コード例 #1
0
def calc_freesurfer_surf(subject, atlas):
    # Clean
    args = fmri.read_cmd_args(
        dict(subject=subject,
             atlas=atlas,
             function='clean_4d_data',
             fmri_file_template='rest.nii*',
             fsd='rest_linda',
             overwrite_4d_preproc=False))
    pu.run_on_subjects(args, fmri.main)
    # save the surf files
    args = fmri.read_cmd_args(
        dict(subject=subject,
             atlas=atlas,
             function='load_surf_files',
             overwrite_surf_data=True,
             fmri_file_template=fs_surf_template.format(subject=subject,
                                                        hemi='{hemi}')))
    pu.run_on_subjects(args, fmri.main)
    # Renaming the files
    root_fol = op.join(fmri.MMVT_DIR, subject, 'fmri')
    for hemi in utils.HEMIS:
        os.rename(
            op.join(root_fol,
                    'fmri_rest_linda.sm6.{}.{}.npy'.format(subject, hemi)),
            op.join(root_fol, 'fmri_freesurfer_{}.npy'.format(hemi)))
    os.rename(
        op.join(root_fol, 'rest_linda.sm6.{}_minmax.pkl'.format(subject)),
        op.join(root_fol, 'freesurfer_minmax.pkl'))
コード例 #2
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def calc_hesheng_surf(subject, atlas):
    subject_fol = op.join(fmri.MMVT_DIR, subject, 'fmri')
    if not (utils.both_hemi_files_exist(
            op.join(subject_fol, 'fmri_hesheng_{hemi}.npy'))
            and op.isfile(op.join(subject_fol, 'hesheng_minmax.pkl'))):
        # Copy and rename Hesheng's files
        hesheng_fnames = glob.glob(
            op.join(hesheng_surf_fol.format(subject=subject),
                    hesheng_template.format(subject=subject)))
        for fname in hesheng_fnames:
            hemi = lu.get_label_hemi_invariant_name(utils.namebase(fname))
            target_file = op.join(fmri.FMRI_DIR, subject,
                                  'hesheng_{}.nii.gz'.format(hemi))
            mgz_target_file = utils.change_fname_extension(target_file, 'mgz')
            if not op.isfile(mgz_target_file):
                shutil.copy(fname, target_file)
                fu.nii_gz_to_mgz(target_file)
                os.remove(target_file)
        # Load Hesheng's files
        args = fmri.read_cmd_args(
            dict(subject=subject,
                 atlas=atlas,
                 function='load_surf_files',
                 overwrite_surf_data=True,
                 fmri_file_template='hesheng_{hemi}.mgz'))
        pu.run_on_subjects(args, fmri.main)
コード例 #3
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def calc_diff(subject, fmri_file_template='*linda_{hemi}*,*hesheng_{hemi}'):
    # Calc diff
    args = fmri.read_cmd_args(
        dict(subject=subject,
             function='calc_files_diff',
             fmri_file_template=fmri_file_template))
    pu.run_on_subjects(args, fmri.main)
コード例 #4
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def project_and_calc_clusters(args):
    if not op.isdir(args.root_fol):
        print('You should first set args.root_fol!')
        return False
    img_files = [
        f for f in glob.glob(op.join(args.root_fol, '*.img')) if op.isfile(f)
    ]
