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LTS5 / cmp_nipype

This repository is meant to host a beta version for the future release of the ConnectomeMapper.
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csf_mask needed after 6/3/2014 commit #34

Open LisaKV opened 10 years ago

LisaKV commented 10 years ago

Hi, After I downloaded the latest commit (on June 6, 2014), ConnectomeMapper is failing at the Parcellation stage because it cannot find csf_mask.nii.gz.This file does not exist, and it was not required before. I am wondering why this change was made and what kind of csf_mask ConnectomeMapper is expecting. I am currently creating a csf_mask using mri_binarize as a work around. I am using existing Freesurfer data (that was created during a previous ConnectomeMapper run) and the Lausanne2008 Parcellation.

Thanks, Lisa

davidrs06 commented 10 years ago

Hi,

Could you send us the error message ? The CSF mask file was added to process functional data. Specifying that it is not required for diffusion data might be missing somewhere.

Thanks for reporting this.

Best regards, David Romascano

From: LisaKV [notifications@github.com] Sent: Wednesday, June 18, 2014 8:46 PM To: LTS5/cmp_nipype Subject: [cmp_nipype] csf_mask needed after 6/3/2014 commit (#34)

Hi, After I downloaded the latest commit (on June 6, 2014), ConnectomeMapper is failing at the Parcellation stage because it cannot find csf_mask.nii.gz.This file does not exist, and it was not required before. I am wondering why this change was made and what kind of csf_mask ConnectomeMapper is expecting. I am currently creating a csf_mask using mri_binarize as a work around. I am using existing Freesurfer data (that was created during a previous ConnectomeMapper run) and the Lausanne2008 Parcellation.

Thanks, Lisa

— Reply to this email directly or view it on GitHubhttps://github.com/LTS5/cmp_nipype/issues/34.

LisaKV commented 10 years ago

Hi David,

Here is the error: array(['Traceback (most recent call last):\n', ' File "/group_shares/FAIR_LAB/usr/CMP_beta_06062014/lib/python2.7/site-packages/nipype/pipeline/plugins/linear.py", line 37, in run\n node.run(updatehash=updatehash)\n', ' File "/group_shares/FAIR_LAB/usr/CMP_beta_06062014/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1128, in run\n self._run_interface()\n', ' File "/group_shares/FAIR_LAB/usr/CMP_beta_06062014/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1226, in _run_interface\n self._result = self._run_command(execute)\n', ' File "/group_shares/FAIR_LAB/usr/CMP_beta_06062014/lib/python2.7/site-packages/nipype/pipeline/engine.py", line 1350, in _run_command\n result = self._interface.run()\n', ' File "/group_shares/FAIR_LAB/usr/CMP_beta_06062014/lib/python2.7/site-packages/nipype/interfaces/base.py", line 823, in run\n runtime = self._run_interface(runtime)\n', ' File "/group_shares/FAIR_LAB/usr/CMP_beta_06062014/lib/python2.7/site-packages/nipype/interfaces/cmtk/parcellation.py", line 128, in _run_interface\n erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,\'mri\',\'csf_mask.nii.gz\'))\n', ' File "/group_shares/FAIR_LAB/usr/CMP_beta_06062014/lib/python2.7/site-packages/nipype/interfaces/cmtk/parcellation.py", line 47, in erode_mask\n mask = ni.load( maskFile ).get_data().astype( np.uint32 )\n', ' File "/usr/global/lib/python2.7/site-packages/nibabel-1.3.0-py2.7.egg/nibabel/loadsave.py", line 54, in load\n return klass.from_filename(filename)\n', ' File "/usr/global/lib/python2.7/site-packages/nibabel-1.3.0-py2.7.egg/nibabel/spatialimages.py", line 411, in from_filename\n return klass.from_file_map(file_map)\n', ' File "/usr/global/lib/python2.7/site-packages/nibabel-1.3.0-py2.7.egg/nibabel/analyze.py", line 869, in from_file_map\n hdrf = hdr_fh.get_prepare_fileobj(mode=\'rb\')\n', ' File "/usr/global/lib/python2.7/site-packages/nibabel-1.3.0-py2.7.egg/nibabel/fileholders.py", line 69, in get_prepare_fileobj\n obj = allopen(self.filename, _args, _kwargs)\n', ' File "/usr/global/lib/python2.7/site-packages/nibabel-1.3.0-py2.7.egg/nibabel/volumeutils.py", line 1284, in allopen\n return opener(fname, _args, _kwargs)\n', ' File "/usr/global/lib/python2.7/gzip.py", line 34, in open\n return GzipFile(filename, mode, compresslevel)\n', ' File "/usr/global/lib/python2.7/gzip.py", line 89, in init\n fileobj = self.myfileobj = builtin.open(filename, mode or \'rb\')\n', "IOError: [Errno 2] No such file or directory: u'/group_shares/FAIR_MCDON/CMP_beta/DIY_Parcellation/2042_S1_1/CMP06062014/FREESURFER/mri/csf_mask.nii.gz'\n"], dtype='|S247')

Please let me know if you need any other additional information. I am not sure if this is a related error, but if I supply a csf mask, I then get an error that /fsmask_1mm_eroded.nii.gz does not exist.

Thanks, Lisa

From: davidrs06 [mailto:notifications@github.com] Sent: Friday, June 20, 2014 9:09 AM To: LTS5/cmp_nipype Cc: Lisa Vingara Subject: Re: [cmp_nipype] csf_mask needed after 6/3/2014 commit (#34)

Hi,

Could you send us the error message ? The CSF mask file was added to process functional data. Specifying that it is not required for diffusion data might be missing somewhere.

Thanks for reporting this.

Best regards, David Romascano

From: LisaKV [notifications@github.com] Sent: Wednesday, June 18, 2014 8:46 PM To: LTS5/cmp_nipype Subject: [cmp_nipype] csf_mask needed after 6/3/2014 commit (#34)

Hi, After I downloaded the latest commit (on June 6, 2014), ConnectomeMapper is failing at the Parcellation stage because it cannot find csf_mask.nii.gz.This file does not exist, and it was not required before. I am wondering why this change was made and what kind of csf_mask ConnectomeMapper is expecting. I am currently creating a csf_mask using mri_binarize as a work around. I am using existing Freesurfer data (that was created during a previous ConnectomeMapper run) and the Lausanne2008 Parcellation.

Thanks, Lisa

— Reply to this email directly or view it on GitHubhttps://github.com/LTS5/cmp_nipype/issues/34.

— Reply to this email directly or view it on GitHubhttps://github.com/LTS5/cmp_nipype/issues/34#issuecomment-46696335.

MarcRamos commented 10 years ago

Same here, I had this problem when running in Non-Linear Registration mode. I have tested with the previous version and it seems to work fine. Thanks!

Save white matter mask: /home/marc2/1_PROJECTS/1present/Repeat**/FREESURFER/mri/fsmask_1mm.nii.gz 140630-21:43:52,206 workflow ERROR: ['Node parcellation failed to run on host connectome-ripper2.'] 140630-21:43:53,718 workflow INFO: Saving crash info to /home/marc2/mojito/cloudn/general/crash-20140630-214353-marc2-parcellation.npz 140630-21:43:53,767 workflow INFO: Traceback (most recent call last): File "/usr/local/lib/python2.7/dist-packages/nipype-0.0.0-py2.7.egg/nipype/pipeline/plugins/multiproc.py", line 15, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/lib/python2.7/dist-packages/nipype-0.0.0-py2.7.egg/nipype/pipeline/engine.py", line 1128, in run self._run_interface() File "/usr/local/lib/python2.7/dist-packages/nipype-0.0.0-py2.7.egg/nipype/pipeline/engine.py", line 1226, in _run_interface self._result = self._run_command(execute) File "/usr/local/lib/python2.7/dist-packages/nipype-0.0.0-py2.7.egg/nipype/pipeline/engine.py", line 1350, in _run_command result = self._interface.run() File "/usr/local/lib/python2.7/dist-packages/nipype-0.0.0-py2.7.egg/nipype/interfaces/base.py", line 823, in run runtime = self._run_interface(runtime) File "/usr/local/lib/python2.7/dist-packages/nipype-0.0.0-py2.7.egg/nipype/interfaces/cmtk/parcellation.py", line 128, in _run_interface erode_mask(op.join(self.inputs.subjects_dir,self.inputs.subject_id,'mri','csf_mask.nii.gz')) File "/usr/local/lib/python2.7/dist-packages/nipype-0.0.0-py2.7.egg/nipype/interfaces/cmtk/parcellation.py", line 47, in erode_mask mask = ni.load( maskFile ).get_data().astype( np.uint32 ) File "/usr/lib/pymodules/python2.7/nibabel/loadsave.py", line 54, in load return klass.from_filename(filename) File "/usr/lib/pymodules/python2.7/nibabel/spatialimages.py", line 411, in from_filename return klass.from_file_map(file_map) File "/usr/lib/pymodules/python2.7/nibabel/analyze.py", line 869, in from_file_map hdrf = hdr_fh.get_prepare_fileobj(mode='rb') File "/usr/lib/pymodules/python2.7/nibabel/fileholders.py", line 69, in get_prepare_fileobj obj = allopen(self.filename, args, _kwargs) File "/usr/lib/pymodules/python2.7/nibabel/volumeutils.py", line 1284, in allopen return opener(fname, _args, *_kwargs) File "/usr/lib/python2.7/gzip.py", line 34, in open return GzipFile(filename, mode, compresslevel) File "/usr/lib/python2.7/gzip.py", line 89, in init fileobj = self.myfileobj = builtin.open(filename, mode or 'rb') IOError: [Errno 2] No such file or directory: u'/home/marc2/1_PROJECTS/1_present/***/FREESURFER/mri/csf_mask.nii.gz'

MarcRamos commented 10 years ago

Any progress in this issue? Thanks!

davidrs06 commented 10 years ago

Good evening,

Sorry for taking so long to answer. The last commit should work now. Could you update your version of the mapper and see if the pipeline executes properly ?

Our branch of nipype has also been updated so you would need to install the last commit also.

Best regards, David Romascano

LisaKV commented 10 years ago

Hi David,

Thanks. I am having trouble installing the latest commit. The version of nipype I am using was downloaded today (11/7/2014) using git clone git://github.com/LTS5/nipype.git, and I installed cmp using git clone https://github.com/LTS5/cmp_nipype.git on the same day. When I attempt to start connectomemapper, I get the error:

Traceback (most recent call last): File "/usr/CMP_beta_11072014/bin/connectomemapper", line 14, in import cmp.gui File "/usr/CMP_beta_11072014/cmp_nipype/cmp/gui.py", line 15, in import project File "/usr/CMP_beta_11072014/cmp_nipype/cmp/project.py", line 22, in import pipelines.functional.functional as fMRI_pipeline File "/usr/CMP_beta_11072014/cmp_nipype/cmp/pipelines/functional/functional.py", line 30, in from cmp.stages.functional.functional import FunctionalStage File "/usr/CMP_beta_11072014/cmp_nipype/cmp/stages/functional/functional.py", line 32, in import statsmodels.api as sm ImportError: No module named statsmodels.api

Can you offer any insight into this error? Or know where is statsmodels.api supposed to be?

Thanks, Lisa

From: davidrs06 [mailto:notifications@github.com] Sent: Tuesday, November 04, 2014 9:08 AM To: LTS5/cmp_nipype Cc: Lisa Karstens Vingara Subject: Re: [cmp_nipype] csf_mask needed after 6/3/2014 commit (#34)

Good evening,

Sorry for taking so long to answer. The last commit should work now. Could you update your version of the mapper and see if the pipeline executes properly ?

Our branch of nipype has also been updated so you would need to install the last commit also.

Best regards, David Romascano

— Reply to this email directly or view it on GitHubhttps://github.com/LTS5/cmp_nipype/issues/34#issuecomment-61676107.

mhough commented 10 years ago

Hi Lisa,

I had the same error on a new machine. If you are on Ubuntu like me I just ran:

sudo apt-get install python-statsmodels

and reran connectomemapper and it was fine.

Cheers,

-Morgan

On Nov 7, 2014, at 2:02 PM, LisaKV notifications@github.com wrote:

Hi David,

Thanks. I am having trouble installing the latest commit. The version of nipype I am using was downloaded today (11/7/2014) using git clone git://github.com/LTS5/nipype.git, and I installed cmp using git clone https://github.com/LTS5/cmp_nipype.git on the same day. When I attempt to start connectomemapper, I get the error:

Traceback (most recent call last): File "/usr/CMP_beta_11072014/bin/connectomemapper", line 14, in import cmp.gui File "/usr/CMP_beta_11072014/cmp_nipype/cmp/gui.py", line 15, in import project File "/usr/CMP_beta_11072014/cmp_nipype/cmp/project.py", line 22, in import pipelines.functional.functional as fMRI_pipeline File "/usr/CMP_beta_11072014/cmp_nipype/cmp/pipelines/functional/functional.py", line 30, in from cmp.stages.functional.functional import FunctionalStage File "/usr/CMP_beta_11072014/cmp_nipype/cmp/stages/functional/functional.py", line 32, in import statsmodels.api as sm ImportError: No module named statsmodels.api

Can you offer any insight into this error? Or know where is statsmodels.api supposed to be?

Thanks, Lisa

From: davidrs06 [mailto:notifications@github.com] Sent: Tuesday, November 04, 2014 9:08 AM To: LTS5/cmp_nipype Cc: Lisa Karstens Vingara Subject: Re: [cmp_nipype] csf_mask needed after 6/3/2014 commit (#34)

Good evening,

Sorry for taking so long to answer. The last commit should work now. Could you update your version of the mapper and see if the pipeline executes properly ?

Our branch of nipype has also been updated so you would need to install the last commit also.

Best regards, David Romascano

— Reply to this email directly or view it on GitHubhttps://github.com/LTS5/cmp_nipype/issues/34#issuecomment-61676107. — Reply to this email directly or view it on GitHub https://github.com/LTS5/cmp_nipype/issues/34#issuecomment-62221929.

ncullen93 commented 8 years ago

August 4, 2016 - this is still an issue.