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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely,
AFNI HQ
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Hi,
I'm trying to map the functional data to surface using 3dVol2Surf and then extract the data within surface ROI. Then I met ** FATAL ERROR: Input and mask datasets are not same dimensions!
I checked their number of nodes and found there's a lack of nodes for the functional data. It's weird because this doesn't happen to another run of this subject (scanned just 2 min
by
Dong
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AFNI Message Board
Dear AFNI experts,
I was using 3dAutomask to get the mask of brain from the epi dataset. I met the problem that some of the skull was included in the mask. Is this acceptable? I'm not sure if the later analysis would be affected if I use this mask. And is there some way to have a cleaner mask?
Many thanks,
Dong
by
Dong
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AFNI Message Board
Thanks for the reply, but it doesn't work.
I have tried and many other index values.
As long as the index value is larger than the max index of ROI, there always
-- Error SUMA_IsCmapOKForLabelDset (SUMA_Color.c:4273):
Have 2 unique values,
have no colormap big enough for this
-- Error SUMA_CreateCmapForLabelDset (SUMA_Color.c:4223):
Provided cmap is no good
-- Err
by
Dong
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AFNI Message Board
Thank you very much for the reply!
I tried to follow the example but met some errors. From my understanding, when using 3dmaskave, the mask (ROI dataset) and input (resting fMRI dataset in my study) should have the same size. So, I checked the size of resting data and used it for -pad_to_node.
After running the command "ROI2dataset -label_dset surfROI_lv1.niml.dset -pad_to_node 135170
by
Dong
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AFNI Message Board
Hello,
I want to do some resting state analysis based on surface data.
I have mapped data from a volume domain to surface domain and drawn several ROIs on surface. I'm wondering 1) which commands I can use to extract the timeseries from each ROI and 2) if 3dDeconvolve can be used for the correlation analysis between two surface ROIs.
Thanks in advance.
by
Dong
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AFNI Message Board
Thanks! Following is the full script. BTW, I got another error if using the full path of surface data, please look at the end.
wf="/media/vpp/DATA/"
s=sbj05
thesession=pre
thecond='restingEyeClosed'
cd ${wf}/${s}/anat/surface_info/surf/
3dVol2Surf -spec ${wf}/${s}/anat/surface_info/SUMA/${s}_lh.spec \
-surf_A smoothwm \
-surf_B pial \
-sv ${wf}/${s}/${thesession}
by
Dong
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AFNI Message Board
Yes, I ran ls -ld in the output directory and got 'drwxrwxrwx 1 vpp vpp 20480'. I can also create or write a file to that directory.
All fMRI data and output were put in D:\ of Windows system, I think they are free to read/write in Linux. I've never met a permission problem when working with those data. Is there any other reason?
Thanks !
by
Dong
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AFNI Message Board
Hi rick,
Thanks for your response.
The output is:
vpp
drwxrwxrwx 1 vpp vpp 20480
by
Dong
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AFNI Message Board
Hi,
I was trying to use the following script to map volume data to surface, but got some errors.
3dVol2Surf -spec ${wf}/${s}/anat/surface_info/SUMA/${s}_lh.spec \
-surf_A smoothwm \
-surf_B pial \
-sv ${s}_surf_volm_aligned+orig \
-grid_parent r06_detrend.nii.gz \
-map_func ave \
-f_steps 10 \
-f_index nodes \
-out_niml ${wf}/${s}/${thesession}/${thecond}/${s}_lvol2surf.niml.dset
by
Dong
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AFNI Message Board