    for img_fname in img_files:
        mgz_fname = fu.mri_convert_to(img_fname, 'mgz', overwrite=False)
        if ' ' in utils.namebase(mgz_fname):
            mgz_new_fname = op.join(
                utils.get_parent_fol(mgz_fname),
                utils.namebase_with_ext(mgz_fname).replace(' ', '_').replace(
                    ',', '').lower())
            os.rename(mgz_fname, mgz_new_fname)
    nii_files = [
        f for f in glob.glob(op.join(args.root_fol, '*'))
        if op.isfile(f) and utils.file_type(f) in ('nii', 'nii.gz', 'mgz')
    ]
    for fname in nii_files:
        fmri_args = fmri.read_cmd_args(
            dict(subject=args.subject,
                 function='project_volume_to_surface,find_clusters',
                 fmri_file_template=fname,
                 threshold=args.cluster_threshold))
        pu.run_on_subjects(fmri_args, fmri.main)
コード例 #5
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def calc_linda_surf(subject, atlas):
    # Check for Linda's output fname
    if not utils.both_hemi_files_exist(op.join(fmri.MMVT_DIR, subject, 'fmri', 'fmri_linda_{}.npy'.format('{hemi}'))) \
            and not op.isfile(op.join(fmri.MMVT_DIR, subject, 'fmri', 'linda_minmax.pkl')):
        # Find Linda's files
        linda_volume_fnames = glob.glob(op.join(
            linda_fol.format(subject=subject), linda_vol_template.format(subject=subject)))
        linda_volume_folder = utils.get_parent_fol(linda_volume_fnames[0])
        # project linda files on the surface
        args = fmri.read_cmd_args(dict(
            subject=subject, function='project_volume_to_surface', remote_fmri_dir=linda_volume_folder,
            fmri_file_template=linda_vol_template.format(subject=subject), overwrite_surf_data=True))
        pu.run_on_subjects(args, fmri.main)
        # rename Linda's files
        linda_fnames = glob.glob(op.join(fmri.MMVT_DIR, subject, 'fmri', 'fmri_{}'.format(
            linda_template_npy.format(subject=subject))))
        for fname in linda_fnames:
            hemi = lu.get_label_hemi(utils.namebase(fname))
            target_file = op.join(fmri.MMVT_DIR, subject, 'fmri', 'fmri_linda_{}.npy'.format(hemi))
            if not op.isfile(target_file):
                os.rename(fname, target_file)
        # rename minmax file
        linda_minmax_name = '{}.pkl'.format(utils.namebase(glob.glob(op.join(
            fmri.MMVT_DIR, subject, 'fmri', '{}_minmax.pkl'.format(
                utils.namebase(linda_vol_template.format(subject=subject)))))[0]))
        os.rename(op.join(fmri.MMVT_DIR, subject, 'fmri', linda_minmax_name),
                  op.join(fmri.MMVT_DIR, subject, 'fmri', 'linda_minmax.pkl'))
        # delete mgz files
        mgz_files = glob.glob(op.join(fmri.MMVT_DIR, subject, 'fmri', 'fmri_{}_?h.mgz'.format(
            utils.namebase(linda_vol_template.format(subject=subject)))))
        for mgz_file in mgz_files:
            os.remove(mgz_file)
コード例 #6
0
ファイル: load_nii.py プロジェクト: Bakikii/blender-importer
def pre_blender_call(args):
    from src.mmvt_addon import load_results_panel
    from src.preproc import fMRI as fmri
    from src.utils import preproc_utils as pu
    from src.utils import utils

    user_fol = op.join(pu.MMVT_DIR, args.subject)
    nii_fname = args.nii
    if not op.isfile(args.nii):
        args.nii = op.join(user_fol, 'fmri', nii_fname)
    if not op.isfile(args.nii):
        fmri_fol = op.join(utils.get_link_dir(utils.get_links_dir(), 'fMRI'),
                           args.subject)
        args.nii = op.join(fmri_fol, nii_fname)
    if not op.isfile(args.nii):
        raise Exception("Can't find the nii file!")
    fmri_file_template, _, _ = load_results_panel.load_surf_files(
        args.nii, run_fmri_preproc=False, user_fol=user_fol)
    preproc_args = fmri.read_cmd_args(
        dict(subject=args.subject,
             atlas=args.atlas,
             function='load_surf_files',
             fmri_file_template=fmri_file_template,
             ignore_missing=True))
    ret = pu.run_on_subjects(preproc_args, fmri.main)
    if ret:
        load_results_panel.clean_nii_temp_files(fmri_file_template, user_fol)
        args.fmri_file_template = fmri_file_template
    else:
        raise Exception("Couldn't load the surface files!")
    return args
コード例 #7
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ファイル: fMRI.py プロジェクト: pelednoam/mmvt
def load_rest_to_colin():
    args = fmri.read_cmd_args(['-s', subject])
    args.task = 'REST'
    args.function = 'project_volume_to_surface,find_clusters'
    args.contrast = 'rest'
    args.volume_name = 'spmT_0001'
    fmri.main(subject, mri_subject, args)
コード例 #8
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ファイル: fMRI.py プロジェクト: pelednoam/mmvt
def fsfast():
    args = fmri.read_cmd_args(['-s', subject])
    args.task = 'MSIT'
    args.function = 'fmri_pipeline'
    args.contrast_name = 'interference'
    args.atlas = 'laus250'
    fmri.main(subject, mri_subject, args)
コード例 #9
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def compare_connectivity(subject, atlas, n_jobs=6):
    for name, fol, template in zip(['hesheng', 'linda', 'freesurfer'],
                                   [hesheng_surf_fol, linda_surf_fol, fs_surf_fol],
                                   [hesheng_template, linda_hemi_template, fs_surf_template]):
        output_fname_template = op.join(
            fmri.MMVT_DIR, subject, 'fmri', '{}_labels_data_laus125_mean_{}.npz'.format(name, '{hemi}'))
        if not utils.both_hemi_files_exist(output_fname_template):
            args = fmri.read_cmd_args(dict(
                subject=subject, atlas=atlas, function='analyze_4d_data', fmri_file_template=template, remote_fmri_dir=fol,
                labels_extract_mode='mean', overwrite_labels_data=False))
            pu.run_on_subjects(args, fmri.main)
            for hemi in utils.HEMIS:
                os.rename(op.join(fmri.MMVT_DIR, subject, 'fmri', 'labels_data_laus125_mean_{}.npz'.format(hemi)),
                          output_fname_template.format(hemi=hemi))

        args = con.read_cmd_args(dict(
            subject=subject, atlas='laus125', function='calc_lables_connectivity',
            connectivity_modality='fmri', connectivity_method='corr,cv', labels_extract_mode='mean',
            windows_length=34, windows_shift=4, save_mmvt_connectivity=False, calc_subs_connectivity=False,
            labels_name=name, recalc_connectivity=True, n_jobs=n_jobs))
        pu.run_on_subjects(args, con.main)
        conn_fol = op.join(con.MMVT_DIR, subject, 'connectivity')
        coloring_fol = op.join(con.MMVT_DIR, subject, 'coloring')
        os.rename(op.join(conn_fol, 'fmri_corr.npy'), op.join(conn_fol, 'fmri_corr_{}.npy'.format(name)))
        os.rename(op.join(conn_fol, 'fmri_corr_cv_mean.npz'), op.join(conn_fol, 'mri_corr_cv_mean_{}.npz'.format(name)))
        os.rename(op.join(conn_fol, 'fmri_corr_cv_mean_mean.npz'), op.join(conn_fol, 'fmri_corr_cv_mean_mean_{}.npz'.format(name)))
        os.rename(op.join(coloring_fol, 'fmri_corr_cv_mean.csv'), op.join(coloring_fol, 'fmri_corr_cv_mean_{}.csv'.format(name)))
コード例 #10
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def fsfast():
    args = fmri.read_cmd_args(['-s', subject])
    args.task = 'MSIT'
    args.function = 'fmri_pipeline'
    args.contrast_name = 'interference'
    args.atlas = 'laus250'
    fmri.main(subject, mri_subject, args)
コード例 #11
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def load_rest_to_colin():
    args = fmri.read_cmd_args(['-s', subject])
    args.task = 'REST'
    args.function = 'project_volume_to_surface,find_clusters'
    args.contrast = 'rest'
    args.volume_name = 'spmT_0001'
    fmri.main(subject, mri_subject, args)
コード例 #12
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def pet():
    args = fmri.read_cmd_args(['-s', subject])
    args.threshold = 0
    args.is_pet = True
    args.symetric_colors = False
    args.atlas = 'laus250'
    fmri.main(subject, mri_subject, args)
    '-s s02 --threshold 0 --is_pet 1 --symetric_colors 0 --overwrite_surf_data 1 --remote_subject_dir /local_mount/space/thibault/1/users/npeled/artur/recon_tese/{subject}'
コード例 #13
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def save_dynamic_activity_map(args):
    args = fmri.read_cmd_args(
        dict(subject=args.subject,
             atlas=args.atlas,
             function='save_dynamic_activity_map',
             fmri_file_template='fmcpr.up.sm6.{subject}.{hemi}.*',
             overwrite_activity_data=True))
    pu.run_on_subjects(args, fmri.main)
コード例 #14
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ファイル: fMRI.py プロジェクト: pelednoam/mmvt
def pet():
    args = fmri.read_cmd_args(['-s', subject])
    args.threshold = 0
    args.is_pet = True
    args.symetric_colors = False
    args.atlas = 'laus250'
    fmri.main(subject, mri_subject, args)
    '-s s02 --threshold 0 --is_pet 1 --symetric_colors 0 --overwrite_surf_data 1 --remote_subject_dir /local_mount/space/thibault/1/users/npeled/artur/recon_tese/{subject}'
コード例 #15
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def calc_subcorticals_activity(args):
    args = fmri.read_cmd_args(
        dict(
            subject=args.subject,
            function='calc_subcorticals_activity',
            # fmri_file_template='rest*',
            fmri_file_template='fmcpr.sm6.mni305.2mm.*',
            labels_extract_mode='mean',  #,pca,pca_2,pca_4,pca_8',
            overwrite_subs_data=True))
    pu.run_on_subjects(args, fmri.main)
コード例 #16
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def fmri_msit_pipeline(args):
    '-s pp009 -a laus250 -f fmri_pipeline -t MSIT --contrast_template "*Interference*"'
    for subject in args.subject:
        args = fmri.read_cmd_args(
            dict(subject=subject,
                 atlas=args.atlas,
                 function='fmri_pipeline',
                 task='MSIT',
                 contrast_template='*Interference*'))
        pu.run_on_subjects(args, fmri.main)
コード例 #17
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def project_volume_to_surface(args):
    args = fmri.read_cmd_args(dict(
        subject=args.subject,
        function='project_volume_to_surface',
        fmri_file_template='f*.gz',
        sftp_username=args.sftp_username,
        sftp_domain=args.sftp_domain,
        sftp=True,
        remote_subject_dir=args.remote_subject_dir,
    ))
    pu.run_on_subjects(args, fmri.main)
コード例 #18
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def get_subject_files_using_sftp(args):
    for subject in args.subject:
        args = fmri.read_cmd_args(
            dict(subject=subject,
                 atlas=args.atlas,
                 sftp_username=args.sftp_username,
                 sftp_domain=args.sftp_domain,
                 sftp=True,
                 remote_subject_dir=args.remote_subject_dir,
                 function='prepare_subject_folder'))
        pu.run_on_subjects(args, fmri.main)
コード例 #19
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def analyze_rest_fmri(args):
    for subject in args.mri_subject:
        remote_rest_fol = get_fMRI_rest_fol(subject, args.remote_fmri_dir)
        local_rest_fname = convert_rest_dicoms_to_mgz(subject, remote_rest_fol)
        if not op.isfile(local_rest_fname):
            print('{}: Can\'t find {}!'.format(subject, local_rest_fname))
            continue
        args = fmri.read_cmd_args(
            dict(
                subject=subject,
                atlas=args.atlas,
                remote_subject_dir=args.remote_subject_dir,
                function='clean_4d_data',
                fmri_file_template=local_rest_fname,
            ))
        fmri.call_main(args)

