[Anand Joshi]

Can you check if the input files exist by typing ls <filename> exactly as in the input command?

[leonidastra86]

Should I type it in terminal? Because I don’t get anything out of it.

The input file (/Users/leonidastra86/Desktop/AAA/Pre/xxx/Normalised/abc.pvc-thickness_0-6mm.left.mid.cortex.dfs) exists for sure, I use the path as always. Should I use the atlas.pvc-thickness_0-6mm.left.mid.cortex.dfs maybe? Because in this case I receive an additional error:##Error using readdfs (line 61)

I apologise for my poor knowledge on programming.

[Anand Joshi]

can you try the following in the terminal
ls /Users/leonidastra86/Desktop/AAA/Pre/xxx/Normalised/abc.pvc-thickness_0-6mm.left.mid.cortex.dfs

Is there any space in the path? If yes, then you should use double quotes around the file name.

[leonidastra86]

There is no space in my path. When I type your suggested path I receive the same back without the ls.
Is it normal?

Thank you so much for your help. It is really important for me to manage the statistical analysis of my results.

[Anand Joshi]

I read your command, I think you are specifying 2 files as inputs.
There should be 3 files. If you are smoothing cortical thickness, then you should specify the input file twice and then the output file.
first file contains geometry
second file contains the function that needs to be smoothed
third file if the output file
fourth argument is the amount of smoothing.

If that doesn’t work, can you share one file with me using dropbox and share the exact command that you are trying so that I can try to reproduce the error?

[leonidastra86]

It worked! That was the problem! I had the input file just once. I did it twice and worked.

Thank you sooooo much!

The right file is the one with the patient name or the one with atlas?

abc.pvc-thickness_0-6mm.left.mid.cortex.dfs

or

atlas.pvc-thickness_0-6mm.left.mid.cortex.dfs

???

[Anand Joshi]

subject file contains cortical thickness on the subject’s surface whereas
atlas file contains subjects cortical thickness coregistered to the atlas.
If you want to perform multisubject or across scan comparison then you can use atlas file as input, whereas if you want to look at only one scan then you can use the subject file.

[leonidastra86]

Perfect! So far so good. I smoothed both hemispheres and wanted to start the analysis. My demographics file is ready, however I cannot install BSS. I already installed R and R Studio but as soon as I type pip install bss I receive the following problem:

Leonidass-Air:~ leonidastra86$ pip install bss
Collecting bss
Using cached bss-0.9.4-py2.py3-none-any.whl
Collecting matplotlib>=1.5.3 (from bss)
Downloading matplotlib-2.1.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (13.2MB)
100% |████████████████████████████████| 13.2MB 89kB/s
Collecting numpy>=1.11 (from bss)
Using cached numpy-1.13.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting statsmodels>=0.6.1 (from bss)
Using cached statsmodels-0.8.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting patsy>=0.4 (from bss)
Using cached patsy-0.4.1-py2.py3-none-any.whl
Collecting scipy>=0.18 (from bss)
Using cached scipy-0.19.1-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting nibabel>=2.1 (from bss)
Using cached nibabel-2.1.0.zip
Collecting pandas>=0.19 (from bss)
Using cached pandas-0.20.3-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.5.3->bss)
Requirement already satisfied: pytz in /System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python (from matplotlib>=1.5.3->bss)
Collecting backports.functools-lru-cache (from matplotlib>=1.5.3->bss)
Downloading backports.functools_lru_cache-1.4-py2.py3-none-any.whl
Collecting six>=1.10 (from matplotlib>=1.5.3->bss)
Using cached six-1.11.0-py2.py3-none-any.whl
Collecting cycler>=0.10 (from matplotlib>=1.5.3->bss)
Using cached cycler-0.10.0-py2.py3-none-any.whl
Collecting subprocess32 (from matplotlib>=1.5.3->bss)
Using cached subprocess32-3.2.7.tar.gz
Collecting python-dateutil>=2.0 (from matplotlib>=1.5.3->bss)
Downloading python_dateutil-2.6.1-py2.py3-none-any.whl (194kB)
100% |████████████████████████████████| 194kB 2.0MB/s
Installing collected packages: numpy, backports.functools-lru-cache, six, cycler, subprocess32, python-dateutil, matplotlib, scipy, patsy, pandas, statsmodels, nibabel, bss
Found existing installation: numpy 1.8.0rc1
DEPRECATION: Uninstalling a distutils installed project (numpy) has been deprecated and will be removed in a future version. This is due to the fact that uninstalling a distutils project will only partially uninstall the project.
Uninstalling numpy-1.8.0rc1:
Exception:
Traceback (most recent call last):
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/basecommand.py”, line 215, in main
status = self.run(options, args)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/commands/install.py”, line 342, in run
prefix=options.prefix_path,
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_set.py”, line 778, in install
requirement.uninstall(auto_confirm=True)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_install.py”, line 754, in uninstall
paths_to_remove.remove(auto_confirm)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/req/req_uninstall.py”, line 115, in remove
renames(path, new_path)
File “/Library/Python/2.7/site-packages/pip-9.0.1-py2.7.egg/pip/utils/__init__.py”, line 267, in renames
shutil.move(old, new)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py”, line 302, in move
copy2(src, real_dst)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py”, line 131, in copy2
copystat(src, dst)
File “/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py”, line 103, in copystat
os.chflags(dst, st.st_flags)
OSError: [Errno 1] Operation not permitted: ‘/var/folders/13/mblgc8t52kx3g229dsds97r00000gn/T/pip-szRNjk-uninstall/System/Library/Frameworks/Python.framework/Versions/2.7/Extras/lib/python/numpy-1.8.0rc1-py2.7.egg-info’

