[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

[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?

[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]

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?

[leonidastra86]

Problem was fixed, analysis was performed without any problems.
Thank you all so much for your help!

[leonidastra86]

Oh God, I now know the problem. I analysed the Data with 2 Computers, half on a Windows computer (C:\Program Files\BrainSuite17a\svreg\BrainSuiteAtlas1\) and half with a MacOs Computer (so the path is not the same).
Is there a solution for this? Do I need the svreg. files for all of the patients and edit the path every time or is it just for the first case? Because in the ICBM25 folder that I downloaded from the Brainsuite page was only on the first patient present.

[leonidastra86]

Hi Yeun and thank you very much for your help.
After some changes that you suggested and some mistakes that I found in my data, I could form the right pathway.
It asks about the atlas, although I used the Brainsuite atlas.

Error: Could not determine the BrainSuite atlas used for registration.
Please check the log file /Users/leonidastra86/Desktop/ICBM25/1001/1001.svreg.log, and check if the subject directory is valid. If using a custom atlas, supply the path in the atlas= argument.

Any ideas?

[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

[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]

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

???

[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.

[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.

[leonidastra86]

The issue is resolved but thank you for your response anyway.
I have to admit, sometimes come Nifti from dcm2nii with the wrong number of bvals und bvecs and I need to do it again or download the dcom files again.

Anyway, now it works and I learn the program and its issues every day a little more. Thank you very much for your support.

[leonidastra86]

It was actually a bundle that included 2 series of 22 images. I had more but I thought it wouldn’t work. My images are all in dicom and I must transform them everytime. The program to transform them is in my opinion the issue. dcm2niigui is the simplest but I am not really sure about the results. I usually receive many files and I don’t know which of them I should include in the path that I use.

Do you have an example for me?

Or should I have one .bvec and one .bval file only?

[leonidastra86]

In addition to my questions above, I have already the next problem in the next 2 patients. I get the following message:

Error message:
Number of volumes in NIfTI file does not equal the number of b-matrices.
Total number of images found: 2
Total number of bmatrices: 1

Error help/resolution:
Check to make sure that bvec/bval or bmat file have correct number of entries
corresponding to the diffusion scan file. Check to make sure gradient file
contains “0, 0, 0” row(s)/col(s) for b=0 images.

I tried to transform the Dicoms with dcm2niigui and the newer mricron but I always get the same results. What do I do false? The .bvec file has values:
0
0
0
and the .bval just 0.

[Author]

Posts