        args = fmri.read_cmd_args(
            dict(subject=args.subject,
                 atlas=args.atlas,
                 function='analyze_4d_data',
                 fmri_file_template='rest.sm6.{subject}.{hemi}.mgz',
                 labels_extract_mode='mean',
                 overwrite_labels_data=False))
        fmri.call_main(args)

        args = connectivity.read_cmd_args(
            dict(subject=args.subject,
                 atlas=args.atlas,
                 function='calc_lables_connectivity',
                 connectivity_modality='fmri',
                 connectivity_method='corr',
                 labels_extract_mode='mean',
                 identifier='',
                 save_mmvt_connectivity=True,
                 calc_subs_connectivity=False,
                 recalc_connectivity=True,
                 n_jobs=args.n_jobs))
        connectivity.call_main(args)
コード例 #20
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def load_labels_ts(args):
    args = fmri.read_cmd_args(
        dict(subject=args.subject,
             atlas=args.atlas,
             function='load_labels_ts',
             labels_order_fname=op.join(fmri.MMVT_DIR, 'labels_order',
                                        'linda_laus125_order.txt'),
             labels_extract_mode='mean',
             excluded_labels='corpuscallosum,unknown',
             labels_indices_to_remove_from_data='0,4,113,117',
             st_template='{subject}_{atlas}_mri.txt',
             backup_existing_files=False,
             pick_the_first_one=True))
    pu.run_on_subjects(args, fmri.main)
コード例 #21
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def clean_4d_data(args):
    '''
    python -m src.preproc.fMRI -s nmr00474,nmr00502,nmr00515,nmr00603,nmr00609,nmr00626,nmr00629,nmr00650,nmr00657,nmr00669,nmr00674,nmr00681,nmr00683,nmr00692,nmr00698,nmr00710
        -a laus125 -f clean_resting_state_data --template_brain fsaverage5 --fmri_file_template "f.nii*" --remote_subject_dir "/space/franklin/1/users/sx424/mem_flex/subjects/{subject}"'
    '''
    args = fmri.read_cmd_args(
        dict(subject=args.subject,
             atlas=args.atlas,
             function='clean_4d_data',
             fmri_file_template='rest.nii*',
             fsd='rest_linda'
             # template_brain='fsaverage5',
             ))
    pu.run_on_subjects(args, fmri.main)
コード例 #22
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ファイル: fMRI.py プロジェクト: Bakikii/blender-importer
def project_and_calc_clusters(args):
    if not op.isdir(args.root_fol):
        print('You should first set args.root_fol!')
        return False
    nii_files = [
        f for f in glob.glob(op.join(args.root_fol, '*'))
        if op.isfile(f) and utils.file_type(f) in ('nii', 'nii.gz', 'mgz')
    ]
    for fname in nii_files:
        args = fmri.read_cmd_args(
            dict(subject=args.subject,
                 function='project_volume_to_surface,find_clusters',
                 fmri_file_template=fname))
        pu.run_on_subjects(args, fmri.main)
コード例 #23
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def analyze_4d_data(args):
    # '-s subject-name -a atlas-name -f analyze_4d_data --fmri_file_template {subject}*{morph_to_subject}.{hemi}.{format}  --morph_labels_to_subject fsaverage'
    # '-f analyze_4d_data -a laus125 -s "file:/homes/5/npeled/space1/Documents/memory_task/subjects.txt"'
    args = fmri.read_cmd_args(dict(
        subject=args.subject,
        atlas=args.atlas,
        function='analyze_4d_data',
        # fmri_file_template='fmcpr.up.sm6.{subject}.{hemi}.nii.gz',
        fmri_file_template='{subject}_bld???_rest_reorient_skip_faln_mc_g1000000000_bpss_resid_{hemi}.mgz',
        # template_brain='fsaverage5',
        # template_brain='fsaverage6',
        # labels_extract_mode='mean,pca,pca_2,pca_4,pca_8',
        labels_extract_mode='mean',
        overwrite_labels_data=True
    ))
    pu.run_on_subjects(args, fmri.main)
コード例 #24
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def calc_labels_mean_freesurfer(args):
    '''
    python -m src.preproc.fMRI -a laus125 -f calc_labels_mean_freesurfer --fmri_file_template "{hemi}.{subject}_bld014_rest_reorient_skip_faln_mc_g1000000000_bpss_resid_fsaverage6_sm6_fsaverage5*.mgz" --excluded_labels corpuscallosum,unknown --overwrite_labels_data 1 --remote_fmri_dir "/autofs/cluster/scratch/tuesday/noam/DataProcessed_memory/{subject}/surf" -s 'nmr00506','nmr00599','nmr00515','nmr00692','nmr00657','nmr00609','nmr00468','nmr00629','nmr00681','nmr00643','nmr00448','nmr00650','nmr00674','nmr00669','nmr00603','nmr00710','nmr00683','nmr00640','nmr00634','nmr00502','nmr00698'
    '''
    args = fmri.read_cmd_args(dict(
        subject=args.subject,
        atlas=args.atlas,
        function='calc_labels_mean_freesurfer',
        fmri_file_template='{hemi}.{subject}_bld???_rest_reorient_skip_faln_mc_g1000000000_bpss_resid_fsaverage6_sm6_fsaverage5*.mgz',
        excluded_labels='corpuscallosum,unknown',
        remote_fmri_dir='/autofs/cluster/neuromind/douw/scans/adults/{subject}/surf',
        overwrite_labels_data=True,
        sftp_username=args.sftp_username,
        sftp_domain=args.sftp_domain,
        sftp=True,
        remote_subject_dir=args.remote_subject_dir,
    ))
    pu.run_on_subjects(args, fmri.main)
コード例 #25
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def language(args):
    # -f language -s nmr01361 --clinical_dir clin_4090354
    # -s nmr01353 -f clean_4d_data --fsd sycabs --remote_fmri_dir "/space/megraid/clinical/MEG-MRI/seder/freesurfer" --nconditions 4
    if args.clinical_dir == '':
        print('You should set the clinical_dir first. Example: clin_4090354')
        return
    clinical_root_dir = op.join(args.remote_fmri_dir, args.clinical_dir)
    if not op.isdir(clinical_root_dir):
        print('{} does not exist!'.format(clinical_root_dir))

    task = 'sycabs'
    fwhm = 6
    subject = args.subject[0]
    remote_mri_dir = args.remote_clinical_subjects_dir
    subject_mri_dir = op.join(remote_mri_dir, subject)
    mri_subject_task_dir = utils.make_dir(op.join(subject_mri_dir, task))
    clinical_dirs = glob.glob(op.join(clinical_root_dir, '*'))
    clinical_dirs = [
        d for d in clinical_dirs if utils.namebase(d) != 'mne_dcm'
    ]
    remote_fmri_dir = utils.select_one_file(clinical_dirs)
    fmri_fols = sorted(glob.glob(op.join(remote_fmri_dir, '*_SyCAbs')))
    par_fol = utils.make_dir(op.join(remote_mri_dir, subject, 'par'))
    par_files = glob.glob(op.join(par_fol, '*.par'))
    sessions = sorted(
        [utils.find_num_in_str(utils.namebase(d))[0] for d in fmri_fols])

    # Warning: You first need to put the original ones in the following folder:
    if len(par_files) == 0:
        print('\n *** Please put the original par files in {} and rerun ***'.
              format(op.join(remote_mri_dir, subject, 'par')))
        return

    par_files.sort(key=lambda x: int(utils.namebase(x).split('_')[-1]))
    ret = input('''
        Patient: {}
        MRI folder: {}
        fMRI root folder: {}
        fMRI sessions: {}
        Session and pars: {}
        Do you want to continue (y/n)? '''.format(
        subject, subject_mri_dir, remote_fmri_dir,
        [utils.namebase(d) for d in fmri_fols],
        list(zip([utils.namebase(f) for f in par_files], sessions))))
    if not au.is_true(ret):
        return

    # You need first to run src.preproc.anatomy
    if not op.isfile(anat.get_blend_fname(subject, args.atlas)):
        args = anat.read_cmd_args(
            dict(
                subject=subject,
                remote_subject_dir=subject_mri_dir,
                ignore_missing=True,
            ))
        pu.run_on_subjects(args, anat.main)

    # convert the fMRI dicom files to nii
    for fmri_fol in fmri_fols:
        ses_num = utils.find_num_in_str(utils.namebase(fmri_fol))[0]
        ses_files = glob.glob(op.join(fmri_fol, '**', '*.*'), recursive=True)
        output_fname = op.join(
            utils.make_dir(op.join(mri_subject_task_dir, ses_num)), 'f.nii.gz')
        if not op.isfile(output_fname):
            fu.mri_convert(ses_files[0], output_fname)

    # Convert and arrange the par file
    from src.misc.fmri_scripts import convert_par
    for par_file, session in zip(par_files, sessions):
        fs_par_fname = op.join(mri_subject_task_dir, session,
                               '{}.par'.format(task))
        # if not op.isfile(fs_par_fname):
        warnings = convert_par.sycabs(par_file, fs_par_fname)
        if warnings != '':
            print(
                '\n *** Please fix the problems with the par convertion ({}) and rerun ***\n'
                .format(par_file))
            return

    for hemi in utils.HEMIS:
        utils.delete_folder_files(
            op.join(remote_mri_dir, '{}_sm{}_{}'.format(task, fwhm, hemi)))

    # Run the FreeSurfer analysis
    args = fmri.read_cmd_args(
        dict(subject=subject,
             atlas=args.atlas,
             function='clean_4d_data',
             fsd=task,
             fwhm=fwhm,
             remote_fmri_dir=remote_mri_dir,
             nconditions=4,
             ignore_missing=True,
             print_only=False,
             overwrite_4d_preproc=False))
    pu.run_on_subjects(args, fmri.main)

    # Load the fMRI results
    args = fmri.read_cmd_args(
        dict(
            subject=subject,
            atlas=args.atlas,
            function='load_surf_files',
            fmri_file_template=op.join(MMVT_DIR, subject, 'fmri',
                                       'words_v_symbols_{hemi}.mgz'),
        ))
    pu.run_on_subjects(args, fmri.main)
コード例 #26
0
def analyze_rest_fmri(gargs):
    good_subjects = []
    for subject in gargs.mri_subject:
        # remote_rest_fol = get_fMRI_rest_fol(subject, gargs.remote_fmri_dir)
        # print('{}: {}'.format(subject, remote_rest_fol))
        # if remote_rest_fol == '':
        #     continue
        # local_rest_fname = convert_rest_dicoms_to_mgz(subject, remote_rest_fol, overwrite=True)
        # if local_rest_fname == '':
        #     continue
        # if not op.isfile(local_rest_fname):
        #     print('{}: Can\'t find {}!'.format(subject, local_rest_fname))
        #     continue
        # args = fmri.read_cmd_args(dict(
        #     subject=subject,
        #     atlas=gargs.atlas,
        #     remote_subject_dir=gargs.remote_subject_dir,
        #     function='clean_4d_data',
        #     fmri_file_template=local_rest_fname,
        #     overwrite_4d_preproc=True
        # ))
        # flags = fmri.call_main(args)
        # if subject not in flags or not flags[subject]['clean_4d_data']:
        #     continue

        output_fname = op.join(MMVT_DIR, subject, 'connectivity',
                               'fmri_corr.npz')
        if op.isfile(output_fname):
            print('{} already exist!'.format(output_fname))
            good_subjects.append(subject)
            continue
        remote_fname = op.join(
            gargs.remote_fmri_rest_dir, subject, 'rest_001', '001',
            'fmcpr.siemens.sm6.{}.{}.nii.gz'.format(subject, '{hemi}'))
        if not utils.both_hemi_files_exist(remote_fname):
            print('Couldn\t find fMRI rest data for {} ({})'.format(
                subject, remote_fname))
            continue
        local_fmri_fol = utils.make_dir(op.join(FMRI_DIR, subject))
        local_fmri_template = op.join(local_fmri_fol,
                                      utils.namebase_with_ext(remote_fname))
        if utils.both_hemi_files_exist(local_fmri_template):
            print('{} al')
        for hemi in utils.HEMIS:
            local_fmri_fname = op.join(local_fmri_fol,
                                       local_fmri_template.format(hemi=hemi))
            if op.isfile(local_fmri_fname):
                os.remove(local_fmri_fname)
            utils.make_link(remote_fname.format(hemi=hemi), local_fmri_fname)

        args = fmri.read_cmd_args(
            dict(subject=subject,
                 atlas=gargs.atlas,
                 function='analyze_4d_data',
                 fmri_file_template=local_fmri_template,
                 labels_extract_mode='mean',
                 overwrite_labels_data=True))
        flags = fmri.call_main(args)
        if subject not in flags or not flags[subject]['analyze_4d_data']:
            continue

        args = connectivity.read_cmd_args(
            dict(
                subject=subject,
                atlas=gargs.atlas,
                function='calc_lables_connectivity',
                connectivity_modality='fmri',
                connectivity_method='corr',
                labels_extract_mode='mean',
                windows_length=34,  # tr = 3 -> 100s
                windows_shift=4,  # 12s
                save_mmvt_connectivity=True,
                calc_subs_connectivity=False,
                recalc_connectivity=True,
                n_jobs=gargs.n_jobs))
        flags = connectivity.call_main(args)
        if subject in flags and flags[subject]['calc_lables_connectivity']:
            good_subjects.append(subject)

    print('{}/{} good subjects'.format(len(good_subjects),
                                       len(gargs.mri_subject)))
    print('Good subject: ', good_subjects)
    print('Bad subjects: ', set(gargs.mri_subject) - set(good_subjects))