As far as I understand it will be installed and afterwards deinstalled. Why?

And one more question, in the USC2015_Brainsuite Workshop there is one more smoothed file in every patient folder, the ABCS.svreg.inv.map.jacdet.smooth2.0mm.nii.gz.

Should I smooth it too? Is it important for the analysis?

Thank you sooo much for your help.

[leonidastra86]

In the slides for BSS, on the required data, says that we need a svreg.inv.jacobian.*mm.nii.gz file. Should I smooth it too?

If yes, how? Because with the way I did the other files doesn’t work. I receive the following message:

Index exceeds matrix dimensions.

Error in readdfsGz>readdfs (line 129)

Error in readdfsGz (line 41)

Error in svreg_smooth_surf_function (line 31)

MATLAB:badsubscript

[Anand Joshi]

For smoothing volumetrically, you can use
svreg_smooth_vol_function.sh

Please type it on the command line without any arguments to see the usage.

svreg_smooth_vol_function : This script performs 3d vol news
Authored by Anand A. Joshi, Signal and Image Processing Institute
Department of Electrical Engineering, Viterbi School of Engineering, USC

usage: svreg_smooth_vol_function.sh in_file stdx stdy stdz out_file

required input:
in_file: input vol file
stdx,stdy,stdz: std dev (in mm) in 3 directions
out_vol: output vol file

[leonidastra86]

Could you please give me an example?

Something like this?

/Applications/BrainSuite17a/svreg/bin/svreg_smooth_surf_function.sh /Users/leonidastra86/Desktop/ABC/Pre/XXX/Normalised/abt.svreg.inv.jacobian.nii.gz stdx stdy stdz /Users/leonidastra86/Desktop/ABC/Pre/XXX/Normalised/abt.svreg.inv.jacobian.smooth2.0mm.nii.gz 2.0

How do I define the std values? What are they exactly?

[Anand Joshi]

svreg_smooth_vol_function.sh uses 3D Gaussian smoothing. The parameters specify standard deviation, in mm, of the Gaussian kernel for the smoothing. One can specify the std dev in three directions separately.
Please make sure to svreg_smooth_vol_function.sh for nii.gz volume files, and svreg_smooth_surf_function.sh for .dfs files for surface based smoothing.

[leonidastra86]

I receive always the following message:

Index exceeds matrix dimensions.

Error in readdfsGz>readdfs (line 129)

Error in readdfsGz (line 41)

Error in svreg_smooth_surf_function (line 31)

MATLAB:badsubscript

I tried std values from 0.5 till 5 but without any success.

Is it the .svreg.inv.jacobian.nii.gz file the right one to perform smoothing?

Is there a path-example to understand how will it be used?

Thanks a lot.

[leonidastra86]

After trying some things out, the last problem that comes out is the following:

Warning: qform is already set. Nothing to do.
> In add_qform (line 69)
In load_nii_BIG_Lab (line 47)
In svreg_smooth_vol_function (line 34)
Error using imgaussfilt3
Expected Sigma to be finite.

Error in imgaussfilt3>validateSigma (line 379)

Error in imgaussfilt3>parseInputs (line 343)

Error in imgaussfilt3 (line 113)

Error in svreg_smooth_vol_function (line 46)

MATLAB:imgaussfilt3:expectedFinite

What does it mean?

[Anand Joshi]

What’s the command line that you tried?

[leonidastra86]

/Applications/BrainSuite17a/svreg/bin/svreg_smooth_vol_function.sh /Users/leonidastra86/Desktop/ABC/Pre/sample1001/Normalised/1001.svreg.inv.jacobian.nii.gz std2 std2 std2 /Users/leonidastra86/Desktop/ABC/Pre/sample1001/Normalised/1001.svreg.inv.map.jacdet.smooth2.0mm.nii.gz

[Anand Joshi]

Instead of std2 try just 2

[leonidastra86]

Warning: qform is already set. Nothing to do.
> In add_qform (line 69)
In load_nii_BIG_Lab (line 47)
In svreg_smooth_vol_function (line 34)

[Anand Joshi]

You can ignore the warning. The output should be correct.

[Author]

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