho the anatomical (if you have a surface recon for the anatomical I hear BBB is the registration method of choice). To overlay statistics result on the anatomical just use the the same “warp” as for the mock template and you should be fine.
Best Regards Sebastian
Hi,
I have a basic question, but the answer can be useful for others as well.
I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So:
My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan)
My EPI data: fmc.nii.gz files in run folders
Now I have three questions:
How can I unpack the fieldmap data? An example command ...
How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
example command would be very useful.
- How will the undistorted volumes be used later on in the FS-FAST
analysis stream?
Your help would be very much appreciated.
Thanks, Reza
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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the commands I gave you will do this On 09/06/2014 07:47 AM, Reza Rajimehr wrote:
I forgot to mention that I want to use undistorted EPI volumes for the functional-anatomical registration.
Hi,
I have a basic question, but the answer can be useful for others as well.
I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So:
My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan)
My EPI data: fmc.nii.gz files in run folders
Now I have three questions:
How can I unpack the fieldmap data? An example command ...
How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
example command would be very useful.
- How will the undistorted volumes be used later on in the FS-FAST
analysis stream?
Your help would be very much appreciated.
Thanks, Reza
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Reza,
On Sep 6, 2014, at 13:10 , Reza Rajimehr reza@nmr.mgh.harvard.edu wrote:
Hi,
I have a basic question, but the answer can be useful for others as well.
I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So:
My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan)
As it should, you need one of the two magnitude images and the actual field map for epidewarp.fsl to work.
My EPI data: fmc.nii.gz files in run folders
Now I have three questions:
- How can I unpack the fieldmap data? An example command …
Exactly like you unpack everything else… (unpacksdcmdir works for siemens data, just make sure you include the sequence in the CFG file for e.g.: “B0_Map fieldmap nii fieldmap.nii”) So basically (if you have siemens data use: unpacksdcmdir -src $srcdir -targ $targdir -seqcfg $cfg_file -fsfast where $srcdir points to the directory with all the sessions dicoms (unpacksdcmdir will figure out which sequence instances are in which files), $cfg_file is just a list of sequence “descriptors” so unpacksdcmdir knows which data to handele and how to name and where to store it in $targdir, I think -fsfast makes sure the output directory is structured the way fsfast expects it...
- How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
example command would be very useful.
For a single 3d volume use:
# non-reversed phase epidewarp.fsl --mag ${fid_dir}/${fid_name_stem}_fid_mag.${out_ext} --dph ${fid_dir}/${fid_name_stem}_fid_phasediff.${out_ext} \ <------> <-->--exf ${mocovol_dir}/${moco_name} --tediff ${TEdiff} --esp ${EPI_echospacing} \ <------> <-->--vsm ${mocovol_dir}/vsm_fmc.${out_ext} \ <------><------>--exfdw ${mocovol_dir}/mocovol_undistorted_non-reversed-phase.${fsl_epi_out_ext} ….
for a full 4d series use: <------><------><------>epidewarp.fsl --mag ${fid_dir}/${fid_name_stem}_fid_mag.${out_ext} --dph ${fid_dir}/${fid_name_stem}_fid_phasediff.${out_ext} \ <------><------> <--><------>--exf ${mocovol_dir}/${moco_name} --epi ${bold_dir}/${epi_run}/${epi_in_stem}.${epi_in_ext} --tediff ${TEdiff} --esp ${EPI_echospacing} \ <------><------> <--><------>--vsm ${bold_dir}/${epi_run}/vsm_fmc.${out_ext} \ <------><------><------><------><------>--epidw ${bold_dir}/${epi_run}/${epi_out_stem}.${fsl_epi_out_ext} \ <------><------><------><------>${fugue_opts_string}
Make sure to test both PE directions (and if needed add —perev as $fugue_opts_string to reverse the phase encode…), —epidw will contain the full unwrapped eli series with the name you give it there
I hope you can figure out meaning of the different shell variables in the two examples if you compare with the output of “epidewarp.fsl” on the shell, just replace my variables with your actual directory and file names.
- How will the undistorted volumes be used later on in the FS-FAST
analysis stream?
Well for all further steps you can either override which functional volumes to take, or you could just rename the initial motion corrected volumes to say fmc_distorted and then have epidewarp.fsl call its output fmc, but that really is open to how you want to go ahead
Your help would be very much appreciated.
Thanks, Reza _______________________________________________ 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.
On 09/06/2014 07:10 AM, Reza Rajimehr wrote:
Hi,
I have a basic question, but the answer can be useful for others as well.
I am doing a customized preprocessing of monkey functional data in FS-FAST v5.3. After motion correction and before functional-anatomical registration, I want to use fieldmap data to correct spatial distortions of EPI data. So:
My fieldmap data: dicom files from a fieldmap scan (there are actually two series of dicom files for that scan)
My EPI data: fmc.nii.gz files in run folders
Now I have three questions:
- How can I unpack the fieldmap data? An example command ...
I think you get two series out, one magnitude and one phase, just convert those to nifti
- How can I use FS-FAST's epidewarp.fsl command for my dataset? Again an
example command would be very useful.
something like epidewarp.fsl --mag mag.nii --dph phase.nii --exf template.nii --o b0dc.nii ... You have to add --tediff and --esp, but those depend on you sequence Put the output (b0dc.nii) into session/bold (or session/rest, or where ever your fmri data are located)
- How will the undistorted volumes be used later on in the FS-FAST
analysis stream?
When you run preproc-sess and mkanalysis-sess add -b0dc to the command line
Your help would be very much appreciated.
Thanks, Reza _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu