leonidastra86

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Viewing 15 posts - 16 through 30 (of 41 total)
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  • in reply to: Problem with smoothing #912
    leonidastra86
    Participant

    /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

    in reply to: Problem with smoothing #910
    leonidastra86
    Participant

    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?

    in reply to: Problem with smoothing #909
    leonidastra86
    Participant

    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.

    in reply to: Problem with smoothing #907
    leonidastra86
    Participant

    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?

    in reply to: Problem with BSSR #906
    leonidastra86
    Participant

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

    in reply to: Problem with BSSR #904
    leonidastra86
    Participant

    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.

    in reply to: Problem with BSSR #901
    leonidastra86
    Participant

    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?

    in reply to: Problem with smoothing #896
    leonidastra86
    Participant

    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

    in reply to: Problem with smoothing #894
    leonidastra86
    Participant

    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.

    in reply to: Problem with smoothing #892
    leonidastra86
    Participant

    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

    ???

    in reply to: Problem with smoothing #890
    leonidastra86
    Participant

    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.

    in reply to: Problem with smoothing #888
    leonidastra86
    Participant

    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.

    in reply to: Error with BDP #690
    leonidastra86
    Participant

    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.

    in reply to: Error with BDP #656
    leonidastra86
    Participant

    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?

    in reply to: Error with BDP #650
    leonidastra86
    Participant

    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.

Viewing 15 posts - 16 through 30 (of 41 total)