Can you run the 2nd command with --debug as the first option and send
the terminal output?
doug
On 6/12/15 12:09 PM, David C. Zhu wrote:
Dear FreeSurfer experts:
I have been using FreeSurfer for segmentation and for volumetric
analyses. I want to give a try to use it for surface-based fMRI analyses.
I encountered some issues with mris_preproc to assemble IRF results to
the fsaverage surface. Please advise on how to resolve these issues.
Here is what I did:
After finishing “recon-all” on each subject, I ran this following on
each subject.
bbregister --mov reg_cat_TSall_before_blur.nii --bold --s freesurfer
--init-fsl --lta register.lta
“reg_cat_TSall_before_blur.nii” is the EPI fMRI time series assembled
together.
Then I calculated the IRF percent signal changes for different
conditions. “sum_all_norm_IRF_EA.nii” is for one condition.
Now I want to assemble the “sum_all_norm_IRF_EA.nii” from each subject
and put them on the fsaverage surface. I got the following errors:
mris_preproc --hemi rh --o rh.fsaverage.sumEA.mgh \
--iv S00720110927_Free/sum_all_norm_IRF_EA.nii
S00720110927_Free/register.lta \
--iv S01420110908_Free/sum_all_norm_IRF_EA.nii
S01420110908_Free/register.lta \
--iv S01520110811_Free/sum_all_norm_IRF_EA.nii
S01520110811_Free/register.lta \
--iv S02520110927_Free/sum_all_norm_IRF_EA.nii
S02520110927_Free/register.lta \
--iv S02720111028_Free/sum_all_norm_IRF_EA.nii
S02720111028_Free/register.lta \
--iv S02820111107_Free/sum_all_norm_IRF_EA.nii
S02820111107_Free/register.lta \
--iv S02920111108_Free/sum_all_norm_IRF_EA.nii
S02920111108_Free/register.lta \
--iv S03020120703_Free/sum_all_norm_IRF_EA.nii
S03020120703_Free/register.lta \
--iv S03120120726_Free/sum_all_norm_IRF_EA.nii
S03120120726_Free/register.lta \
--iv S03620120727_Free/sum_all_norm_IRF_EA.nii
S03620120727_Free/register.lta \
--iv S03720120809_Free/sum_all_norm_IRF_EA.nii
S03720120809_Free/register.lta \
--iv S03920120807_Free/sum_all_norm_IRF_EA.nii
S03920120807_Free/register.lta
ERROR: number of input volumes (12) does not equal number of subjects (48)
mris_preproc --hemi rh --o rh.fsaverage.sumEA.mgh \
--iv S00720110927_Free/sum_all_norm_IRF_EA.nii
S00720110927_Free/register.dat \
--iv S01420110908_Free/sum_all_norm_IRF_EA.nii
S01420110908_Free/register.dat \
--iv S01520110811_Free/sum_all_norm_IRF_EA.nii
S01520110811_Free/register.dat \
--iv S02520110927_Free/sum_all_norm_IRF_EA.nii
S02520110927_Free/register.dat \
--iv S02720111028_Free/sum_all_norm_IRF_EA.nii
S02720111028_Free/register.dat \
--iv S02820111107_Free/sum_all_norm_IRF_EA.nii
S02820111107_Free/register.dat \
--iv S02920111108_Free/sum_all_norm_IRF_EA.nii
S02920111108_Free/register.dat \
--iv S03020120703_Free/sum_all_norm_IRF_EA.nii
S03020120703_Free/register.dat \
--iv S03120120726_Free/sum_all_norm_IRF_EA.nii
S03120120726_Free/register.dat \
--iv S03620120727_Free/sum_all_norm_IRF_EA.nii
S03620120727_Free/register.dat \
--iv S03720120809_Free/sum_all_norm_IRF_EA.nii
S03720120809_Free/register.dat \
--iv S03920120807_Free/sum_all_norm_IRF_EA.nii
S03920120807_Free/register.dat
nsubjects = 12
ERROR: cannot find ./freesurfer
Under each subject directory, for example, “S00720110927_Free”, I have
the following data structure (The “freesurfer” storing the “recon-all”
FreeSurfer results.):
circ2:/fmri/PI/liu/rdl_afni/S00720110927_Free> ls
freesurfer lh.sum_all_norm_IRF_MA.mgh register.dat.mincost
rh.sum_all_norm_IRF_HA.mgh sum_all_norm_IRF_HS.nii
fsaverage lh.sum_all_norm_IRF_MS.mgh register.dat.param
rh.sum_all_norm_IRF_HS.mgh sum_all_norm_IRF_MA.nii
lh.EC_average mprage_nudge_RAI.nii.gz
register.dat.sum rh.sum_all_norm_IRF_MA.mgh
sum_all_norm_IRF_MS.nii
lh.sum_all_norm_IRF_EA.mgh reg_cat_TSall_before_blur.nii register.lta
rh.sum_all_norm_IRF_MS.mgh surfer.log
lh.sum_all_norm_IRF_ES.mgh register.dat
rh.EC_average sum_all_norm_IRF_EA.nii
lh.sum_all_norm_IRF_HA.mgh register.dat~
rh.sum_all_norm_IRF_EA.mgh sum_all_norm_IRF_ES.nii
lh.sum_all_norm_IRF_HS.mgh register.dat.log
rh.sum_all_norm_IRF_ES.mgh sum_all_norm_IRF_HA.nii
Thank you.
David Zhu
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