Dear FSL email list,
I have some questions regarding the interpretation of Oxford_asl output. I am using the latest version of Oxford_asl (version 3.9.13 for CentOS 7) downloaded from GitHub.
1) I understand from previous posts that in the folder containing partial volume corrected results (/.../native_space/pvcorr), the perfusion_calib_masked.nii.gz image is CBF for GM only, and perfusion_wm_calib_masked.nii.gz is CBF for WM. I tried to use "fslstats perfusion_calib_masked -M" and "fslstats perfusion_wm_calib_masked -M" to get the mean CBF for GM and WM, respectively. However, the output is different from the numbers in perfusion_calib_gm_mean.txt and perfusion_wm_calib_wm_mean.txt. For example:
[jiyang@dhcp pvcorr]$ fslstats perfusion_calib_masked.nii.gz -M
60.859487
[jiyang@dhcp pvcorr]$ fslstats perfusion_wm_calib_masked.nii.gz -M
4.719992
[jiyang@dhcp pvcorr]$ cat perfusion_calib_gm_mean.txt
30.913142
[jiyang@dhcp pvcorr]$ cat perfusion_wm_calib_wm_mean.txt
4.747511
I was wondering why this is so, and which one is the current GM/WM CBF?
2) Is it correct to get the global CBF from the perfusion_calib.nii.gz in "/.../native_space" folder (i.e. non-partial-volume-corrected), by using
fslstats /.../native_space/perfusion_calib -M?
3) In order to calculate lobar CBF and CBF in subcortical structures, is it correct to warp MNI Structural Atlas to /.../native_space/pvcorr/perfusion_calib_masked.nii.gz, and use fslstats -M to get the mean CBF in each region?
4) I got the following error/warning messages when running Oxford_asl. Are they concerns or something I can ignore?
Cannot open volume /tmp/fsl_Ry3Ru2_ox_asl/init/basil/step2/mean_fwm for reading!
Cannot open volume /tmp/fsl_Ry3Ru2_ox_asl/init/basil/step2/mean_deltwm for reading!
Cannot open volume /tmp/fsl_Ry3Ru2_ox_asl/basil/step2/mean_fwm for reading!
Cannot open volume /tmp/fsl_Ry3Ru2_ox_asl/basil/step2/mean_deltwm for reading!
/bin/cp: '/tmp/fsl_Ry3Ru2_ox_asl/mask.nii.gz' and '/tmp/fsl_Ry3Ru2_ox_asl/mask.nii.gz' are the same file
/bin/cp: '/tmp/fsl_Ry3Ru2_ox_asl/tissseg.nii.gz' and '/tmp/fsl_Ry3Ru2_ox_asl/tissseg.nii.gz' are the same file
Cannot open volume /data_pub/jiyang/ASLprocessing/reconvertedRawData_reprocessing/pCASL_FSL/test11004/subjects/11004/11004_invKineticMdl_wT1/native_space/pvcorr/deltwm for reading!
The command I ran to processing was:
${newOxfordAsl_folder}/oxford_asl \
-i ${indFolder}/${ID}_pCASL \
--iaf ${acq_order} \
--tis ${TI} \
--casl \
--bolus ${bolus} \
--bat ${BAT} \
--slicedt=${slicedt} \
--fslanat=${indFolder}/${ID}_T1.anat \
--sbrain ${indFolder}/${ID}_T1_brain \
-c ${indFolder}/${ID}_M0 \
--tr ${TR} \
--cmethod single \
--tissref csf \
--csf ${indFolder}/${ID}_M0_ventricle \
--te ${TE} \
--fixbolus \
--pvcorr \
--spatial \
--mc \
-o ${indFolder}/${ID}_invKineticMdl_wT1 \
>> ${indFolder}/${ID}_logfile.txt
Any help is much appreciated!
Best regards,
Jiyang
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